Sort all includes in src/gromacs

Used:
  admin/reformat_all.sh --pattern=src/gromacs includesort -B=../build
after building the doc-check target (whose dependencies are needed for
the sorter).

Change-Id: Icde0fb5cb5bc082fb4381d4cba1211329bad3fa5

diff --git a/src/gromacs/analysisdata.h b/src/gromacs/analysisdata.h
index 51f2d44156bf4bafca88a7c300620858f7cc5b64..0bea9203648896c3878f61bce320110f75502e00 100644 (file)
--- a/src/gromacs/analysisdata.h
+++ b/src/gromacs/analysisdata.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -201,13 +201,13 @@
 #ifndef GMX_ANALYSISDATA_H
 #define GMX_ANALYSISDATA_H
 
-#include "analysisdata/analysisdata.h"
-#include "analysisdata/arraydata.h"
-#include "analysisdata/dataframe.h"
-#include "analysisdata/modules/average.h"
-#include "analysisdata/modules/displacement.h"
-#include "analysisdata/modules/histogram.h"
-#include "analysisdata/modules/lifetime.h"
-#include "analysisdata/modules/plot.h"
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/displacement.h"
+#include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/analysisdata/modules/lifetime.h"
+#include "gromacs/analysisdata/modules/plot.h"
 
 #endif

diff --git a/src/gromacs/analysisdata/abstractdata.cpp b/src/gromacs/analysisdata/abstractdata.cpp
index bdc43b4536c40b80cfe1e276d4b20e191ee34144..9d21ccad6c9c8d890e3d43fedea8db140b02017a 100644 (file)
--- a/src/gromacs/analysisdata/abstractdata.cpp
+++ b/src/gromacs/analysisdata/abstractdata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/abstractdata.h"
+#include "abstractdata.h"
 
 #include <vector>
 

diff --git a/src/gromacs/analysisdata/abstractdata.h b/src/gromacs/analysisdata/abstractdata.h
index 6a122f58e22813c64c1fe2594d4716b1f383330f..07dc2ed0e45a0ea7fc4f8d9a56453c77d343818d 100644 (file)
--- a/src/gromacs/analysisdata/abstractdata.h
+++ b/src/gromacs/analysisdata/abstractdata.h
@@ -45,7 +45,7 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/analysisdata.cpp b/src/gromacs/analysisdata/analysisdata.cpp
index 1d9f023999930ead737fae906eb524a53242b481..300b2bd56f6fbf94c989bec8c6338c2386f6df53 100644 (file)
--- a/src/gromacs/analysisdata/analysisdata.cpp
+++ b/src/gromacs/analysisdata/analysisdata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/analysisdata.h"
+#include "analysisdata.h"
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datastorage.h"

diff --git a/src/gromacs/analysisdata/analysisdata.h b/src/gromacs/analysisdata/analysisdata.h
index 4de2c116bb112bba5ffd68a6e32267901675481d..b8849769ea847b06f19d5f4e32e9d0e95f185f2d 100644 (file)
--- a/src/gromacs/analysisdata/analysisdata.h
+++ b/src/gromacs/analysisdata/analysisdata.h
@@ -43,9 +43,8 @@
 #ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
 #define GMX_ANALYSISDATA_ANALYSISDATA_H
 
-#include "../utility/real.h"
-
-#include "abstractdata.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/arraydata.cpp b/src/gromacs/analysisdata/arraydata.cpp
index 6124ce6d677e486a41ca486314cb1aea85aa8df0..60d4c89cfd906f28eed43237355de96d97c0ca90 100644 (file)
--- a/src/gromacs/analysisdata/arraydata.cpp
+++ b/src/gromacs/analysisdata/arraydata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/arraydata.h"
+#include "arraydata.h"
 
 #include <algorithm>
 

diff --git a/src/gromacs/analysisdata/arraydata.h b/src/gromacs/analysisdata/arraydata.h
index 71efadf6edf385ce8424dce4a53cdc736b50b206..f255ae70f612e34f2e1dd7829fbccbdcb97854c0 100644 (file)
--- a/src/gromacs/analysisdata/arraydata.h
+++ b/src/gromacs/analysisdata/arraydata.h
@@ -45,10 +45,9 @@
 
 #include <vector>
 
-#include "../utility/gmxassert.h"
-
-#include "abstractdata.h"
-#include "dataframe.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/dataframe.h b/src/gromacs/analysisdata/dataframe.h
index b5d0da65e69fd354fbfc06bd254172e82b7409d4..5502063042bdf347db0e104c194bfd92ea28c926 100644 (file)
--- a/src/gromacs/analysisdata/dataframe.h
+++ b/src/gromacs/analysisdata/dataframe.h
@@ -45,10 +45,10 @@
 
 #include <vector>
 
-#include "../utility/arrayref.h"
-#include "../utility/flags.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/flags.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/datamodule.cpp b/src/gromacs/analysisdata/datamodule.cpp
index 694aeff0e881497af079f6739fe69465ea732f78..dde3922dbdd5f93398bb720dc8ec8657ab0d56ac 100644 (file)
--- a/src/gromacs/analysisdata/datamodule.cpp
+++ b/src/gromacs/analysisdata/datamodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/datamodule.h"
+#include "datamodule.h"
 
 #include "gromacs/analysisdata/paralleloptions.h"
 

diff --git a/src/gromacs/analysisdata/datamodulemanager.cpp b/src/gromacs/analysisdata/datamodulemanager.cpp
index 3a22614b7d83418accfeae4fd83d91049dbe7d23..5946a4f637ad7e45d1d6bd0626720ad66c8cf18f 100644 (file)
--- a/src/gromacs/analysisdata/datamodulemanager.cpp
+++ b/src/gromacs/analysisdata/datamodulemanager.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/datamodulemanager.h"
+#include "datamodulemanager.h"
 
 #include <vector>
 

diff --git a/src/gromacs/analysisdata/datamodulemanager.h b/src/gromacs/analysisdata/datamodulemanager.h
index 81ebbbbeee1ec429466e62380131934d4818a87d..4688ce01b3476461ba7472500fee627c68bf75b7 100644 (file)
--- a/src/gromacs/analysisdata/datamodulemanager.h
+++ b/src/gromacs/analysisdata/datamodulemanager.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,9 +43,8 @@
 #ifndef GMX_ANALYSISDATA_DATAMODULEMANAGER_H
 #define GMX_ANALYSISDATA_DATAMODULEMANAGER_H
 
-#include "abstractdata.h"
-
-#include "../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/dataproxy.h b/src/gromacs/analysisdata/dataproxy.h
index 50f6d52d5b861ebeb55e1c6512fbf9b79fae5115..d4c6af3b8fbe148eee8858ce68cdd1a86fa0bae8 100644 (file)
--- a/src/gromacs/analysisdata/dataproxy.h
+++ b/src/gromacs/analysisdata/dataproxy.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,8 +45,8 @@
 #ifndef GMX_ANALYSISDATA_DATAPROXY_H
 #define GMX_ANALYSISDATA_DATAPROXY_H
 
-#include "abstractdata.h"
-#include "datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/datastorage.h b/src/gromacs/analysisdata/datastorage.h
index 9c32aa8c8ff70a8cde37e3648adcb4dd829f817f..8fd2b00ff04ef2ee6de9d4dc2620fe64c0273b7c 100644 (file)
--- a/src/gromacs/analysisdata/datastorage.h
+++ b/src/gromacs/analysisdata/datastorage.h
@@ -45,11 +45,10 @@
 
 #include <vector>
 
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
-
-#include "dataframe.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/average.h b/src/gromacs/analysisdata/modules/average.h
index 3f8f583f06af68de7dbb3bb267cc35cf0d3daa87..558ee1e57b86d82e997d239cb1b7c9f3de558080 100644 (file)
--- a/src/gromacs/analysisdata/modules/average.h
+++ b/src/gromacs/analysisdata/modules/average.h
@@ -45,10 +45,10 @@
 
 #include <vector>
 
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/displacement.cpp b/src/gromacs/analysisdata/modules/displacement.cpp
index 1320d40eaf5c105b2ae51220853512f1cb3ea469..9b9b2f468d142476098947a1fc85a9f169308264 100644 (file)
--- a/src/gromacs/analysisdata/modules/displacement.cpp
+++ b/src/gromacs/analysisdata/modules/displacement.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/displacement.h"
+#include "displacement.h"
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datamodulemanager.h"

diff --git a/src/gromacs/analysisdata/modules/displacement.h b/src/gromacs/analysisdata/modules/displacement.h
index 88cac9ba508ff465eedc21cd605349648f445b4e..398acf11ad1e0254e4b11335dbc257353ab23005 100644 (file)
--- a/src/gromacs/analysisdata/modules/displacement.h
+++ b/src/gromacs/analysisdata/modules/displacement.h
@@ -43,10 +43,9 @@
 #ifndef GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
 #define GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
 
-#include "../../utility/real.h"
-
-#include "../abstractdata.h"
-#include "../datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/frameaverager.h b/src/gromacs/analysisdata/modules/frameaverager.h
index 7531abeb5d67e2980d44da52c1b4f3651222fa70..61867c24c4c084750d1c785d72413bb3675ebb3d 100644 (file)
--- a/src/gromacs/analysisdata/modules/frameaverager.h
+++ b/src/gromacs/analysisdata/modules/frameaverager.h
@@ -44,8 +44,8 @@
 
 #include <vector>
 
-#include "../../utility/gmxassert.h"
-#include "../../utility/real.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/histogram.cpp b/src/gromacs/analysisdata/modules/histogram.cpp
index 48df0079f7e8c1c40fd748e942f6426e75cc352a..cc9c601e962dd34123bf9ca57a3ad5746f9e8c88 100644 (file)
--- a/src/gromacs/analysisdata/modules/histogram.cpp
+++ b/src/gromacs/analysisdata/modules/histogram.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/histogram.h"
+#include "histogram.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/analysisdata/modules/histogram.h b/src/gromacs/analysisdata/modules/histogram.h
index c577dae07d12d132ef0071a5f85cbb35d4102ca2..280c4784f73a7be8412c0662d62b0366dc442a76 100644 (file)
--- a/src/gromacs/analysisdata/modules/histogram.h
+++ b/src/gromacs/analysisdata/modules/histogram.h
@@ -45,9 +45,9 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/lifetime.h b/src/gromacs/analysisdata/modules/lifetime.h
index 64560fdcdb525d058807c8bec034c050a35ea6cb..128fbfc0534eed05357fef46118c3033e6f7c8cb 100644 (file)
--- a/src/gromacs/analysisdata/modules/lifetime.h
+++ b/src/gromacs/analysisdata/modules/lifetime.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,9 +43,9 @@
 #ifndef GMX_ANALYSISDATA_MODULES_LIFETIME_H
 #define GMX_ANALYSISDATA_MODULES_LIFETIME_H
 
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/modules/plot.cpp b/src/gromacs/analysisdata/modules/plot.cpp
index 9ef70050f5edebe781f6ae05415909246f97c034..e421e2d64a85aea39d64679b758993531f6265a9 100644 (file)
--- a/src/gromacs/analysisdata/modules/plot.cpp
+++ b/src/gromacs/analysisdata/modules/plot.cpp
@@ -41,21 +41,20 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/plot.h"
-
-#include <string>
-#include <vector>
+#include "plot.h"
 
 #include <cstdio>
 #include <cstring>
 
-#include <boost/shared_ptr.hpp>
+#include <string>
+#include <vector>
 
-#include "gromacs/legacyheaders/oenv.h"
+#include <boost/shared_ptr.hpp>
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"

diff --git a/src/gromacs/analysisdata/modules/plot.h b/src/gromacs/analysisdata/modules/plot.h
index 916fa4a151eaba6e3ebe6ced0a6b9474cbf8bb6b..9696d54e66627f73d782c2c395aa771828964563 100644 (file)
--- a/src/gromacs/analysisdata/modules/plot.h
+++ b/src/gromacs/analysisdata/modules/plot.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,9 +47,9 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../datamodule.h"
-#include "../../options/timeunitmanager.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/tests/analysisdata.cpp b/src/gromacs/analysisdata/tests/analysisdata.cpp
index d8949f6c8a0c73b6e70935289628feaad6e44e63..7cdd8baffa67df33e607a06d0a96e06c14e94cd3 100644 (file)
--- a/src/gromacs/analysisdata/tests/analysisdata.cpp
+++ b/src/gromacs/analysisdata/tests/analysisdata.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/analysisdata.h"
+
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/paralleloptions.h"
 #include "gromacs/utility/exceptions.h"
 

diff --git a/src/gromacs/analysisdata/tests/arraydata.cpp b/src/gromacs/analysisdata/tests/arraydata.cpp
index eec3aa3f08ca2baf4c1e56d84f0ae1b0eade741e..56b73ecedfd6c48c7578e9c09e4beacdce48f22a 100644 (file)
--- a/src/gromacs/analysisdata/tests/arraydata.cpp
+++ b/src/gromacs/analysisdata/tests/arraydata.cpp
@@ -46,10 +46,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/analysisdata/arraydata.h"
 
+#include <gtest/gtest.h>
+
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"
 

diff --git a/src/gromacs/analysisdata/tests/average.cpp b/src/gromacs/analysisdata/tests/average.cpp
index 64d3eeccddcd5d841e71a367baf6b2c91e6f1cfa..cbfc91cd2aa5e8523104ade246b20d579889b1dd 100644 (file)
--- a/src/gromacs/analysisdata/tests/average.cpp
+++ b/src/gromacs/analysisdata/tests/average.cpp
@@ -48,10 +48,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/average.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/analysisdata/tests/histogram.cpp b/src/gromacs/analysisdata/tests/histogram.cpp
index baf6774786dff981295a91a577a78a58e67b50b1..491568b49f84ef21bc5ce8924de779e728ef9272 100644 (file)
--- a/src/gromacs/analysisdata/tests/histogram.cpp
+++ b/src/gromacs/analysisdata/tests/histogram.cpp
@@ -48,10 +48,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/histogram.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/histogram.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/analysisdata/tests/lifetime.cpp b/src/gromacs/analysisdata/tests/lifetime.cpp
index c15421392222a1e0315635c89066f20aca24d72d..7364b1c7d587211a193a180d36b6429923a6cfb8 100644 (file)
--- a/src/gromacs/analysisdata/tests/lifetime.cpp
+++ b/src/gromacs/analysisdata/tests/lifetime.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/lifetime.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/lifetime.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/bonded/bonded.cpp b/src/gromacs/bonded/bonded.cpp
index 0ad3139599b1f8aa49333ea3e932247626d4e381..481c34ae8a75ca9e1a305112dbea8582e8b0e5fa 100644 (file)
--- a/src/gromacs/bonded/bonded.cpp
+++ b/src/gromacs/bonded/bonded.cpp
@@ -41,22 +41,23 @@
 #include "config.h"
 
 #include <assert.h>
+
 #include <cmath>
 
 #include <algorithm>
 
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/bonded/restcbt.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -66,8 +67,6 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "restcbt.h"
-
 /* Find a better place for this? */
 const int cmap_coeff_matrix[] = {
     1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4,

diff --git a/src/gromacs/bonded/bonded.h b/src/gromacs/bonded/bonded.h
index 542f57976735446611b9a1859f12915324820720..0fdc81d9fcc7637d86c07aac40b2a5a2e558f252 100644 (file)
--- a/src/gromacs/bonded/bonded.h
+++ b/src/gromacs/bonded/bonded.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/bonded/restcbt.h b/src/gromacs/bonded/restcbt.h
index 9f2490c19b07f02c9ea0efbeb044e260558875b9..66a5f96fde7c6c743bace9d69262887af59908bd 100644 (file)
--- a/src/gromacs/bonded/restcbt.h
+++ b/src/gromacs/bonded/restcbt.h
@@ -52,8 +52,8 @@
 #define GMX_BONDED_RESTCBT_H
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/topology/idef.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/commandline.h b/src/gromacs/commandline.h
index d29ba2668f63a35b2bae5a2cd1d9d17e67ba27c5..eeba8f3ab33773a709346eed965afe1ce33555e5 100644 (file)
--- a/src/gromacs/commandline.h
+++ b/src/gromacs/commandline.h
@@ -78,10 +78,10 @@
 #ifndef GMX_COMMANDLINE_H
 #define GMX_COMMANDLINE_H
 
-#include "commandline/cmdlinehelpwriter.h"
-#include "commandline/cmdlineinit.h"
-#include "commandline/cmdlinemodule.h"
-#include "commandline/cmdlineparser.h"
-#include "commandline/pargs.h"
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/commandline/cmdlineinit.h"
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/commandline/pargs.h"
 
 #endif

diff --git a/src/gromacs/commandline/cmdlinehelpcontext.cpp b/src/gromacs/commandline/cmdlinehelpcontext.cpp
index e90ede652c95bb292dbd844b847cf748d47d0f9b..e98997e5bf0aef0b68d44cc85f11d56bb82fcc2a 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpcontext.cpp
+++ b/src/gromacs/commandline/cmdlinehelpcontext.cpp
@@ -43,9 +43,10 @@
 
 #include "cmdlinehelpcontext.h"
 
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/utility/gmxassert.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlinehelpcontext.h b/src/gromacs/commandline/cmdlinehelpcontext.h
index 154facababb6da14390e4f388c45bdfecdfff4d0..57aa7363c3275f9ab531844fcbd834eabea490c7 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpcontext.h
+++ b/src/gromacs/commandline/cmdlinehelpcontext.h
@@ -43,8 +43,8 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
 #define GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
 
-#include "../onlinehelp/helpwritercontext.h"
-#include "../utility/common.h"
+#include "gromacs/onlinehelp/helpwritercontext.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlinehelpmodule.cpp b/src/gromacs/commandline/cmdlinehelpmodule.cpp
index 585413df04e3a2c8879780cf4edf5b32a910cda0..3a67a1ff4ab4008f77a9d825c305bc561abca3ac 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpmodule.cpp
+++ b/src/gromacs/commandline/cmdlinehelpmodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/cmdlinehelpmodule.h"
+#include "cmdlinehelpmodule.h"
 
 #include <string>
 #include <vector>
@@ -51,7 +51,6 @@
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/cmdlinehelpwriter.h"
 #include "gromacs/commandline/cmdlineparser.h"
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/onlinehelp/helpformat.h"
 #include "gromacs/onlinehelp/helpmanager.h"
 #include "gromacs/onlinehelp/helptopic.h"
@@ -65,6 +64,8 @@
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlinehelpmodule.h b/src/gromacs/commandline/cmdlinehelpmodule.h
index 9fa23b9f31ba9d0ea50fcf3e1e9acac5fa9cce04..6b6d33413c96d48793b412410bf31ef98ab8bc87 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpmodule.h
+++ b/src/gromacs/commandline/cmdlinehelpmodule.h
@@ -42,12 +42,12 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPMODULE_H
 #define GMX_COMMANDLINE_CMDLINEHELPMODULE_H
 
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager-impl.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
 #include "gromacs/onlinehelp/helptopicinterface.h"
 #include "gromacs/utility/common.h"
 
+#include "cmdlinemodulemanager-impl.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlinehelpwriter.cpp b/src/gromacs/commandline/cmdlinehelpwriter.cpp
index b410e904af8441624f1aabe08a60fb4ab476d8cf..0c79bd393451006b0e4c5161ced2b0ab4170a1dd 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpwriter.cpp
+++ b/src/gromacs/commandline/cmdlinehelpwriter.cpp
@@ -51,7 +51,6 @@
 #include <boost/scoped_ptr.hpp>
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/onlinehelp/helpformat.h"
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/options/basicoptions.h"
@@ -64,6 +63,8 @@
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlinehelpwriter.h b/src/gromacs/commandline/cmdlinehelpwriter.h
index 1ab3add95268e8c93e084541a96bbda11c9be7d5..3ffd581c7e415cb86bba081ab046e142c3f27cd0 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpwriter.h
+++ b/src/gromacs/commandline/cmdlinehelpwriter.h
@@ -43,7 +43,7 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPWRITER_H
 #define GMX_COMMANDLINE_CMDLINEHELPWRITER_H
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlineinit.cpp b/src/gromacs/commandline/cmdlineinit.cpp
index 853901386c8bc495de91d6a608ec38b749633515..8fe171ee058c34e3ba807a752211baea35b95afd 100644 (file)
--- a/src/gromacs/commandline/cmdlineinit.cpp
+++ b/src/gromacs/commandline/cmdlineinit.cpp
@@ -41,25 +41,24 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/cmdlineinit.h"
+#include "cmdlineinit.h"
+
+#include "config.h"
 
 #include <cstring>
 
 #include <boost/scoped_ptr.hpp>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/init.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlineinit.h b/src/gromacs/commandline/cmdlineinit.h
index 5c0fc026eb2b3aae9c9b84c96242502b6916b76e..ae4089f4aea58c462297cb1a50de6e5683a944da 100644 (file)
--- a/src/gromacs/commandline/cmdlineinit.h
+++ b/src/gromacs/commandline/cmdlineinit.h
@@ -47,7 +47,7 @@
 
 // Forward declaration of class CommandLineProgramContext is not sufficient for
 // MSVC if the return value of initForCommandLine() is ignored(!)
-#include "cmdlineprogramcontext.h"
+#include "gromacs/commandline/cmdlineprogramcontext.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlinemodulemanager-impl.h b/src/gromacs/commandline/cmdlinemodulemanager-impl.h
index 5a56b68f5c4643f9afed62b66fadae4889438667..847b623a751ecec3ef51df615de3dc839b1b6c3e 100644 (file)
--- a/src/gromacs/commandline/cmdlinemodulemanager-impl.h
+++ b/src/gromacs/commandline/cmdlinemodulemanager-impl.h
@@ -46,9 +46,8 @@
 #include <string>
 #include <vector>
 
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/options/options.h"
 #include "gromacs/utility/common.h"

diff --git a/src/gromacs/commandline/cmdlinemodulemanager.cpp b/src/gromacs/commandline/cmdlinemodulemanager.cpp
index b026f8b0db6382f5ac1fec59895ca35c8d7c8188..8fee8aa10e28ca0cef593bdd1b1d1a8ffc6410e5 100644 (file)
--- a/src/gromacs/commandline/cmdlinemodulemanager.cpp
+++ b/src/gromacs/commandline/cmdlinemodulemanager.cpp
@@ -43,26 +43,23 @@
 
 #include "cmdlinemodulemanager.h"
 
+#include "config.h"
+
 #include <cstdio>
 
 #include <string>
 #include <utility>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpmodule.h"
 #include "gromacs/commandline/cmdlineinit.h"
 #include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager-impl.h"
 #include "gromacs/commandline/cmdlineparser.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/utility/basenetwork.h"
@@ -71,6 +68,9 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "cmdlinehelpmodule.h"
+#include "cmdlinemodulemanager-impl.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/commandline/cmdlinemodulemanager.h b/src/gromacs/commandline/cmdlinemodulemanager.h
index 9fb4432f826cca2518897862e31ab3d12a1456cd..62b39488ca28461e37673d088c16cbd36b9bc236 100644 (file)
--- a/src/gromacs/commandline/cmdlinemodulemanager.h
+++ b/src/gromacs/commandline/cmdlinemodulemanager.h
@@ -43,9 +43,9 @@
 #ifndef GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
 #define GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
 
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlineparser.h b/src/gromacs/commandline/cmdlineparser.h
index 7f4768c04ede6b0e0e7f50c8db7f97530de75d48..c497410e5077f8f6dc7cfc842286b115355c9245 100644 (file)
--- a/src/gromacs/commandline/cmdlineparser.h
+++ b/src/gromacs/commandline/cmdlineparser.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlineprogramcontext.h b/src/gromacs/commandline/cmdlineprogramcontext.h
index 206585669aebbcd832e78f2021d317858fc19670..bfcc17322c5b6e7f192d5b4b61961d402a273aac 100644 (file)
--- a/src/gromacs/commandline/cmdlineprogramcontext.h
+++ b/src/gromacs/commandline/cmdlineprogramcontext.h
@@ -53,8 +53,8 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../utility/common.h"
-#include "../utility/programcontext.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/programcontext.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/pargs.cpp b/src/gromacs/commandline/pargs.cpp
index 5a16f3cf48ba90b203322c83f95f3f9e4dd419a5..8b7a459d8f3561038cbd1b4bf6f250c2922bb5b3 100644 (file)
--- a/src/gromacs/commandline/pargs.cpp
+++ b/src/gromacs/commandline/pargs.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/pargs.h"
+#include "pargs.h"
 
 #include <cstdlib>
 #include <cstring>

diff --git a/src/gromacs/commandline/pargs.h b/src/gromacs/commandline/pargs.h
index f6a2ab680cc0f5f23605ab15365b06aa5816e237..9c81a77cb229eb2e14d01cf4289da62b71e3e06a 100644 (file)
--- a/src/gromacs/commandline/pargs.h
+++ b/src/gromacs/commandline/pargs.h
@@ -44,11 +44,11 @@
 #ifndef GMX_COMMANDLINE_PARGS_H
 #define GMX_COMMANDLINE_PARGS_H
 
-#include "../legacyheaders/oenv.h"
-#include "../fileio/filenm.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/commandline/shellcompletions.cpp b/src/gromacs/commandline/shellcompletions.cpp
index e047cf256041b12e731df316ac96ece1e3d8fa24..1eefeda1cf6fd282965b63511aab391030368ca4 100644 (file)
--- a/src/gromacs/commandline/shellcompletions.cpp
+++ b/src/gromacs/commandline/shellcompletions.cpp
@@ -43,7 +43,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/shellcompletions.h"
+#include "shellcompletions.h"
 
 #include <cstdio>
 
@@ -53,10 +53,10 @@
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
 #include "gromacs/options/optionsvisitor.h"
-#include "gromacs/fileio/filenm.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"

diff --git a/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp b/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
index c5db3a916cc70f57325ef3ff17f92c27e3ecd8ca..a545dcc835556abd1b4c2bfaf3883ed2c7c55bf7 100644 (file)
--- a/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
+++ b/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpwriter.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"

diff --git a/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp b/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
index 0d8f4fc4cc35f463cf8afc5d92be1c4794639b5f..ebb3ee1f5fb67d5dce49bdaafc21b23baa943a41 100644 (file)
--- a/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
+++ b/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
@@ -42,6 +42,8 @@
 // For GMX_BINARY_SUFFIX
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlinemodulemanager.h"
+
 #include "config.h"
 
 #include <vector>
@@ -50,7 +52,6 @@
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
 #include "gromacs/utility/file.h"
 

diff --git a/src/gromacs/commandline/tests/cmdlineparser.cpp b/src/gromacs/commandline/tests/cmdlineparser.cpp
index 6e408528c53b9deb2b719c843ffbb8725aca895a..719e69d34f71917e67a1c1a2198387b44eee4e99 100644 (file)
--- a/src/gromacs/commandline/tests/cmdlineparser.cpp
+++ b/src/gromacs/commandline/tests/cmdlineparser.cpp
@@ -44,11 +44,12 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlineparser.h"
+
 #include <vector>
 
 #include <gtest/gtest.h>
 
-#include "gromacs/commandline/cmdlineparser.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 

diff --git a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
index c7ee818a48a2dfbfbee565bab616970bdea8a87e..f31c3ea405220bacb8763ec947771fe9b3415e12 100644 (file)
--- a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
+++ b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
@@ -41,20 +41,21 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlineprogramcontext.h"
+
+#include "config.h"
+
 #include <string>
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
 #include <gtest/gtest.h>
 
-#include "gromacs/commandline/cmdlineprogramcontext.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/path.h"
 
 #include "testutils/cmdlinetest.h"
 
-#include "config.h"
-
 using gmx::test::CommandLine;
 using gmx::Path;
 

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 38be02d5236b9e5780088ebd2e8f17b16d074410..e6cab41f9c7a5d50c7dbb2c190f7fa70305a5076 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "edsam.h"
+
 #include <stdio.h>
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/mdlib/groupcoord.h"
-
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))

diff --git a/src/gromacs/essentialdynamics/edsam.h b/src/gromacs/essentialdynamics/edsam.h
index 32322ad580513eb63423b65cbc6aab5ec6dbf155..20cbaf442b0e3e2ed59abf8a06b282466389c6d1 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.h
+++ b/src/gromacs/essentialdynamics/edsam.h
@@ -48,8 +48,8 @@
 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fft/fft.cpp b/src/gromacs/fft/fft.cpp
index 26ac29acbe2da25a871ebc14d53c0a6d13c14972..2d8a81e17b58b2df9c82c4429eb7e1bbc966842f 100644 (file)
--- a/src/gromacs/fft/fft.cpp
+++ b/src/gromacs/fft/fft.cpp
@@ -35,7 +35,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fft/fft.h"
+#include "fft.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/fft/fft.h b/src/gromacs/fft/fft.h
index cfce41baab2aaa0555706fbf68a021d93eba2f62..69fe46289b18bfe3b73bc7d6354b3bade249d2ce 100644 (file)
--- a/src/gromacs/fft/fft.h
+++ b/src/gromacs/fft/fft.h
@@ -54,8 +54,8 @@
 
 #include <stdio.h>
 
-#include "../math/gmxcomplex.h"
-#include "../utility/real.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fft/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
index 1e9e11bd70a7757568d5115bf35726db5f5072f2..d22662291698cee874c6e2ef6788e27e25b609cd 100644 (file)
--- a/src/gromacs/fft/fft5d.cpp
+++ b/src/gromacs/fft/fft5d.cpp
@@ -36,6 +36,8 @@
 
 #include "fft5d.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <float.h>
 #include <math.h>
@@ -49,8 +51,6 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 #ifdef NOGMX
 #define GMX_PARALLEL_ENV_INITIALIZED 1
 #else

diff --git a/src/gromacs/fft/fft_fftpack.cpp b/src/gromacs/fft/fft_fftpack.cpp
index c0f412bf6ebd8f688cbdeabe6b2c1b3c8beb6fc9..1301723da1aeddeceb2bc0b0cd00185c23907f9e 100644 (file)
--- a/src/gromacs/fft/fft_fftpack.cpp
+++ b/src/gromacs/fft/fft_fftpack.cpp
@@ -35,18 +35,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fft/fft.h"
-
 #include <errno.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "external/fftpack/fftpack.h"
+
+#include "gromacs/fft/fft.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/real.h"
 
-#include "external/fftpack/fftpack.h"
-
 /*! \internal
  * \brief
  * Contents of the FFTPACK fft datatype.

diff --git a/src/gromacs/fft/fft_fftw3.cpp b/src/gromacs/fft/fft_fftw3.cpp
index d83d0f591b0604f7a8cdec3dc5a988eec0d9fce2..dee2ff284b473c41aa250438cbde4f824cf9dd53 100644 (file)
--- a/src/gromacs/fft/fft_fftw3.cpp
+++ b/src/gromacs/fft/fft_fftw3.cpp
@@ -35,6 +35,8 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdlib.h>
 
@@ -46,8 +48,6 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 
-#include "config.h"
-
 #ifdef GMX_DOUBLE
 #define FFTWPREFIX(name) fftw_ ## name
 #else

diff --git a/src/gromacs/fft/parallel_3dfft.cpp b/src/gromacs/fft/parallel_3dfft.cpp
index f721bab65f500464461f2b75dfd5445a9c250eba..3c04fb24fc57d7ad177f927519555b9c124ed735 100644 (file)
--- a/src/gromacs/fft/parallel_3dfft.cpp
+++ b/src/gromacs/fft/parallel_3dfft.cpp
@@ -35,19 +35,18 @@
  */
 #include "gmxpre.h"
 
+#include "parallel_3dfft.h"
+
+#include <errno.h>
 #include <stdlib.h>
 #include <string.h>
-#include <errno.h>
 
 #include "gromacs/fft/fft.h"
-#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fft/fft5d.h"
 #include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
-
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "fft5d.h"
 
 struct gmx_parallel_3dfft  {
     fft5d_plan p1, p2;

diff --git a/src/gromacs/fft/parallel_3dfft.h b/src/gromacs/fft/parallel_3dfft.h
index 2a3fe97d5fa49ee8a410cf382b9341b465e4fd28..145b0a97b7bb241ffa35f3f217125cdc5c5a5e64 100644 (file)
--- a/src/gromacs/fft/parallel_3dfft.h
+++ b/src/gromacs/fft/parallel_3dfft.h
@@ -37,13 +37,12 @@
 #ifndef GMX_FFT_PARALLEL_3DFFT_H
 #define GMX_FFT_PARALLEL_3DFFT_H
 
-#include "../math/gmxcomplex.h"
-#include "../timing/wallcycle.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/gmxmpi.h"
-#include "../utility/real.h"
-
-#include "fft.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fft/tests/fft.cpp b/src/gromacs/fft/tests/fft.cpp
index e0d80ad9743f257b0f34a62d4be42b76f10777c5..446d50307f9e2bf2da800be03ed2a2550f264f2d 100644 (file)
--- a/src/gromacs/fft/tests/fft.cpp
+++ b/src/gromacs/fft/tests/fft.cpp
@@ -44,11 +44,12 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/fft/fft.h"
+
 #include <vector>
 
 #include <gtest/gtest.h>
 
-#include "gromacs/fft/fft.h"
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 57aff53965f5fc2b76fe05a452ee05cafbd51cad..ef01aa45f771f253c55c0b94b7ee93e5ce333e86 100644 (file)
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -42,25 +42,24 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
-#include "xdrf.h"
-#include "filenm.h"
-#include "pdbio.h"
-#include "tpxio.h"
-#include "trxio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gmxfio.h"
-
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define CHAR_SHIFT 24

diff --git a/src/gromacs/fileio/confio.h b/src/gromacs/fileio/confio.h
index 6fbafb3ee485e1bcbf146f0ed14cce99dc8fa761..2b149c23a82b59884c77e6b218554834b8e03e24 100644 (file)
--- a/src/gromacs/fileio/confio.h
+++ b/src/gromacs/fileio/confio.h
@@ -40,9 +40,8 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
-
-#include "trx.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 /* For reading coordinate files it is assumed that enough memory
  * has been allocated beforehand.

diff --git a/src/gromacs/fileio/enxio.c b/src/gromacs/fileio/enxio.c
index d6dce5f4ab98e589d84a9c33cf08f3a2d5f0cf36..c9b34b1da1f0538caabee990e9f9d6e0caaa1c46 100644 (file)
--- a/src/gromacs/fileio/enxio.c
+++ b/src/gromacs/fileio/enxio.c
@@ -41,15 +41,14 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* The source code in this file should be thread-safe.

diff --git a/src/gromacs/fileio/enxio.h b/src/gromacs/fileio/enxio.h
index acf41f05f1a1e9e2e44f696a4ef3233f4c72db9a..c8434ab2b53135cb6b2c2639b5b4f75f9f14509e 100644 (file)
--- a/src/gromacs/fileio/enxio.h
+++ b/src/gromacs/fileio/enxio.h
@@ -37,11 +37,11 @@
 #ifndef GMX_FILEIO_ENXIO_H
 #define GMX_FILEIO_ENXIO_H
 
-#include "../legacyheaders/types/energy.h"
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/state.h"
-#include "gmxfio.h"
-#include "xdr_datatype.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.c
index bf8212d2c85468be4e88b97aa65d9cf92146be9c..782424df600a423c45856ff35feda0a4e24b246c 100644 (file)
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.c
@@ -43,7 +43,6 @@
 
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/fileio/filenm.h b/src/gromacs/fileio/filenm.h
index e4dfab80ae8c1a64e05008b557c5fedb5ab2f511..0dcfd73b9d57fed2ad9f624724de42c0f28f3561 100644 (file)
--- a/src/gromacs/fileio/filenm.h
+++ b/src/gromacs/fileio/filenm.h
@@ -38,8 +38,8 @@
 #ifndef GMX_FILEIO_FILENM_H
 #define GMX_FILEIO_FILENM_H
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/gmx_system_xdr.c b/src/gromacs/fileio/gmx_system_xdr.c
index cb10ba0abbfbdac6e428507390cf6f8161119cec..9839291218526b1bbfa188a44f7795ec8d5bfc73 100644 (file)
--- a/src/gromacs/fileio/gmx_system_xdr.c
+++ b/src/gromacs/fileio/gmx_system_xdr.c
@@ -41,12 +41,12 @@
 #ifdef GMX_INTERNAL_XDR
 
 
-#include <stdlib.h>
+#include "gmx_system_xdr.h"
+
 #include <limits.h>
+#include <stdlib.h>
 #include <string.h>
 
-#include "gmx_system_xdr.h"
-
 
 /* NB - THIS FILE IS ONLY USED ON MICROSOFT WINDOWS, since that
  * system doesn't provide any standard XDR system libraries. It will

diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index e191b217e96d614f1ac6eb276dc5d1fe817a456b..cad0b389519d0ce2e7b5b6a5844a04cfba9266c6 100644 (file)
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -38,12 +38,12 @@
 
 #include "gmxfio.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif

diff --git a/src/gromacs/fileio/gmxfio.h b/src/gromacs/fileio/gmxfio.h
index 8f6401da230b7a197777d4bbd8112ba9406ed419..bc656d2ef98fda4fbaae00711778d25d4d713078 100644 (file)
--- a/src/gromacs/fileio/gmxfio.h
+++ b/src/gromacs/fileio/gmxfio.h
@@ -40,10 +40,10 @@
 
 #include <stdio.h>
 
-#include "../utility/cstringutil.h"
-#include "../utility/futil.h"
-#include "../utility/real.h"
-#include "../math/vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/gmxfio_asc.c b/src/gromacs/fileio/gmxfio_asc.c
index b2f04b7ff8464de349ee1e459a4fa9e9b3e29e4e..153e345726ea88667aa6d80022eea5efd1e6160c 100644 (file)
--- a/src/gromacs/fileio/gmxfio_asc.c
+++ b/src/gromacs/fileio/gmxfio_asc.c
@@ -36,13 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <ctype.h>
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif

diff --git a/src/gromacs/fileio/gmxfio_bin.c b/src/gromacs/fileio/gmxfio_bin.c
index 498a795eb4da99a8bf5544e08da2f17a8b793ac9..9238af5fa137a37ce3e2428ac359f48e3f31ff00 100644 (file)
--- a/src/gromacs/fileio/gmxfio_bin.c
+++ b/src/gromacs/fileio/gmxfio_bin.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif

diff --git a/src/gromacs/fileio/gmxfio_int.h b/src/gromacs/fileio/gmxfio_int.h
index cedde9ae907317e4960af5a66ddbf6df88dcc871..e7010b15f32fbecc34189362cb6f11e9712f0f16 100644 (file)
--- a/src/gromacs/fileio/gmxfio_int.h
+++ b/src/gromacs/fileio/gmxfio_int.h
@@ -58,7 +58,7 @@
 
 #include "thread_mpi/lock.h"
 
-#include "xdrf.h"
+#include "gromacs/fileio/xdrf.h"
 
 /* the reader/writer functions  for t_iotype */
 typedef gmx_bool read_func (t_fileio *fio, void *item, int nitem, int eio,

diff --git a/src/gromacs/fileio/gmxfio_rw.c b/src/gromacs/fileio/gmxfio_rw.c
index d41d19176a953be2c43d9a4b14625ad23ca79612..bdfa1ec4d80b9d3bc2e061dc2becc3f316bfac01 100644 (file)
--- a/src/gromacs/fileio/gmxfio_rw.c
+++ b/src/gromacs/fileio/gmxfio_rw.c
@@ -36,11 +36,11 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif

diff --git a/src/gromacs/fileio/gmxfio_xdr.c b/src/gromacs/fileio/gmxfio_xdr.c
index 6054be42f9db211b2e9f7bad508407feadbb1d0e..ca1b70d21e43521ea239790646026fcd292672ed 100644 (file)
--- a/src/gromacs/fileio/gmxfio_xdr.c
+++ b/src/gromacs/fileio/gmxfio_xdr.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif

diff --git a/src/gromacs/fileio/libxdrf.c b/src/gromacs/fileio/libxdrf.c
index 98957275c014e2dd401ed5f8a54168f262951832..90e58d4ee251c740b9281b023a106ac9b24e326c 100644 (file)
--- a/src/gromacs/fileio/libxdrf.c
+++ b/src/gromacs/fileio/libxdrf.c
@@ -42,8 +42,8 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "xdrf.h"
-#include "xdr_datatype.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
 #include "gromacs/utility/futil.h"
 
 /* This is just for clarity - it can never be anything but 4! */

diff --git a/src/gromacs/fileio/matio.h b/src/gromacs/fileio/matio.h
index 988d751d267dc1bc18c7683518aa9ae83141235b..1facdf56086fcbad3a0d94bca628f5e9cf4abb01 100644 (file)
--- a/src/gromacs/fileio/matio.h
+++ b/src/gromacs/fileio/matio.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/rgb.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/md5.c b/src/gromacs/fileio/md5.c
index ad3c36aaad3262af62c7c7bb4d110a4c2c59ecfc..ff74cc68d073b5a4b4c5b73926a7c8424b48e48c 100644 (file)
--- a/src/gromacs/fileio/md5.c
+++ b/src/gromacs/fileio/md5.c
@@ -99,6 +99,7 @@
  */
 
 #include "md5.h"
+
 #include <string.h>
 
 #undef BYTE_ORDER   /* 1 = big-endian, -1 = little-endian, 0 = unknown */

diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.c
index 4532b7d65b1ee1b9a9290fc8efece4a83328c680..844c84602e5eec689f081782194c2f331d6e5701 100644 (file)
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.c
@@ -36,22 +36,21 @@
 
 #include "mdoutf.h"
 
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "tngio.h"
-#include "trajectory_writing.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/timing/wallcycle.h"
 
 struct gmx_mdoutf {
     t_fileio         *fp_trn;

diff --git a/src/gromacs/fileio/mdoutf.h b/src/gromacs/fileio/mdoutf.h
index 7c9f2a3309188c12cbf4f7fd1b7f725b25c6355a..8e241f4e3e366425ceba47533ddaa23192802f50 100644 (file)
--- a/src/gromacs/fileio/mdoutf.h
+++ b/src/gromacs/fileio/mdoutf.h
@@ -38,15 +38,14 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/oenv.h"
-#include "../legacyheaders/network.h"
-
-#include "../math/vectypes.h"
-#include "../timing/wallcycle.h"
-#include "../utility/basedefinitions.h"
-#include "filenm.h"
-#include "enxio.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/mtxio.h b/src/gromacs/fileio/mtxio.h
index abbe0fb67488730cda650f14cc2d2b35ea00fe6f..4f9216e5d3728f3d09962d86d7a334b9316e6889 100644 (file)
--- a/src/gromacs/fileio/mtxio.h
+++ b/src/gromacs/fileio/mtxio.h
@@ -43,8 +43,8 @@
 #ifndef GMX_FILEIO_MTXIO_H
 #define GMX_FILEIO_MTXIO_H
 
-#include "../linearalgebra/sparsematrix.h"
-#include "../utility/real.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index 05c0cf13222ce646afd0e0049ea179cb8c795764..d5b8a00517490597e4026700b86545834708fff4 100644 (file)
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -42,12 +42,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -57,6 +55,7 @@
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {

diff --git a/src/gromacs/fileio/pdbio.h b/src/gromacs/fileio/pdbio.h
index 241239a8a6aa27039b43b75b254f9682d9a45a9e..3e13161126c3d9c07b9765b303f720c8a21cb8b1 100644 (file)
--- a/src/gromacs/fileio/pdbio.h
+++ b/src/gromacs/fileio/pdbio.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/strdb.c b/src/gromacs/fileio/strdb.c
index 21f70b014f3f0f8a65529eeeb8789cc151e8410d..7d6ff971f8f0b88bc3ae6c359a0ffe271b1a87da 100644 (file)
--- a/src/gromacs/fileio/strdb.c
+++ b/src/gromacs/fileio/strdb.c
@@ -42,11 +42,10 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
-
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 gmx_bool get_a_line(FILE *fp, char line[], int n)
 {

diff --git a/src/gromacs/fileio/strdb.h b/src/gromacs/fileio/strdb.h
index bcc2cf98e6d6280239fabe6000f992a07f1ae4d2..dc35b915adeec5d2e2bef526cfff4559d8c69de7 100644 (file)
--- a/src/gromacs/fileio/strdb.h
+++ b/src/gromacs/fileio/strdb.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/tests/tngio.cpp b/src/gromacs/fileio/tests/tngio.cpp
index 1eab0e4c8667f4be02fa9cddfc9838ab10a7d848..6c5cbef3498731ad88b6e7074bce1c9f10b96629 100644 (file)
--- a/src/gromacs/fileio/tests/tngio.cpp
+++ b/src/gromacs/fileio/tests/tngio.cpp
@@ -41,10 +41,12 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
+#include "gromacs/fileio/tngio.h"
+
 #include <string>
 
-#include "gromacs/fileio/tngio.h"
+#include <gtest/gtest.h>
+
 #include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/utility/path.h"
 

diff --git a/src/gromacs/fileio/timecontrol.c b/src/gromacs/fileio/timecontrol.c
index 4c355ae13b71d6217f4cc1aac446d1ac7ad760d6..735d649423d480023d3a93757770078d8244b5f4 100644 (file)
--- a/src/gromacs/fileio/timecontrol.c
+++ b/src/gromacs/fileio/timecontrol.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fileio/timecontrol.h"
+#include "timecontrol.h"
 
 #include "thread_mpi/threads.h"
 

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index b677014564098d9ab2c65d5d4cf6a220ea1ec600..1303872d3d8364a0ee2a3405b1efc82a2d0c9ee8 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -46,10 +46,9 @@
 #include "tng/tng_io.h"
 #endif
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index cdc1263badc34a153dd42962508eb19d2150c77f..b4cfc5f011924f0ab868360e2c7e06be94da68bd 100644 (file)
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -36,10 +36,10 @@
 
 #include "tngio_for_tools.h"
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #ifdef GMX_USE_TNG
 #include "tng/tng_io.h"
 #endif

diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index db684d369936b2908e6bdccb073710b58ad0496b..4fba747508fc6bb1bec86b89c7fd93924bf11bf7 100644 (file)
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -38,19 +38,18 @@
 
 /* This file is completely threadsafe - keep it that way! */
 
+#include "tpxio.h"
+
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "tpxio.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "confio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
@@ -59,6 +58,7 @@
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define TPX_TAG_RELEASE  "release"

diff --git a/src/gromacs/fileio/tpxio.h b/src/gromacs/fileio/tpxio.h
index 433742fdcdafa5b470f26005591e0d44aa5e7446..0b3ca43e312d08841fb44c7c0725ea8f92664363 100644 (file)
--- a/src/gromacs/fileio/tpxio.h
+++ b/src/gromacs/fileio/tpxio.h
@@ -47,9 +47,9 @@
  * can also be used with the routines in gmxfio.h
  *
  **************************************************************/
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/state.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/trajectory_writing.c b/src/gromacs/fileio/trajectory_writing.c
index c28a834bb52c0f7d0624723e334437ba99084d11..01b83b7de14a6aba03bb4fcfe95f21185761284a 100644 (file)
--- a/src/gromacs/fileio/trajectory_writing.c
+++ b/src/gromacs/fileio/trajectory_writing.c
@@ -34,17 +34,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "confio.h"
 #include "trajectory_writing.h"
-#include "mdoutf.h"
 
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/smalloc.h"
 
 void
 do_md_trajectory_writing(FILE           *fplog,

diff --git a/src/gromacs/fileio/trajectory_writing.h b/src/gromacs/fileio/trajectory_writing.h
index e604eb58b22b89ff2dd74edfe40e41c7978ee932..37956342b12935f467d4e37efff681e0969a0748 100644 (file)
--- a/src/gromacs/fileio/trajectory_writing.h
+++ b/src/gromacs/fileio/trajectory_writing.h
@@ -40,12 +40,11 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/mdebin.h"
-#include "../timing/wallcycle.h"
-
-#include "filenm.h"
-#include "mdoutf.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/trnio.c b/src/gromacs/fileio/trnio.c
index a85a82f3c98cefc6f326370f77b3569b4b10af4a..a1d6c8cbd7730ee617dbb51351c39ef689e3b425 100644 (file)
--- a/src/gromacs/fileio/trnio.c
+++ b/src/gromacs/fileio/trnio.c
@@ -36,14 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "trnio.h"
+
 #include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "trnio.h"
-#include "gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 #define BUFSIZE     128
 #define GROMACS_MAGIC   1993

diff --git a/src/gromacs/fileio/trnio.h b/src/gromacs/fileio/trnio.h
index 59bf1d4122ad51b7e2284099c1c01cad4ae57c69..0dcc1e03993b579fc6bfa0f0f22d62f76baa104d 100644 (file)
--- a/src/gromacs/fileio/trnio.h
+++ b/src/gromacs/fileio/trnio.h
@@ -53,7 +53,7 @@
  *
  **************************************************************/
 
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/trx.h b/src/gromacs/fileio/trx.h
index dbbfc4b94982083210b32698d9d84280c947d8a1..9e551b5405c2f48a16b99182e77061140f3a0ddd 100644 (file)
--- a/src/gromacs/fileio/trx.h
+++ b/src/gromacs/fileio/trx.h
@@ -43,9 +43,9 @@
 #ifndef GMX_FILEIO_TRX_H
 #define GMX_FILEIO_TRX_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index b6098ce5b39e829833f13fa8fbf002650fed27ee..8e70f73716fc8a234b7446db8e5b2a2b27d31de4 100644 (file)
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -38,6 +38,8 @@
 
 #include "trxio.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 
@@ -60,8 +62,6 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 #ifdef GMX_USE_PLUGINS
 #include "gromacs/fileio/vmdio.h"
 #endif

diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index f66b4c37f10f81b9f0c83c75284852ecfd8c746a..0d32e364051a95bccbe9a4cecb6bae2050dc91e4 100644 (file)
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -38,12 +38,11 @@
 #ifndef GMX_FILEIO_TRXIO_H
 #define GMX_FILEIO_TRXIO_H
 
-#include "../legacyheaders/readinp.h"
-#include "../legacyheaders/oenv.h"
-
-#include "filenm.h"
-#include "gmxfio.h"
-#include "pdbio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/readinp.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/vmdio.c b/src/gromacs/fileio/vmdio.c
index b4ed95239e8e7eb757ca71064385ad310a290a16..621160a9e8f91fe49085b0e71be53b01d8c1eb43 100644 (file)
--- a/src/gromacs/fileio/vmdio.c
+++ b/src/gromacs/fileio/vmdio.c
@@ -86,10 +86,10 @@
 /*                                                                           */
 /*****************************************************************************/
 
-#include <stdlib.h>
+#include <assert.h>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
-#include <assert.h>
 
 /*
  * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
@@ -102,8 +102,8 @@
 #ifndef _WIN32_IE
 #define _WIN32_IE 0x0500 /* SHGetFolderPath is available since WinXP/IE5 */
 #endif
-#include <windows.h>
 #include <shlobj.h>
+#include <windows.h>
 #endif
 
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/fileio/writeps.c b/src/gromacs/fileio/writeps.c
index cd9d1b407fb5e17ceb77d94dc54b3848642d05b2..a0ae4e15cb9719aa319be7a9eafbef634b198fdc 100644 (file)
--- a/src/gromacs/fileio/writeps.c
+++ b/src/gromacs/fileio/writeps.c
@@ -40,11 +40,10 @@
 
 #include <stdio.h>
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 const char *fontnm[efontNR] = {
     "Times-Roman", "Times-Italic",     "Times-Bold",    "Times-BoldItalic",

diff --git a/src/gromacs/fileio/writeps.h b/src/gromacs/fileio/writeps.h
index 9572efdd9ffebc2ea0ae9f3bbd86b0c539ab66f3..33b8dadde2be052507bdb54a8d36414895ed9283 100644 (file)
--- a/src/gromacs/fileio/writeps.h
+++ b/src/gromacs/fileio/writeps.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/rgb.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/xdrd.c b/src/gromacs/fileio/xdrd.c
index 7edfe5911a1a17ceddb26af239d88d8610a3adc8..5af573e7b3b9ef1a698dcca7d95a397283c72397 100644 (file)
--- a/src/gromacs/fileio/xdrd.c
+++ b/src/gromacs/fileio/xdrd.c
@@ -36,8 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "xdrf.h"
-
+#include "gromacs/fileio/xdrf.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/fileio/xdrf.h b/src/gromacs/fileio/xdrf.h
index 5563c58e86804fb0ee803b369d9c8b25329e92ef..dd2959e9863924c8b3f5e9ae6ebdffe0d0fcfba2 100644 (file)
--- a/src/gromacs/fileio/xdrf.h
+++ b/src/gromacs/fileio/xdrf.h
@@ -49,7 +49,7 @@
 #include "config.h"
 
 #ifdef GMX_INTERNAL_XDR
-#include "gmx_system_xdr.h"
+#include "gromacs/fileio/gmx_system_xdr.h"
 #else
 #include <rpc/rpc.h>
 #include <rpc/xdr.h>

diff --git a/src/gromacs/fileio/xtcio.h b/src/gromacs/fileio/xtcio.h
index 18ebc044c983253956080f4865d1ccd83533ff95..2c50fb89f0bc5300b79069b29f7e84593636ea39 100644 (file)
--- a/src/gromacs/fileio/xtcio.h
+++ b/src/gromacs/fileio/xtcio.h
@@ -38,10 +38,10 @@
 #ifndef GMX_FILEIO_XTCIO_H
 #define GMX_FILEIO_XTCIO_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/fileio/xvgr.cpp b/src/gromacs/fileio/xvgr.cpp
index dddebce5a1c73e78c2739d19cb94e3bd4d83f846..fc65cf8d02b6dda047a9c1944512f82718df7fcb 100644 (file)
--- a/src/gromacs/fileio/xvgr.cpp
+++ b/src/gromacs/fileio/xvgr.cpp
@@ -36,22 +36,21 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fileio/xvgr.h"
+#include "xvgr.h"
 
 #include "config.h"
 
-#include <string.h>
 #include <ctype.h>
+#include <string.h>
 #include <time.h>
 
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/oenv.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"

diff --git a/src/gromacs/fileio/xvgr.h b/src/gromacs/fileio/xvgr.h
index 8aa6c35cc73d48d2f13e7eac7360081713616c87..542387b1892575cb8a4e38bf519a9df5ef1a6807 100644 (file)
--- a/src/gromacs/fileio/xvgr.h
+++ b/src/gromacs/fileio/xvgr.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/oenv.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxana/anadih.c b/src/gromacs/gmxana/anadih.c
index a73525d6768b5d8025a11513c3990b435f8bda71..c967c601c85b036aab9128d755a2531fc43dd813 100644 (file)
--- a/src/gromacs/gmxana/anadih.c
+++ b/src/gromacs/gmxana/anadih.c
@@ -39,20 +39,20 @@
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gstat.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/bonded/bonded.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 void print_one(const output_env_t oenv, const char *base, const char *name,
                const char *title, const char *ylabel, int nf, real time[],

diff --git a/src/gromacs/gmxana/autocorr.c b/src/gromacs/gmxana/autocorr.c
index 5e829a986d6d8884cf267c5869847dcbd80dd91d..9b0a13b69103c833f5407b0bd0ca0b38d93344ba 100644 (file)
--- a/src/gromacs/gmxana/autocorr.c
+++ b/src/gromacs/gmxana/autocorr.c
@@ -40,16 +40,16 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "correl.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define MODE(x) ((mode & (x)) == (x))
 

diff --git a/src/gromacs/gmxana/cmat.c b/src/gromacs/gmxana/cmat.c
index fab169f798f615da7d29813a213db408372b9570..672a2b60b22a1795f414a289ff85bb1d52770a7c 100644 (file)
--- a/src/gromacs/gmxana/cmat.c
+++ b/src/gromacs/gmxana/cmat.c
@@ -37,12 +37,13 @@
 #include "gmxpre.h"
 
 #include "cmat.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/fileio/matio.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 t_mat *init_mat(int n1, gmx_bool b1D)
 {

diff --git a/src/gromacs/gmxana/correl.c b/src/gromacs/gmxana/correl.c
index b223ad0adb1b5339a387436880b009f15aac2054..a8c8c430ff8a005ea59f8eddfe9293a59a86d5a6 100644 (file)
--- a/src/gromacs/gmxana/correl.c
+++ b/src/gromacs/gmxana/correl.c
@@ -37,13 +37,14 @@
 
 #include "gmxpre.h"
 
+#include "correl.h"
+
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
 
 #include "gromacs/fft/fft.h"
 #include "gromacs/utility/smalloc.h"
-#include "correl.h"
 
 #define SWAP(a, b) tempr = (a); (a) = (b); (b) = tempr
 

diff --git a/src/gromacs/gmxana/correl.h b/src/gromacs/gmxana/correl.h
index bdc8f5078d2c9f5dd86a20ce69e55a36e02f8db1..5851d6c28c2c569b8234a8a75a544974684a2cf9 100644 (file)
--- a/src/gromacs/gmxana/correl.h
+++ b/src/gromacs/gmxana/correl.h
@@ -39,8 +39,8 @@
 #ifndef _correl_h
 #define _correl_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fft/fft.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 typedef struct {
     int        n;

diff --git a/src/gromacs/gmxana/dens_filter.c b/src/gromacs/gmxana/dens_filter.c
index 0bf0bfc7d2959bfca99098b5dba2afd0d65bcef8..bd08b5247a0b1b43d76416a7c22ea2d6dad709c7 100644 (file)
--- a/src/gromacs/gmxana/dens_filter.c
+++ b/src/gromacs/gmxana/dens_filter.c
@@ -39,11 +39,13 @@
  * Routines for Filters and convolutions
  */
 
+#include "dens_filter.h"
+
 #include <math.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
-#include "dens_filter.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_DOUBLE
 #define EXP(x) (exp(x))

diff --git a/src/gromacs/gmxana/dlist.c b/src/gromacs/gmxana/dlist.c
index d1e1d27a3bb6f223d128af72186e8907446c9696..b7578cef623f03e97c71f8f2dd82ae9b537ae70a 100644 (file)
--- a/src/gromacs/gmxana/dlist.c
+++ b/src/gromacs/gmxana/dlist.c
@@ -39,8 +39,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gstat.h"
-
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/edittop.c b/src/gromacs/gmxana/edittop.c
index 9902937cedfca0a03d71dfd6d99c30f6a480decd..3a5357c731391c6711b76f87aeb7a406f4a88088 100644 (file)
--- a/src/gromacs/gmxana/edittop.c
+++ b/src/gromacs/gmxana/edittop.c
@@ -38,8 +38,8 @@
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/symtab.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
                   real q, real m, int type)

diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c
index b645b777ca43a4df37168e82d6ec6e28433b70cd..8d65ffbc59ab3123577f8604cf5b7af5a2a8f26e 100644 (file)
--- a/src/gromacs/gmxana/eigio.c
+++ b/src/gromacs/gmxana/eigio.c
@@ -36,12 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "eigio.h"
-#include "gromacs/fileio/trnio.h"
+
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
                        rvec **xref, gmx_bool *bDMR,

diff --git a/src/gromacs/gmxana/expfit.c b/src/gromacs/gmxana/expfit.c
index b9d57723a104139b486943997ef3f96a97b82dbc..61f9f7699ec8615a5078478faebdbf6cbd51f046 100644 (file)
--- a/src/gromacs/gmxana/expfit.c
+++ b/src/gromacs/gmxana/expfit.c
@@ -39,14 +39,13 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 const int   nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3};
 

diff --git a/src/gromacs/gmxana/fitahx.c b/src/gromacs/gmxana/fitahx.c
index 02816002294db37caff1d30480663fabb9487528..24b5a955d1a8c23ee37335083f0ad023bc7c16ba 100644 (file)
--- a/src/gromacs/gmxana/fitahx.c
+++ b/src/gromacs/gmxana/fitahx.c
@@ -37,9 +37,9 @@
 #include "gmxpre.h"
 
 #include "fitahx.h"
-#include "gromacs/math/vec.h"
 
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/fitahx.h b/src/gromacs/gmxana/fitahx.h
index 01d1c7c3deb90afbfc04d288ad0c706e1ed5dc6c..399028ef054e7de3da18a4b06e4ff7e98d124395 100644 (file)
--- a/src/gromacs/gmxana/fitahx.h
+++ b/src/gromacs/gmxana/fitahx.h
@@ -39,8 +39,8 @@
 #define _fitahx_h
 
 
+#include "gromacs/gmxana/hxprops.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "hxprops.h"
 
 extern real fit_ahx(int nres, t_bb bb[], int natoms, int nall, atom_id allindex[],
                     rvec x[], int nca, atom_id caindex[], gmx_bool bFit);

diff --git a/src/gromacs/gmxana/geminate.c b/src/gromacs/gmxana/geminate.c
index 273f7ae92ab03f29d17af30bc6f2f9f98e11cec6..2b8603dfe68e59f02168eec0086eaf6f975c277e 100644 (file)
--- a/src/gromacs/gmxana/geminate.c
+++ b/src/gromacs/gmxana/geminate.c
@@ -34,16 +34,16 @@
  */
 #include "gmxpre.h"
 
+#include "geminate.h"
+
 #include <math.h>
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "geminate.h"
-
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 static void missing_code_message()
 {

diff --git a/src/gromacs/gmxana/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
index b0e506085cb71da42227998db5cbadbabd0eb13f..98675b56879fd89d976eff6c3b85c36b35add6f8 100644 (file)
--- a/src/gromacs/gmxana/gmx_anadock.c
+++ b/src/gromacs/gmxana/gmx_anadock.c
@@ -39,18 +39,18 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/statistics/statistics.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static const char *etitles[] = { "E-docked", "Free Energy" };
 

diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index dde9815f2a3322cfbfca087f19ba341c43d3a121..4a219adf2cc4247d90b625639a963f60656a30a9 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -41,27 +41,26 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
 {

diff --git a/src/gromacs/gmxana/gmx_analyze.c b/src/gromacs/gmxana/gmx_analyze.c
index 94400867e5f00bfd2efafa911010a57991817292..a2f9799621121539723b8758fdf3377a8a05f378 100644 (file)
--- a/src/gromacs/gmxana/gmx_analyze.c
+++ b/src/gromacs/gmxana/gmx_analyze.c
@@ -41,23 +41,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
 #include "gromacs/linearalgebra/matrix.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* must correspond to char *avbar_opt[] declared in main() */
 enum {

diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 8064d062f104d40ff76e41e7f1cd8befd8bec31b..2a093478e48932698edd6c70f55137a963b5a9d7 100644 (file)
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -39,21 +39,21 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/fileio/trnio.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void dump_dih_trn(int nframes, int nangles, real **dih, const char *fn,

diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index e366081d07f85b3931b0c2c5946df218068e6ff9..2a2b8fd8cb212cfaa1f36a9d373cbf992afd0fac 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -40,21 +40,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Structure for the names of lambda vector components */

diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index d98f7d600ee969c141171257ab93e201c95812c2..4b55d0d4068a794c9fea6cbede726defc82155e9 100644 (file)
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -40,20 +40,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define MAX_ENDS 3
 

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 0c5a02a21c618429bd73bbd6a394f99e02fa3ac4..8c377df06afe31642c6b944f64a07c1051f94332 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -40,25 +40,25 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/residuetypes.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool bAllowed(real phi, real psi)
 {

diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index d1984d58e5cb74aa4061a1c44bffb48c77691ad9..e93a10f95ea4a38949ee8805dfa02ffdc8961d53 100644 (file)
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -40,30 +40,28 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "cmat.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* print to two file pointers at once (i.e. stderr and log) */
 static gmx_inline

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index 3800dceca998cc86a3c53348e66e8387ca0a33d0..2f9d219d7d7a489a0e0bcbcc73b1958d0b0ea806 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -38,27 +38,26 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/pme.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void clust_size(const char *ndx, const char *trx, const char *xpm,
                        const char *xpmw, const char *ncl, const char *acl,

diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index 8923544657bdfe61c10c9b314b994aa1706af9d6..3cc6dc6d14b295a6b1129f87b88ad892af016228 100644 (file)
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-
-#include "gromacs/math/do_fit.h"
+#include "gromacs/utility/smalloc.h"
 
 void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
 {

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 59411cd54980dca7aed26f1851b1400f6c0bc588..57756726ed606c51d904c15df3099d8a758926c1 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -47,26 +47,25 @@
 #endif
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/matio.h"
-#include "eigio.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_covar(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 42d316bb2ea8ed651c38839b21963bd0dba403b5..e27cf05233ae6e631a3a8f446de276a20f4295f3 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -38,21 +38,20 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/statistics/statistics.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define SQR(x) (pow(x, 2.0))
 #define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 43a3180d678f69ba5d2cdae8a48dcc3e29d3a9d2..f74611b940d81c0c1832b47449d222e4bbc24d41 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -41,23 +41,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index a71c04137f4f622bf3b3852232f5fefeb390ffa0..03bc88dd11495173ec16d5a96cd86ae0aafab9bf 100644 (file)
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -40,22 +40,21 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_densmap(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 5d8a8d9bb16a67e4226cdee03ce8964541d10bb2..99f68079920b4084ee6dfc0173034af85a1b4511 100644 (file)
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -38,29 +38,28 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "dens_filter.h"
-#include "binsearch.h"
-#include "powerspect.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/dens_filter.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_DOUBLE

diff --git a/src/gromacs/gmxana/gmx_dielectric.c b/src/gromacs/gmxana/gmx_dielectric.c
index e9c6445dd6a2f20a281d527f0be540bcf99f0a1b..5f4ce8844609862a753050b9da8b6464a1154dbc 100644 (file)
--- a/src/gromacs/gmxana/gmx_dielectric.c
+++ b/src/gromacs/gmxana/gmx_dielectric.c
@@ -40,20 +40,19 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gstat.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "gromacs/utility/futil.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Determines at which point in the array the fit should start */
 int calc_nbegin(int nx, real x[], real tbegin)

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 68e338fe04be79a85f0791000612763be85e6277..b930a6115e98f83f47ed3ca845b2d8eb78bbbedc 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -36,37 +36,36 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <math.h>
+#include <string.h>
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/statistics/statistics.h"
-#include "gstat.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/fileio/enxio.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/bonded/bonded.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define e2d(x) ENM2DEBYE*(x)

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index d7e1dd8af8e04a5a8ab76444975d9f3908da4a0f..e6d0f2985417e46b78b1f854d0bcf624245e5e8b 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -40,34 +40,33 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 45e7a876631c25ccf6d8895976d6f9e1d266698e..610f52a10e9642de15147dba777f50f5168226f2 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -40,20 +40,19 @@
 
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/viewit.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 07439151bc47948254d0bfb5265cf17923b82e28..65b6eaad3d211c7bd560d8843c1b33406c39f47f 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -39,25 +39,25 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fft/fft.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 enum {
     VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR

diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index 424c73842e1e7fc2bb30cfa2e9d2f073ad7e4252..57f2e47dca8b9ede552df98a1397cd453f999249 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -34,15 +34,14 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 7b2ac8e4993c2884e3ffdba910bdd161c5451ae1..5a727cb1c2317a7e5391eabde550148b8bd02964 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -36,17 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index abe79cb071fbe1d88efcc0525130e13c2f735e20..02069c9945bc1408e8716b7724899fa341416125 100644 (file)
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/math/units.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "princ.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_eneconv.c b/src/gromacs/gmxana/gmx_eneconv.c
index 34dea5935738d8c995594dca0461d92d62e6f397..9a1e775ef66077cdc21fdb281c22ac810e1d8334 100644 (file)
--- a/src/gromacs/gmxana/gmx_eneconv.c
+++ b/src/gromacs/gmxana/gmx_eneconv.c
@@ -40,17 +40,17 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1

diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
index bae15a8ae00c89d21593a43d1c3f53683ccde442..576cb221ebc4fde1261a8ea511e8c10aa6d200ac 100644 (file)
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.c
@@ -36,25 +36,25 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <math.h>
+#include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static int search_str2(int nstr, char **str, char *key)

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index 96a153cf0c08ff075463eb33b7060555a2f060a6..3319c96e81e0a98a7c0dcc89e7ef2c5d6a58d5eb 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -40,25 +40,25 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static real       minthird = -1.0/3.0, minsixth = -1.0/6.0;
 

diff --git a/src/gromacs/gmxana/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
index 4b1909c8a3c28d31e3e3e49eb62f5ffaef164173..cb26f11be0dd05705b2c6955dc73fa5467b0b844 100644 (file)
--- a/src/gromacs/gmxana/gmx_filter.c
+++ b/src/gromacs/gmxana/gmx_filter.c
@@ -40,18 +40,17 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_filter(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 1301d8e01a92c7de5b5990531472fcb3c2d5c25d..befd4b4bbc5f0893c09248413e1ac1afb5e4971b 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -40,22 +40,22 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void insert_ion(int nsa, int *nwater,
                        gmx_bool bSet[], int repl[], atom_id index[],

diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index a883f697a8c96dd993235a9ba07fba555e48b465..1dbe1e35e57d6a0723fb5bbd7d5a689178288f62 100644 (file)
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.c
@@ -40,16 +40,16 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_genpr(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index f8bb1f3758a1634ed0d747d318b579929ea4ace7..a1f3622fdcc50286a41cf0bc0998f35d857f524d 100644 (file)
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -40,23 +40,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "princ.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
                rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)

diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 27e918b8d3e700b1355356d31ec94e3249592440..284ca5517b65b40a992ea4fc0432854c9cccd7c2 100644 (file)
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -39,21 +39,20 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /****************************************************************************/
 /* This program calculates the ordering of water molecules across a box, as */

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 46a4da6497421dd91dff67852d91e383d69a6ab3..06911ed582214ded1cc8209f72bbfe11e3a569bb 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <math.h>
 
 #include "gromacs/commandline/pargs.h"
@@ -61,8 +63,6 @@
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 /*#define HAVE_NN_LOOPS*/
 
 typedef short int t_E;

diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index b1bbcb8d6dca382a1b9c315eb7ae197fcaffeb98..3d18d53f3cb9d84ee1041e840e2e46261a3e4ec2 100644 (file)
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "fitahx.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "hxprops.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/fitahx.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/hxprops.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_helix(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index dfd3a1f7cfc7c7bc2948a523db111fde4433f370..7946fd306f844b724bfcbee13d6c4ad5cb36b094 100644 (file)
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -38,19 +38,18 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index 74de61fc814fb52841ea9ed6de793e4746d36b2a..37038b0af4cddef9acaec5e815272eeb6df09eab 100644 (file)
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -38,23 +38,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "binsearch.h"
-#include "powerspect.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* Print name of first atom in all groups in index file */

diff --git a/src/gromacs/gmxana/gmx_lie.c b/src/gromacs/gmxana/gmx_lie.c
index 250256d475dd523b7dd75ed653d9d17582991e9f..f6ab7c1033610a41a13e4cfc4e1b8ac5317e4651 100644 (file)
--- a/src/gromacs/gmxana/gmx_lie.c
+++ b/src/gromacs/gmxana/gmx_lie.c
@@ -42,18 +42,18 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/fileio/enxio.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int  nlj, nqq;

diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index 7c1ec8411c9443f5838ec253b7836984c13d02d6..9665117ac134f7b24f296a073bfeb44ae0358288 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -38,26 +38,27 @@
  */
 #include "gmxpre.h"
 
+#include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
-#include <ctype.h>
 #include <string.h>
-#include "gromacs/legacyheaders/readinp.h"
+
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct
 {

diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index be16251aefdbd1ded43fa13387901390e7025564..55dc3ab47b4027dda9599d1634b2d3994fb9d124 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -39,17 +39,16 @@
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* It's not nice to have size limits, but we should not spend more time

diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index cc0a6e2becd0df019bb5834520598008f9b4516e..960049e5cf843a3d20e637a1a039c6ca823ef44b 100644 (file)
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -39,22 +39,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/filenm.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gmx_ana.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #define FARAWAY 10000

diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 3b732ffe0a8e549191962b0f7d3598f2724a4f79..920f6cc3a7465e6044e37091d1786049027016b7 100644 (file)
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -40,21 +40,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void periodic_dist(int ePBC,

diff --git a/src/gromacs/gmxana/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
index d27546891a013354a37e9a8c2e310471843c02f3..21af93c9b029f207ab2f0c25c7cf115abd9dd240 100644 (file)
--- a/src/gromacs/gmxana/gmx_mk_angndx.c
+++ b/src/gromacs/gmxana/gmx_mk_angndx.c
@@ -37,13 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static int calc_ntype(int nft, int *ft, t_idef *idef)
 {

diff --git a/src/gromacs/gmxana/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
index 8e77699e8935121e8ee27e6bc965fa690644dc9b..fe1153db71794105bd1fe58811d92c1744f9892e 100644 (file)
--- a/src/gromacs/gmxana/gmx_morph.c
+++ b/src/gromacs/gmxana/gmx_morph.c
@@ -36,17 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/topology/index.h"
-#include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index 701f412114e164f4963288aee2fa1c41b8205439..6913929759c83a52aaf579d3c62049646d2cfb85 100644 (file)
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define FACTOR  1000.0  /* Convert nm^2/ps to 10e-5 cm^2/s */

diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 519f44a3bfe3d5ca8de21d2c2b214cd9a302d77e..eb727c8fa2ef8ac41d81311b0f3b5162fbc83884 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -39,23 +39,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/mtxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static double cv_corr(double nu, double T)

diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index a734478f8df100652ac3eda5e6be5a89db44b4f4..0d005fe5cd4088a62aa8771b52fd9b9b215106f8 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -40,21 +40,21 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_nmens(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index 661caf2749d696f9419980273f7ac10c27c5d3fd..2fbe5cdb1f5ba111e9f4cca0d500fa5696835b89 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -41,19 +41,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_nmtraj(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_options.c b/src/gromacs/gmxana/gmx_options.c
index addcdc5f4b10bb699b6e524626eb8eecb2e9b242..52b99ead39f30cc2a1cee50e2d94935b4f9787ed 100644 (file)
--- a/src/gromacs/gmxana/gmx_options.c
+++ b/src/gromacs/gmxana/gmx_options.c
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 /*
  * This program is needed to create the files:

diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 7c2b600d058b57a4bb0481ef50c0c4a3c2c5dd17..28c3e777226fe247b068cdc07656851a1192b767 100644 (file)
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/confio.h"
-#include "cmat.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /****************************************************************************/

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 0dc23d9f85d43c5b6cba79fb90b8e9c2eb9b3dff..0b0373833e6f6f5de3b56712705aaa0dd8664cfe 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -34,31 +34,30 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/calcgrid.h"
 #include "gromacs/legacyheaders/checkpoint.h"
-#include "gmx_ana.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
-
-#include "config.h"
+#include "gromacs/utility/smalloc.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))

diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index 367c1c5ff643f7c17ac12ff55121178aa6f377dc..ece18dc4d198743cde35822d8b3ea3b3602aeab7 100644 (file)
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -39,21 +39,20 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void gyro_eigen(double **gyr, double *eig, double **eigv, int *ord)
 {

diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index ba223b01ccf4640dca81995783c3895e053576a2..9991682a450471ab97d4769602f5ee6047229d12 100644 (file)
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -40,22 +40,21 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define EPS0 8.85419E-12
 #define ELC 1.60219E-19

diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index 5be044744ab095602cdf27bac3fd8dff8ccffa50..9780027dd6448d7bad708d6593db57dc0da1529e 100644 (file)
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -40,20 +40,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 void

diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index 711bac7ecef0f4c535fda56af6d579694de6d8fc..5198b0c730502b0d05651f3a56a1a56cf19b5f67 100644 (file)
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -39,17 +39,17 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/nrama.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "nrama.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void plot_rama(FILE *out, t_xrama *xr)

diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index db06a912796122df176f76a9a0a3f4834034b603..47c4bc0c6fdb45e6165e0ec4884ac8738768c99e 100644 (file)
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -39,25 +39,24 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gstat.h"
-#include "gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void check_box_c(matrix box)

diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 24af686324c5c1ba96a3c2dc424c946abf0dc117..dccad9e472458a25f2b947ec369f7cb02bb08ac0 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "cmat.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void norm_princ(t_atoms *atoms, int isize, atom_id *index, int natoms,
                        rvec *x)

diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
index 504ba2abc285f8e307414267199abeb111665d8e..ea98add60a3ab047dba946a426f00be662aaaa28 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsdist.c
+++ b/src/gromacs/gmxana/gmx_rmsdist.c
@@ -38,23 +38,22 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/strdb.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void calc_dist(int nind, atom_id index[], rvec x[], int ePBC, matrix box,

diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index de56950586c5fc53507decd4665a0b9dc9ba1958..c4398533cd3de8b584675a8e890b4782097e0cf0 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -38,25 +38,24 @@
 
 #include <math.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/futil.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static real find_pdb_bfac(t_atoms *atoms, t_resinfo *ri, char *atomnm)
 {

diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 0895c01bb259b86b11552e2b88642f98908680d4..4eb9a6ec18f871da561d2c3b1b38d9da4fe9e424 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -39,19 +39,18 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 int gmx_rotacf(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
index e4606039b4fc5433773f42297e8d0f825f9c4447..3eddfe424c22a3853be8afce61c412b4f7a73279 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotmat.c
+++ b/src/gromacs/gmxana/gmx_rotmat.c
@@ -38,20 +38,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
                      int gnx, int *index,

diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
index 47b3e6cca7da83a2173b726647833137fbacc006..46fd1409e178e628c4414ecc238a010bec8d4790 100644 (file)
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.c
@@ -39,20 +39,18 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char *label;

diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index a91af5888bbf27e5308f0ba395065c145ff9086d..797652dd8d76d0c6fc689b3a03e3a450a0e4acff 100644 (file)
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -37,20 +37,19 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-#include "nsfactor.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/nsfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"

diff --git a/src/gromacs/gmxana/gmx_saxs.c b/src/gromacs/gmxana/gmx_saxs.c
index 73ab9694db1cbaa36eb65588c06d8c9231e62e2f..30967feab71464ac42c24f784e2984a6f2594ab8 100644 (file)
--- a/src/gromacs/gmxana/gmx_saxs.c
+++ b/src/gromacs/gmxana/gmx_saxs.c
@@ -39,12 +39,11 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gmx_ana.h"
-#include "sfactor.h"
-
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/sfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/smalloc.h"
 
 int gmx_saxs(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
index c2a0ae7423f9e7e75b8fa638c60fd83e1172edb6..863e820489311dce7ea8895d4dcc76ca563e3551 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.c
+++ b/src/gromacs/gmxana/gmx_sham.c
@@ -41,20 +41,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gstat.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static int index2(int *ibox, int x, int y)

diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
index a4860c8d70e6a1266ae506ffb6a77802a21279f5..4eaae62fb613f12cb7883be302717c6856f10eb4 100644 (file)
--- a/src/gromacs/gmxana/gmx_sigeps.c
+++ b/src/gromacs/gmxana/gmx_sigeps.c
@@ -39,19 +39,19 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 real pot(real x, real qq, real c6, real cn, int npow)
 {

diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index 5c3781322839f1d5103d5cffd907d6c0f5812851..a81a8265d581b86020a38cd757e1b369ffa82933 100644 (file)
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index 4eb86003d4e6c0b8ba8dc112c019fbbae7b65028..600608d2e322611aba964abde422bf08db57bc9b 100644 (file)
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -38,16 +38,16 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
 
 static const double bohr = 0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */
 

diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index e715f578c35b6dc12cdd7d0c4343a1b308d8e2cf..2def7422e5720f45d407115844a82978cb89c263 100644 (file)
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -36,20 +36,19 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index cf72122974457feb48e2ae1505d0eaa0555b26b6..b676ffc6a2deba541021747d1c64ff300852cb59 100644 (file)
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -40,24 +40,24 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #define NK  24

diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 86e9a006f96516cb03acb568e7403b8468ae6207..cd3d0b5ccf1ef7842f20faf4e7054bcd260e7d71 100644 (file)
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -41,23 +41,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
                            gmx_bool bDim[], const char *sffmt)

diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index 5a011c992ccd64feb2f85ce8fd296b72ce1abaee..e13434df5543e92f9d6659320b0a1836c13aaabc 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -40,27 +40,26 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1

diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index f0aa6b5d808eac396d8d787f63fc9cb64717fcf8..4a0be116817ffac64439101c149293314751277f 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index bdf5cb3569232023f399224bf44cb621021cdb7c..ed383bf2f4cabde6f2af7cf4876c251ee01f6278 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -41,22 +41,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     atom_id i;

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 990ec4738dfcaaafd09ddffba4034c3add6a19e6..b9c2af3e717863e654c243f8cd299c582023a742 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -34,11 +34,11 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <stdlib.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif

diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index 781fc5cf1f37f22d329395c82682f2799f4bec41..fb372b77e1fc777443db8b9d1333adf9c787a6b3 100644 (file)
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -41,21 +41,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_vanhove(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index b6567a4813defbafb2bf39c5bfa1abbac644e874..34c378d3a406dfa324a2f232797803146a9aa20e 100644 (file)
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -40,24 +40,24 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fft/fft.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void index_atom2mol(int *n, atom_id *index, t_block *mols)
 {

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index eea360649502ea108c938eb85dc1fb79f5ec6828..7a5b0a4333403b67af100b7fd78fb35d2466949f 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -53,19 +53,18 @@
 #include <sstream>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/xvgr.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 //! longest file names allowed in input files
 #define WHAM_MAXFILELEN 2048

diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index d990df1180674e64d9a8703ce6816c693ec79760..457b1a17a03c6d8e29c6587815d14e933416e52a 100644 (file)
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -41,19 +41,18 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gstat.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/writeps.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool *bPhobics(int nres, char *resnm[])
 {

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
index 0e2bd1f6767a3576d94682fa2ffd2a7007564017..53c67ac0160f18670642f0c97771c6dfc938a4af 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.c
+++ b/src/gromacs/gmxana/gmx_xpm2ps.c
@@ -36,21 +36,21 @@
  */
 #include "gmxpre.h"
 
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define FUDGE 1.2
 #define DDD   2

diff --git a/src/gromacs/gmxana/gstat.h b/src/gromacs/gmxana/gstat.h
index 0d490d9ab14e16d946cc28b678f29daef4d144dc..a07b3ed51307e063669b58aa15f280744273312f 100644 (file)
--- a/src/gromacs/gmxana/gstat.h
+++ b/src/gromacs/gmxana/gstat.h
@@ -37,10 +37,10 @@
 #ifndef GMX_GMXANA_GSTAT_H
 #define GMX_GMXANA_GSTAT_H
 
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/oenv.h"
-#include "../commandline/pargs.h"
-#include "../topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/index.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxana/hxprops.c b/src/gromacs/gmxana/hxprops.c
index bad612044ae8d1f41bf1e256b75b72bcccee1e54..57acd55c76bb653afecbbfb0d9a0261cb011b382 100644 (file)
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.c
@@ -36,19 +36,19 @@
  */
 #include "gmxpre.h"
 
+#include "hxprops.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/bonded/bonded.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
-#include "hxprops.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "gromacs/bonded/bonded.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 real ellipticity(int nres, t_bb bb[])
 {

diff --git a/src/gromacs/gmxana/hxprops.h b/src/gromacs/gmxana/hxprops.h
index 1229b5e5800912165481d9fc12d5d63ccb72b13e..c6242d76b7aff725d19d8418ccf49c7485cc6345 100644 (file)
--- a/src/gromacs/gmxana/hxprops.h
+++ b/src/gromacs/gmxana/hxprops.h
@@ -39,6 +39,7 @@
 #define _hxprops_h
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #define PHI_AHX (-55.0)

diff --git a/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp b/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
index 7c96a96f3cbc83fee8cdd2f1e0dc1f6f0c1951c2..4af681f2f6064ac7ae873e68a4ac21641c83c683 100644 (file)
--- a/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
+++ b/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
@@ -41,12 +41,13 @@
 
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include "gromacs/gmxana/gmx_ana.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
 #include "gromacs/utility/arrayref.h"
 
-#include "config.h"
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
 
 namespace
 {

diff --git a/src/gromacs/gmxana/nrama.c b/src/gromacs/gmxana/nrama.c
index a69fc8a3bd837111065f7547aaea6879c7072420..0c34aeeca73bf5f8e9c6378aba23abd37882087f 100644 (file)
--- a/src/gromacs/gmxana/nrama.c
+++ b/src/gromacs/gmxana/nrama.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nrama.h"
+
 #include <math.h>
 #include <stdlib.h>
 
-#include "nrama.h"
-
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/rmpbc.h"
 
 static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
 #define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))

diff --git a/src/gromacs/gmxana/nrama.h b/src/gromacs/gmxana/nrama.h
index 901c0847c690cdb55b40febf1a62c53b6ee086ba..03ee81418128f796dd0bdf9d979df40003589b58 100644 (file)
--- a/src/gromacs/gmxana/nrama.h
+++ b/src/gromacs/gmxana/nrama.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXANA_NRAMA_H
 #define GMX_GMXANA_NRAMA_H
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/oenv.h"
-#include "../fileio/trxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxana/polynomials.c b/src/gromacs/gmxana/polynomials.c
index 91cd15ff8925f0b78ddee4b95bc0ef7090281c04..9f6257bfbe7adfe6645d630f7583760e8124f34d 100644 (file)
--- a/src/gromacs/gmxana/polynomials.c
+++ b/src/gromacs/gmxana/polynomials.c
@@ -36,11 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <math.h>
+#include <stdio.h>
+
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gstat.h"
 
 real LegendreP(real x, unsigned long m)
 

diff --git a/src/gromacs/gmxana/powerspect.c b/src/gromacs/gmxana/powerspect.c
index 071e50afaddd7daf1732a021362465720fdde496..67674959c7cceb5f39b903cf11dc70e86f3c5eb8 100644 (file)
--- a/src/gromacs/gmxana/powerspect.c
+++ b/src/gromacs/gmxana/powerspect.c
@@ -35,12 +35,13 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
+#include "powerspect.h"
+
 #include "gromacs/fft/fft.h"
+#include "gromacs/gmxana/interf.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "interf.h"
-#include "powerspect.h"
+#include "gromacs/utility/smalloc.h"
 
 void addtoavgenergy(t_complex *list, real *result, int size, int tsteps)
 {

diff --git a/src/gromacs/gmxana/powerspect.h b/src/gromacs/gmxana/powerspect.h
index 9f64cc5cfed567088d89a9a3c85ff027ae030648..5f9bbc324146a6f259cb324f8f6691371c32c5fc 100644 (file)
--- a/src/gromacs/gmxana/powerspect.h
+++ b/src/gromacs/gmxana/powerspect.h
@@ -36,8 +36,8 @@
 #ifndef _powerspect_h
 #define _powerspect_h
 
+#include "gromacs/gmxana/interf.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "interf.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxana/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
index 4c7fdb951d647a07c14a0426c4075f93ed4a4db2..fa12f6d0b6afed5d822f886780f87ceb6719b0ea 100644 (file)
--- a/src/gromacs/gmxana/pp2shift.c
+++ b/src/gromacs/gmxana/pp2shift.c
@@ -36,17 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include <stdlib.h>
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
+#include <stdlib.h>
+
 #include "gromacs/fileio/matio.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int    nx, ny;

diff --git a/src/gromacs/gmxana/princ.c b/src/gromacs/gmxana/princ.c
index e3906590a4febe3986c34ac74a74b3eb7b458462..fb7dcad1d7002380832aabf44ff4d2ea75d01f7a 100644 (file)
--- a/src/gromacs/gmxana/princ.c
+++ b/src/gromacs/gmxana/princ.c
@@ -37,13 +37,13 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "princ.h"
 
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 static void m_op(matrix mat, rvec x)
 {

diff --git a/src/gromacs/gmxana/sfactor.c b/src/gromacs/gmxana/sfactor.c
index 8d027fe4a52cbe945223c5fd103a3618f5044308..8cc7492d771b83ab909984ba6f144ba551e689ba 100644 (file)
--- a/src/gromacs/gmxana/sfactor.c
+++ b/src/gromacs/gmxana/sfactor.c
@@ -36,22 +36,23 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
+#include "sfactor.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "sfactor.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 typedef struct gmx_structurefactors {

diff --git a/src/gromacs/gmxana/sfactor.h b/src/gromacs/gmxana/sfactor.h
index 9df62afd8890a9c02d9ca6043f62f115b517c3aa..0550909596862023457d8225edc28e48763f249f 100644 (file)
--- a/src/gromacs/gmxana/sfactor.h
+++ b/src/gromacs/gmxana/sfactor.h
@@ -37,9 +37,9 @@
 #ifndef _sfactor_h
 #define _sfactor_h
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "../math/gmxcomplex.h"
 #include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/gmxcomplex.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxlib/calcgrid.c b/src/gromacs/gmxlib/calcgrid.c
index 62d25e1ce88839af9cf52dfcad8f95565d21ba8d..1de1f57efed3998ac8ce36a36d0b67c833dee457 100644 (file)
--- a/src/gromacs/gmxlib/calcgrid.c
+++ b/src/gromacs/gmxlib/calcgrid.c
@@ -36,12 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/calcgrid.h"
+
 #include <math.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/utility/smalloc.h"
 
 /* The grid sizes below are based on timing of a 3D cubic grid in fftw
  * compiled with SSE using 4 threads in fft5d.c.

diff --git a/src/gromacs/gmxlib/chargegroup.c b/src/gromacs/gmxlib/chargegroup.c
index 00dbf09dcfa342420d3774b9cf9f392f1a39269f..41e152518dda92a4a98f119b3f0cf06aa6256170 100644 (file)
--- a/src/gromacs/gmxlib/chargegroup.c
+++ b/src/gromacs/gmxlib/chargegroup.c
@@ -36,13 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/chargegroup.h"
+
 #include <math.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/utility/smalloc.h"
 
 
 void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,

diff --git a/src/gromacs/gmxlib/checkpoint.cpp b/src/gromacs/gmxlib/checkpoint.cpp
index bec5b71652101e227368ff40e1adaf74889d425f..c1a806c42dc785c6bb80ba0fbc0c0b865bbe9b5c 100644 (file)
--- a/src/gromacs/gmxlib/checkpoint.cpp
+++ b/src/gromacs/gmxlib/checkpoint.cpp
@@ -39,6 +39,8 @@
 
 #include "gromacs/legacyheaders/checkpoint.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdlib.h>
 #include <string.h>
@@ -46,8 +48,6 @@
 
 #include <fcntl.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif

diff --git a/src/gromacs/gmxlib/conformation-utilities.c b/src/gromacs/gmxlib/conformation-utilities.c
index 59f433fa5d8a5b269cbac0e7e4bda9caad34fde5..d21efa4cde0a00dae3f51dd55e597715e35e5cd4 100644 (file)
--- a/src/gromacs/gmxlib/conformation-utilities.c
+++ b/src/gromacs/gmxlib/conformation-utilities.c
@@ -40,6 +40,7 @@
 #include "conformation-utilities.h"
 
 #include <math.h>
+
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/gmxlib/conformation-utilities.h b/src/gromacs/gmxlib/conformation-utilities.h
index 8aa337b69c0e3041566e14c6f0a57950e744d71c..0fbe271f04714d0cc2eb649bf2c689d1d2f3d0de 100644 (file)
--- a/src/gromacs/gmxlib/conformation-utilities.h
+++ b/src/gromacs/gmxlib/conformation-utilities.h
@@ -37,9 +37,9 @@
 #ifndef GMX_CONFORMATION_UTILITIES_H
 #define GMX_CONFORMATION_UTILITIES_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index c1b94f0ebec12e6d5f45cfeb5e70c3e60babffcb..fe7045a22e5881c53800a34b3656a48024c36cd0 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -38,13 +38,13 @@
 
 #include "gromacs/legacyheaders/copyrite.h"
 
+#include "config.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_LIBMKL
 #include <mkl.h>
 #endif

diff --git a/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu b/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
index 76f92224126a517cfd7d2b58ecff725765d0f2fb..4b5bca9d6f42c2b4812e5b0dfb15210e2065a944 100644 (file)
--- a/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
+++ b/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
@@ -36,6 +36,7 @@
 #include "gmxpre.h"
 
 #include <stdio.h>
+
 #include <cuda.h>
 #include <cuda_runtime_api.h>
 

diff --git a/src/gromacs/gmxlib/cuda_tools/cudautils.cu b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
index f92a53f07db4d1453eb775ae8a23b2269d0189be..44a18eaec48ca2bf09ef6900aa3b95c44f7a9657 100644 (file)
--- a/src/gromacs/gmxlib/cuda_tools/cudautils.cu
+++ b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
@@ -35,11 +35,12 @@
 
 #include "gmxpre.h"
 
+#include "cudautils.cuh"
+
 #include <stdlib.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "cudautils.cuh"
+#include "gromacs/utility/smalloc.h"
 
 /*** Generic CUDA data operation wrappers ***/
 

diff --git a/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu b/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
index cc221cfe24765f26d8a03c0c079a242591fc59e7..d0c684d4ae0ae29b44d0891e79f673fb23202d68 100644 (file)
--- a/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
+++ b/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
@@ -35,11 +35,11 @@
 
 #include "gmxpre.h"
 
-#include <stdlib.h>
-
-#include "cudautils.cuh"
 #include "gromacs/legacyheaders/pmalloc_cuda.h"
 
+#include <stdlib.h>
+
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/utility/cstringutil.h"
 
 /*! Allocates nbytes of page-locked memory.

diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index 764e8e13961fe1619a46e8fdcd5dfa6a3b12a8a8..8e2fefd24f61135c711984d5bee998eadba38eb0 100644 (file)
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -37,25 +37,25 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/disre.h"
+
 #include "config.h"
 
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/topology/mtop_util.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 void init_disres(FILE *fplog, const gmx_mtop_t *mtop,

diff --git a/src/gromacs/gmxlib/ewald_util.c b/src/gromacs/gmxlib/ewald_util.c
index 44dc2271f36d33af2151cf657a655ab9a10a98ef..d3bb07b6e3fe65539870db6af2e5a01bdebd333c 100644 (file)
--- a/src/gromacs/gmxlib/ewald_util.c
+++ b/src/gromacs/gmxlib/ewald_util.c
@@ -36,19 +36,20 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <math.h>
-#include "gromacs/math/utilities.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
 
 real calc_ewaldcoeff_q(real rc, real dtol)
 {

diff --git a/src/gromacs/gmxlib/gmx_cpuid.c b/src/gromacs/gmxlib/gmx_cpuid.c
index 0e69251321b32dfe64b5bd0a8aadee0daf016069..18109192d9cd1410f7b4119f83aa4e6c1bd2089a 100644 (file)
--- a/src/gromacs/gmxlib/gmx_cpuid.c
+++ b/src/gromacs/gmxlib/gmx_cpuid.c
@@ -45,10 +45,10 @@
 #  include <sched.h>
 #endif
 
+#include <ctype.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <ctype.h>
 #ifdef GMX_NATIVE_WINDOWS
 /* MSVC definition for __cpuid() */
     #ifdef _MSC_VER

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.cpp b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
index e05629a5122d20532c97e034ed17a15914f5b5c3..bc7817d5f614b2d16b704f1efa321a4c76097f67 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.cpp
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
@@ -36,6 +36,8 @@
 
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <errno.h>
 #include <stdlib.h>
@@ -44,8 +46,6 @@
 #include <string>
 #include <vector>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 /* For sysconf */
 #include <unistd.h>

diff --git a/src/gromacs/gmxlib/gmx_omp_nthreads.c b/src/gromacs/gmxlib/gmx_omp_nthreads.c
index 76824dee392284ae76893bd3c5a40f5b5389553e..e9a415c403a9473a22cb230aba6119ffd0048d1c 100644 (file)
--- a/src/gromacs/gmxlib/gmx_omp_nthreads.c
+++ b/src/gromacs/gmxlib/gmx_omp_nthreads.c
@@ -35,21 +35,21 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+#include "config.h"
+
+#include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <assert.h>
-
-#include "config.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/md_logging.h"
-
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"

diff --git a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
index 542e3a8fb954c392dcc889e541648e80988b5a3d..f8b741923eb6827ed853639308f7e4e29bee18c1 100644 (file)
--- a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
+++ b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
@@ -35,15 +35,14 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/gpu_utils.h"
+
+#include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/legacyheaders/types/hw_info.h"
-
-#include "gromacs/legacyheaders/gpu_utils.h"
-#include "../cuda_tools/cudautils.cuh"
-
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxlib/ifunc.c b/src/gromacs/gmxlib/ifunc.c
index e27b78aa22c23e51d52228a0b2e185a039bed094..5a649c0bb02ef7e92317e1193a790b61578c6379 100644 (file)
--- a/src/gromacs/gmxlib/ifunc.c
+++ b/src/gromacs/gmxlib/ifunc.c
@@ -38,10 +38,10 @@
 #include "gmxpre.h"
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #define  def_bonded(str, lstr, nra, nrpa, nrpb, ind, func) \
     {str, lstr, (nra), (nrpa), (nrpb), IF_BOND,                        (ind), (func)}

diff --git a/src/gromacs/gmxlib/inputrec.c b/src/gromacs/gmxlib/inputrec.c
index d55f8e4ed57b6d045db20f9052a9dfd18f9e4bb0..ad48b85814f6b411515fe72a08af9b275188caa0 100644 (file)
--- a/src/gromacs/gmxlib/inputrec.c
+++ b/src/gromacs/gmxlib/inputrec.c
@@ -36,9 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/inputrec.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
 
 

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index a91b41e2e4e54f0147e9397c53aaac320071aaa7..9a3078310dfad84821c6d5c76fc25737b80e5b87 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -38,14 +38,14 @@
 
 #include "gromacs/legacyheaders/main.h"
 
+#include "config.h"
+
 #include <limits.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <process.h>
 #endif

diff --git a/src/gromacs/gmxlib/md_logging.c b/src/gromacs/gmxlib/md_logging.c
index 36eb06d964799359be249274f296eea082b798b3..cee3c06ba60857198e07f177b20e004692e186d9 100644 (file)
--- a/src/gromacs/gmxlib/md_logging.c
+++ b/src/gromacs/gmxlib/md_logging.c
@@ -36,10 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "gromacs/legacyheaders/md_logging.h"
+
 #include <stdarg.h>
+#include <stdio.h>
+
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/md_logging.h"
 
 
 void md_print_info(const t_commrec *cr, FILE *fplog,

diff --git a/src/gromacs/gmxlib/mvdata.c b/src/gromacs/gmxlib/mvdata.c
index 8885b13c0e267613c2ec46010b72a397c2bf829d..41aeaeaf15e7267d1bbb475c44d016d6e6ddd7f0 100644 (file)
--- a/src/gromacs/gmxlib/mvdata.c
+++ b/src/gromacs/gmxlib/mvdata.c
@@ -37,16 +37,16 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/mvdata.h"
+
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/tgroup.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxlib/names.c b/src/gromacs/gmxlib/names.c
index 0e048d42db8325c0dd8d7a7f6309ab16ff21c2a3..6e63f2fb62be84d75825dd35b6d1cfdd456e669d 100644 (file)
--- a/src/gromacs/gmxlib/names.c
+++ b/src/gromacs/gmxlib/names.c
@@ -36,9 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/names.h"
 
+#include "gromacs/legacyheaders/typedefs.h"
+
 /* note: these arrays should correspond to enums in include/types/enums.h */
 
 const char *epbc_names[epbcNR+1] =

diff --git a/src/gromacs/gmxlib/network.c b/src/gromacs/gmxlib/network.c
index f43d7789430e993a1a1f923d94394d02fe15506d..94905661e1c4b89bc11b4cc88c76f18b043f9d62 100644 (file)
--- a/src/gromacs/gmxlib/network.c
+++ b/src/gromacs/gmxlib/network.c
@@ -45,10 +45,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
index 35175bc2173467d481facccb09de6ad684eb74b2..93f1d1c361be497d0e69eb0d4bec4650359d847a 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nb_free_energy.h"
+
 #include <math.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "nb_free_energy.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 
 void

diff --git a/src/gromacs/gmxlib/nonbonded/nb_free_energy.h b/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
index efc98d173e832ab63e3dcd397721e001eae1ca13..8b76221810e86d7f4af9ae2984987c4d07da04a0 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
@@ -38,7 +38,7 @@
 #ifndef _nb_free_energy_h_
 #define _nb_free_energy_h_
 
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
 
 void

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic.c b/src/gromacs/gmxlib/nonbonded/nb_generic.c
index dca18ad4fa08645054239d97e89921af7f1b31fc..55fdb28a01f334790ca3605d4b49a544fbe2d7cf 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic.h"
+
 #include <math.h>
 
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
-
 void
 gmx_nb_generic_kernel(t_nblist *                nlist,
                       rvec *                    xx,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic.h b/src/gromacs/gmxlib/nonbonded/nb_generic.h
index d68aebe1b8441d7a0fd95634e68d318a538c557b..65785f2bda286ff942a7528fa961010c93b7bf7a 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic.h
@@ -38,9 +38,9 @@
 #ifndef _nb_generic_h_
 #define _nb_generic_h_
 
-#include "nb_kernel.h"
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_kernel(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
index eedffd8645d45a89748f9c0eed79f137e2f80ade..4334a04c7a9355da1555ac1ba95a17177026aaad 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic_adress.h"
+
 #include <math.h>
 
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic_adress.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
-
 #define ALMOST_ZERO 1e-30
 #define ALMOST_ONE 1-(1e-30)
 void

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
index 17eabeeb29534dc63c011191a4946031c7453605..fd838f2e630e139a081d39faa5cba30136d0fb14 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
@@ -38,9 +38,9 @@
 #ifndef _nb_generic_adress_h_
 #define _nb_generic_adress_h_
 
-#include "nb_kernel.h"
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_adress_kernel(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
index 97c43c2b0b9b86df012bcae8a0841508badb6b6a..fe14f9586a278a65b8234eac961f62ea5d369cac 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic_cg.h"
+
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 
 void

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
index fa4e25768d528966f869d83a870ba987be5cf80d..2ef87893d834f107519a1f2f5c933284f64c6bfb 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
@@ -38,10 +38,10 @@
 #ifndef _nb_generic_cg_h_
 #define _nb_generic_cg_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_cg_kernel(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.c b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
index 60f73652a2a7ab1283ae918756e3268bed7570d7..29b01659bcde7ce98602e708874b5159d7778771 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
@@ -34,13 +34,14 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel.h"
+
 #include <stdio.h>
 #include <string.h>
 
-#include "nb_kernel.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Static data structures to find kernels */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.h b/src/gromacs/gmxlib/nonbonded/nb_kernel.h
index c5d489949abd4cdb05007a205bdeb1dc38f32ab6..76f884aa868bd679af18c9d39741f2ea79f6648e 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.h
@@ -43,8 +43,8 @@ extern "C" {
 #endif
 
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 /* Structure to collect kernel data not available in forcerec or mdatoms structures.
  * This is only used inside the nonbonded module.

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
index 5b931327a505e7512d887c64bded64a7cb31415c..dba59bbf0e948b19edd68776a319007681bfb816 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
@@ -36,6 +36,7 @@
 #define _kernelutil_x86_avx_128_fma_double_h_
 
 #include <math.h>
+
 #include <immintrin.h>
 #ifdef _MSC_VER
 #    include <intrin.h>

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
index bfadf92430785d957357884b80ab61047ba657db..e12ba84a318a60bf1fafcd246540908bd44ef201 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_double;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
index 14c3771d7ef0b6264e4d620b8125f1abf5b8d796..e6f9e12486f4827e091de9cd539def71b7da84ea 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_128_fma_double_h
 #define nb_kernel_avx_128_fma_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
index 1715f97cbc0d28939b0109262860937bfcb25bb7..6aadac8d352ad17cc0cfd2df5c00bd3476f38bdd 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
@@ -38,6 +38,7 @@
 #include "config.h"
 
 #include <math.h>
+
 #include <immintrin.h>
 #ifdef _MSC_VER
 #    include <intrin.h>

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
index 1a7c473b67b41065859a5758eed167351993313a..9dfb2dcf53242433c1bccc3cb79fc94e747ecb89 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_single;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
index 8c2387aa36d2973523ee19ac38134a5d9e8d542e..a96f66b81ea503143fd7459198efb704f531499c 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_128_fma_single_h
 #define nb_kernel_avx_128_fma_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
index dfa412bf84e0df5ee9e2d78cd92210f7d86e9009..b536da526a630731118bdcd568e24eba0546a2ee 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_double;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
index 308256944e686a25a231cbc1a77d372e1bd092c4..97a60c168efe3b0616112f113bef2802affc685e 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_256_double_h
 #define nb_kernel_avx_256_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
index 77093dad3feb5afd1f84b75fb035cc164e10c821..02155949561dc58d2286f4f5e9fd0828c7655d55 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_single;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
index 35c2c3b514ff9ceff693b7c4f5aa7b8137d25e47..bcbb42de557b2c2e325085ceb51c260d03f3091d 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_256_single_h
 #define nb_kernel_avx_256_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
index 0c0dcb7205c6b923f1c5fc7a6af689bd92d38b29..92335ff0c0965190be85fe1344db5b73f4bdb6c4 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel_allvsall.h"
+
 #include "config.h"
 
 #include <math.h>
 
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel_allvsall.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 typedef struct
 {
     real **    pvdwparam;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
index bf5e34b4bb2b8aed561c2e7b622053b302b29318..62b60ca939f3770c5341beec8da4f6d9ce4fc6ce 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
@@ -37,9 +37,9 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 nb_kernel_allvsall(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
index 3557e825e6b8d0a9e5460b93692a12e367f06178..be401ee7bc86d6a4e0c7d764a89cde4ae2257342 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel_allvsallgb.h"
+
 #include "config.h"
 
 #include <math.h>
 
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel_allvsallgb.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 typedef struct
 {
     real **    pvdwparam;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
index 6083fb22952ece84fa5192c7f4196089863576e2..318b103008b324d6193c721f0a31e8d3518715b5 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
@@ -37,9 +37,9 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 nb_kernel_allvsallgb(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
index 361dd233a0a4fcbd1d4d070225ed6a0633ba18ea..ca9b753a792243d902da57962c3db301a9971bab 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_c;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_c;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
index 32640c7d443d66d5e24459de7247c87f9794d846..e524079cd62af3c491e58b4230be449e60728024 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_c_h
 #define nb_kernel_c_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
index c63a233ef7f3af84a986c3b66320b0e8ae9f2087..bd2e022fe867ba2c406b5f14d9a47461ab2df3cb 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
index 67ace2f0e7400de7daad22475f1af9ac209bb992..a18c8857577211e64b7d17f6bbf3e5baff1253ff 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sparc64_hpc_ace_double_h
 #define nb_kernel_sparc64_hpc_ace_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
index 415fee6de3c09e1f20590e87b03839c8b158fbf6..4885d6df1a4bda18cde9df1e745a949f1f470f15 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
@@ -35,11 +35,11 @@
 #ifndef _kernelutil_x86_sse2_double_h_
 #define _kernelutil_x86_sse2_double_h_
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 
-#include "config.h"
-
 
 /* Normal sum of four ymm registers */
 #define gmx_mm_sum4_pd(t0, t1, t2, t3)  _mm_add_pd(_mm_add_pd(t0, t1), _mm_add_pd(t2, t3))

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
index 02ce4ef4173f56420486c58fd2dc22cfe951b2cc..ce36e1c56d528cccc2970d2b2a9fc50d0fe8cf3e 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_double;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
index 1720d436fc1546b835d2a593fa4b3906b25a4b69..3d45667bd2462bc4034a5fc2ee969b8ed2214236 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse2_double_h
 #define nb_kernel_sse2_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
index 31f1230c80a04647a279e03b270a013736953977..3356a780c17fa141901a580346a3e332a91b20ca 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
@@ -37,10 +37,10 @@
 
 /* We require SSE2 now! */
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #define gmx_mm_castsi128_ps   _mm_castsi128_ps
 
 #define gmx_mm_extract_epi32(x, imm) _mm_cvtsi128_si32(_mm_srli_si128((x), 4 * (imm)))

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
index a66eb382cdae35dc2a59769185fe37888be9808d..3bff2be8b3070b32f57d1bc615888ec79485d26f 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_single;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
index 331870820c5f4ab1ed9598890ca72ba9fbdeab8f..82b0ca887b9ba6e74bc8e1e8350ed42807edebad 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse2_single_h
 #define nb_kernel_sse2_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
index a235cd48bcf6c7f461837affa80c04a9bcea951d..449fe3666eb77e81513f56496619abdeae643170 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
@@ -35,11 +35,11 @@
 #ifndef _kernelutil_x86_sse4_1_double_h_
 #define _kernelutil_x86_sse4_1_double_h_
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 
-#include "config.h"
-
 #define gmx_mm_extract_epi32(x, imm) _mm_extract_epi32((x), (imm))
 #define gmx_mm_castsi128_pd(a) _mm_castsi128_pd(a)
 

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
index c30d8005471b3d7322eedf92ee0cd79f4cb71290..2a7f2fc9f7df40b7fae7fecd8fecc6afec8e7159 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_double;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
index 49113b2ab6d81242a403f25e858fbf104de6a733..413731884191ccc165b24fa86ece4760848074e9 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse4_1_double_h
 #define nb_kernel_sse4_1_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
index 2d83de317af084c63f9903ecb3e89793209b01cd..7028cef224036fb9503a4f664d324f69ae0fbd1e 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
@@ -35,10 +35,10 @@
 #ifndef _kernelutil_x86_sse4_1_single_h_
 #define _kernelutil_x86_sse4_1_single_h_
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #undef gmx_restrict
 #define gmx_restrict
 

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
index 95b0055d6ba6a873204db23394addfc2248c9987..79546e1b1b3f59c015621894bd70de59711012a6 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_single;

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
index c70ec17440fd8cd625f275d69b7b506b6407885e..22160f86a2cc935251f5414f1692c656478d7a0b 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse4_1_single_h
 #define nb_kernel_sse4_1_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index baaf1184f238ede7a4dfee96bc253f78492f25bc..7bcf2a66b18337c9c75ffdaed7808e54970afdfe 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nonbonded.h"
+
 #include "config.h"
 
 #include <stdio.h>
@@ -44,61 +46,57 @@
 #include "thread_mpi/threads.h"
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/simd/simd.h"
-
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel.h"
-#include "nb_free_energy.h"
-#include "nb_generic.h"
-#include "nb_generic_cg.h"
-#include "nb_generic_adress.h"
-
 /* Different default (c) and SIMD instructions interaction-specific kernels */
-#include "nb_kernel_c/nb_kernel_c.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h"
 
 #if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
 #endif
 #if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
-#    include "nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
 #endif
 
 

diff --git a/src/gromacs/gmxlib/nrnb.c b/src/gromacs/gmxlib/nrnb.c
index 54925d85ed4d95591c22e3dbd0b0ea8053048d8d..f77bd43a80a642464e9aff0ad13f00ef6e0cf17c 100644 (file)
--- a/src/gromacs/gmxlib/nrnb.c
+++ b/src/gromacs/gmxlib/nrnb.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nrnb.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxlib/oenv.cpp b/src/gromacs/gmxlib/oenv.cpp
index d7fcc05037414e3762aaf20921bcf46151ce319d..89201b8064ae4e746c653177bcae8a4781eb436b 100644 (file)
--- a/src/gromacs/gmxlib/oenv.cpp
+++ b/src/gromacs/gmxlib/oenv.cpp
@@ -38,10 +38,9 @@
 
 #include "gromacs/legacyheaders/oenv.h"
 
-#include "gromacs/utility/smalloc.h"
-
-#include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 
 struct output_env
 {

diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index 3c4f3e5db53d54e5e66277d9d0e6c8023a020f96..1d15a6a4cced171f4ff07036b3507da8aec92670 100644 (file)
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -36,20 +36,20 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
 
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxlib/rbin.c b/src/gromacs/gmxlib/rbin.c
index 5ef4d5d229aabe7de030cf7cbe227ea7ef4aeb66..754c648cb278a65923cd1b2807c0e8aab74ce32f 100644 (file)
--- a/src/gromacs/gmxlib/rbin.c
+++ b/src/gromacs/gmxlib/rbin.c
@@ -37,9 +37,10 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/rbin.h"
+
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/smalloc.h"
 
 t_bin *mk_bin(void)

diff --git a/src/gromacs/gmxlib/readinp.c b/src/gromacs/gmxlib/readinp.c
index 0f2e4196d7dead9aae3527463905c1f420920a96..10a2c7cc366e2932d179af5824894e3de7b2d494 100644 (file)
--- a/src/gromacs/gmxlib/readinp.c
+++ b/src/gromacs/gmxlib/readinp.c
@@ -36,18 +36,20 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/readinp.h"
+
 #include <stdio.h>
 #include <stdlib.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/macros.h"
+
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 t_inpfile *read_inpfile(const char *fn, int *ninp,
                         warninp_t wi)

diff --git a/src/gromacs/gmxlib/sighandler.c b/src/gromacs/gmxlib/sighandler.c
index 2149787465d6d5e961d67353cce18537cfc5d99d..75ff86caba063cd5da802bd6b82451637c34a5eb 100644 (file)
--- a/src/gromacs/gmxlib/sighandler.c
+++ b/src/gromacs/gmxlib/sighandler.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/sighandler.h"
+
 #include "config.h"
 
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/sighandler.h"
 
 const char *gmx_stop_cond_name[] =
 {

diff --git a/src/gromacs/gmxlib/splitter.c b/src/gromacs/gmxlib/splitter.c
index b9557b54a74231e2f12832604bade7e517be4d30..cb2eb90f6b976fb595d82462a4baaf291760d9c1 100644 (file)
--- a/src/gromacs/gmxlib/splitter.c
+++ b/src/gromacs/gmxlib/splitter.c
@@ -43,7 +43,6 @@
 #include <string.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"

diff --git a/src/gromacs/gmxlib/txtdump.c b/src/gromacs/gmxlib/txtdump.c
index b8d3088c736a04d647dd62c7918709c6866d9b95..9b3eec687ef43eeecb59054f67c906161f2a8559 100644 (file)
--- a/src/gromacs/gmxlib/txtdump.c
+++ b/src/gromacs/gmxlib/txtdump.c
@@ -38,16 +38,16 @@
 
 /* This file is completely threadsafe - please keep it that way! */
 
+#include "gromacs/legacyheaders/txtdump.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxlib/viewit.c b/src/gromacs/gmxlib/viewit.c
index c7284534393af48dfd36749ab96f0040d97b673d..c6a3a690bb47fe76e4111561750b200a6f258615 100644 (file)
--- a/src/gromacs/gmxlib/viewit.c
+++ b/src/gromacs/gmxlib/viewit.c
@@ -44,9 +44,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 

diff --git a/src/gromacs/gmxlib/warninp.c b/src/gromacs/gmxlib/warninp.c
index 9d9b5b79b69b516fadf5d764af58f68da4ab48c4..1721a470123534f1a1fe8012642d08aa8ac7b931 100644 (file)
--- a/src/gromacs/gmxlib/warninp.c
+++ b/src/gromacs/gmxlib/warninp.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/warninp.h"
+
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct warninp {
     gmx_bool bAllowWarnings;

diff --git a/src/gromacs/gmxpreprocess/add_par.c b/src/gromacs/gmxpreprocess/add_par.c
index 26926a91d4f8213febc266f19adac64c57e4a229..cf471c4641e40693d73cef372453199e72c89640 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.c
+++ b/src/gromacs/gmxpreprocess/add_par.c
@@ -38,14 +38,15 @@
 #include "gmxpre.h"
 
 #include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "grompp-impl.h"
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "toputil.h"
-#include "hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void clear_atom_list(int i0, atom_id a[])
 {

diff --git a/src/gromacs/gmxpreprocess/add_par.h b/src/gromacs/gmxpreprocess/add_par.h
index ae2b2eca0d1844714c22ec5a82c03e0129a75ed3..92a0d8be4d432853825564648e0fa42c5977864a 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.h
+++ b/src/gromacs/gmxpreprocess/add_par.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_ADD_PAR_H
 #define GMX_GMXPREPROCESS_ADD_PAR_H
 
+#include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "pdb2top.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c
index b2d1f3a751324474be505a5c681500f35102505b..7a6e0b0b7f2a96adecb013edddb678c0b6a15260 100644 (file)
--- a/src/gromacs/gmxpreprocess/addconf.c
+++ b/src/gromacs/gmxpreprocess/addconf.c
@@ -41,20 +41,19 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/calc_verletbuf.c b/src/gromacs/gmxpreprocess/calc_verletbuf.c
index 8d1313a4083a8fc3d976f91dfab58e06cfdee47c..dbdcab9074edab4ed3344c9c91c022a5b266756e 100644 (file)
--- a/src/gromacs/gmxpreprocess/calc_verletbuf.c
+++ b/src/gromacs/gmxpreprocess/calc_verletbuf.c
@@ -34,20 +34,20 @@
  */
 #include "gmxpre.h"
 
+#include "calc_verletbuf.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdlib.h>
 
 #include <sys/types.h>
 
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "calc_verletbuf.h"
-#include "../mdlib/nbnxn_consts.h"
-
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/calch.c b/src/gromacs/gmxpreprocess/calch.c
index dfab85b064e1e74aceb6e736e389b3e4f541c1a7..d171bbd34b85d99be060f2b883fb38626a834ca6 100644 (file)
--- a/src/gromacs/gmxpreprocess/calch.c
+++ b/src/gromacs/gmxpreprocess/calch.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "calch.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-
 #include "gromacs/utility/fatalerror.h"
 
 #define xAI xa[0]

diff --git a/src/gromacs/gmxpreprocess/compute_io.c b/src/gromacs/gmxpreprocess/compute_io.c
index 8de74782b7055b5dfff81fc554628761e430c36d..51a73d1a845aa5666dc869041927c29256579b85 100644 (file)
--- a/src/gromacs/gmxpreprocess/compute_io.c
+++ b/src/gromacs/gmxpreprocess/compute_io.c
@@ -38,6 +38,7 @@
 
 #include <signal.h>
 #include <stdlib.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 static int div_nsteps(int nsteps, int nst)

diff --git a/src/gromacs/gmxpreprocess/convparm.c b/src/gromacs/gmxpreprocess/convparm.c
index 3ae40c2a840f04633487f665dbe40ae60a0c0e71..e3bac959634c99ccff527314da7705448b8453cc 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.c
+++ b/src/gromacs/gmxpreprocess/convparm.c
@@ -37,20 +37,21 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "convparm.h"
+
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "topio.h"
-#include "toputil.h"
-#include "convparm.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gpp_atomtype.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
 
 static int round_check(real r, int limit, int ftype, const char *name)
 {

diff --git a/src/gromacs/gmxpreprocess/fflibutil.cpp b/src/gromacs/gmxpreprocess/fflibutil.cpp
index b47aa18b7c86c5acc632c6561c94a64c1186b4f5..e87fb8f659a5183e0acac7ef7fbd4a02abae6390 100644 (file)
--- a/src/gromacs/gmxpreprocess/fflibutil.cpp
+++ b/src/gromacs/gmxpreprocess/fflibutil.cpp
@@ -36,6 +36,8 @@
 
 #include "fflibutil.h"
 
+#include "config.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -44,8 +46,6 @@
 #include <sys/stat.h>
 #include <sys/types.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/gmxpreprocess/fflibutil.h b/src/gromacs/gmxpreprocess/fflibutil.h
index f49d96327b075c078011a17bd73a5980b73723da..6703c2b7b0a9032dd9b9cc5c9d8822fc4ff5354f 100644 (file)
--- a/src/gromacs/gmxpreprocess/fflibutil.h
+++ b/src/gromacs/gmxpreprocess/fflibutil.h
@@ -37,6 +37,7 @@
 #define GMX_GMXPREPROCESS_FFLIBUTIL_H
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/gmxpreprocess/gen_ad.c b/src/gromacs/gmxpreprocess/gen_ad.c
index c110bc7a3e4a31963416a849307e1a9256152a08..61dc0f9cd71054b75324978d805b6e2249525407 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.c
+++ b/src/gromacs/gmxpreprocess/gen_ad.c
@@ -37,24 +37,24 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gen_ad.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "topio.h"
-#include "gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "gen_ad.h"
+#include "gromacs/utility/smalloc.h"
 
 #define DIHEDRAL_WAS_SET_IN_RTP 0
 static gmx_bool was_dihedral_set_in_rtp(t_param *dih)

diff --git a/src/gromacs/gmxpreprocess/gen_ad.h b/src/gromacs/gmxpreprocess/gen_ad.h
index a2829d7ad348686ae46bb0d47268b9f50d479a59..e8814a5cabe8491f960b7b543bafe0dfa9ad9712 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.h
+++ b/src/gromacs/gmxpreprocess/gen_ad.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_GEN_AD_H
 #define GMX_GMXPREPROCESS_GEN_AD_H
 
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "toputil.h"
-#include "gpp_nextnb.h"
-#include "resall.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
index 609650f4a13aa21e4811bcefdc5d08be81681027..02522be85facfea72c534ecfbc500d2fcfff594e 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
@@ -36,14 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "gen_maxwell_velocities.h"
+
 #include <math.h>
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gen_maxwell_velocities.h"
+#include "gromacs/random/random.h"
 #include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/smalloc.h"
 
 static void low_mspeed(real tempi,
                        gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index 9743f690a6d7a7a271d2df1c703aa92a2f0154ea..4d0e990044c17b47b9faf3c0d269383e98ceef72 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -36,26 +36,26 @@
  */
 #include "gmxpre.h"
 
+#include "gen_vsite.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gen_vsite.h"
-#include "resall.h"
-#include "add_par.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define MAXNAME 32

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.h b/src/gromacs/gmxpreprocess/gen_vsite.h
index 98d668b1758a1e31e61a39a64eaae1ac9187fde4..6a350ef7093b373f8e8eded985adee4b06f76078 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.h
+++ b/src/gromacs/gmxpreprocess/gen_vsite.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_GEN_VSITE_H
 #define GMX_GMXPREPROCESS_GEN_VSITE_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "hackblock.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxpreprocess/genconf.c b/src/gromacs/gmxpreprocess/genconf.c
index 13ee6050362798679a140596aa52620aef0d7c82..9f9a57ce8cda8b3f08e81d47b2aa7b9273ffca21 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.c
+++ b/src/gromacs/gmxpreprocess/genconf.c
@@ -38,17 +38,16 @@
 
 #include "genconf.h"
 
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/names.h"
-#include "sortwater.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
index 9ac5b4d4448c573ab1f8032520d6f85c0eb5aa1c..3a85fa12094f8a8201a5647d3174d605c1619db1 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.c
+++ b/src/gromacs/gmxpreprocess/genhydro.c
@@ -36,24 +36,24 @@
  */
 #include "gmxpre.h"
 
+#include "genhydro.h"
+
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "calch.h"
-#include "genhydro.h"
-#include "h_db.h"
-#include "ter_db.h"
-#include "resall.h"
-#include "pgutil.h"
+#include "gromacs/gmxpreprocess/calch.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
 #include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)

diff --git a/src/gromacs/gmxpreprocess/genhydro.h b/src/gromacs/gmxpreprocess/genhydro.h
index ed5b07f37dae5179453313e761b1f2316617ca44..9161a33324d63b8786358f7ed2b5ca285818a0d5 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.h
+++ b/src/gromacs/gmxpreprocess/genhydro.h
@@ -39,7 +39,7 @@
 #define GMX_GMXPREPROCESS_GENHYDRO_H
 
 #include "gromacs/fileio/pdbio.h"
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/gmxcpp.c b/src/gromacs/gmxpreprocess/gmxcpp.c
index 81795e98054c763b97a2eb8eda83a77ca965ef52..42fd453757e26f6897498a16f21ce5413cf92261 100644 (file)
--- a/src/gromacs/gmxpreprocess/gmxcpp.c
+++ b/src/gromacs/gmxpreprocess/gmxcpp.c
@@ -36,21 +36,23 @@
  */
 #include "gmxpre.h"
 
-#include <sys/types.h>
+#include "gmxcpp.h"
+
+#include <ctype.h>
+#include <errno.h>
+#include <limits.h>
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
 #include <string.h>
-#include <errno.h>
-#include <limits.h>
-#include <ctype.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
+#include <sys/types.h>
+
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gmxcpp.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char *name;

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.c b/src/gromacs/gmxpreprocess/gpp_atomtype.c
index 8ef380fd04d7ab65191ceabaec731488abb409a5..4a9c932b0f93c8dd01f095bbc21acf0d006e4108 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.c
@@ -36,14 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gpp_atomtype.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "topdirs.h"
-#include "toputil.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gpp_atomtype.h"
-
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.h b/src/gromacs/gmxpreprocess/gpp_atomtype.h
index 5a902db7afcdcbc08f6356281c8670058d73d79f..9dd46548b3ae6fa8eece4e85583559e92ed09e62 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.h
@@ -39,8 +39,9 @@
 #define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
 
 #include <stdio.h>
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
index 905308b3be91ff1d1d2beb3f97226e049964d18d..6a39e71f88de1d02f7979549a9bac577772bb61e 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "gpp_bond_atomtype.h"
 
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
index cd88c07a81d8e584dda44e6090f4a64334d665a2..c901d9b1f07484ab890e755a1ff22eb92cbb157c 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
@@ -39,6 +39,7 @@
 #define GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.h b/src/gromacs/gmxpreprocess/gpp_nextnb.h
index e06a3824171e72b1c8e882013f5ee93432765213..c5dde3865e4d3451ddf8a87fd2b98297d1ed38fc 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.h
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_GPP_NEXTNB_H
 #define GMX_GMXPREPROCESS_GPP_NEXTNB_H
 
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 7e32feb2f6d1e0ee545ce072a2e499068ee3fbfd..8a7c681315351031ca616b21b16f926420c07532 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -38,53 +38,52 @@
 
 #include "grompp.h"
 
-#include <sys/types.h>
-#include <math.h>
-#include <string.h>
+#include <assert.h>
 #include <errno.h>
 #include <limits.h>
-#include <assert.h>
+#include <math.h>
+#include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "readir.h"
-#include "toputil.h"
-#include "topio.h"
+#include <sys/types.h>
+
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "readir.h"
-#include "gromacs/legacyheaders/names.h"
-#include "grompp-impl.h"
-#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/splitter.h"
-#include "gromacs/gmxpreprocess/sortwater.h"
-#include "convparm.h"
-#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-#include "vsite_parm.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/gmxpreprocess/convparm.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/gmxpreprocess/tomorse.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/calcgrid.h"
-#include "add_par.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/legacyheaders/perf_est.h"
-#include "compute_io.h"
-#include "gpp_atomtype.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/genborn.h"
-#include "calc_verletbuf.h"
-#include "tomorse.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/utility/cstringutil.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])

diff --git a/src/gromacs/gmxpreprocess/h_db.c b/src/gromacs/gmxpreprocess/h_db.c
index 85bacf8a3f95274892bf20cf8657dd963ad36ff4..f630ae787608c69c80730c6cd01c4e4ce7aee2e2 100644 (file)
--- a/src/gromacs/gmxpreprocess/h_db.c
+++ b/src/gromacs/gmxpreprocess/h_db.c
@@ -37,17 +37,18 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "h_db.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "h_db.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Number of control atoms for each 'add' type.
  *

diff --git a/src/gromacs/gmxpreprocess/h_db.h b/src/gromacs/gmxpreprocess/h_db.h
index f297506765f1e06dfbef013178b541483a79de12..24f873b6c2e3fb913b269d925e7c479f024c92a7 100644 (file)
--- a/src/gromacs/gmxpreprocess/h_db.h
+++ b/src/gromacs/gmxpreprocess/h_db.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/hackblock.c b/src/gromacs/gmxpreprocess/hackblock.c
index ff7f0fdf2e742c565c4b0043d7351afefc8f5741..c30a69851b82c6b85476b52c3bab218c1dfd0571 100644 (file)
--- a/src/gromacs/gmxpreprocess/hackblock.c
+++ b/src/gromacs/gmxpreprocess/hackblock.c
@@ -37,12 +37,14 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include <string.h>
 #include "hackblock.h"
+
+#include <string.h>
+
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/names.h"
 
 /* these MUST correspond to the enum in hackblock.h */
 const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };

diff --git a/src/gromacs/gmxpreprocess/hackblock.h b/src/gromacs/gmxpreprocess/hackblock.h
index 52c138ced6b9e8838acdb1b7754fd7dd54fb67d5..294dcec86c486006856beeae573b874907c00fb9 100644 (file)
--- a/src/gromacs/gmxpreprocess/hackblock.h
+++ b/src/gromacs/gmxpreprocess/hackblock.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
 #define GMX_GMXPREPROCESS_HACKBLOCK_H
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/pdbio.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/symtab.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/gmxpreprocess/hizzie.c b/src/gromacs/gmxpreprocess/hizzie.c
index e7b637a21be99924791c2453333add47953a2614..0aff84f7a41b04bac8fbf85c3ebeac82ef960f50 100644 (file)
--- a/src/gromacs/gmxpreprocess/hizzie.c
+++ b/src/gromacs/gmxpreprocess/hizzie.c
@@ -39,16 +39,16 @@
 
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-#include "toputil.h"
-#include "pdb2top.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert-molecules.cpp
index 32d5908987e4e7eb53000cf4f087f79f9eb9cdc0..5818fbbbea234c6a8ebf27eaf8a52ede9ed15d53 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert-molecules.cpp
@@ -38,18 +38,17 @@
 
 #include "insert-molecules.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/addconf.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"

diff --git a/src/gromacs/gmxpreprocess/nm2type.c b/src/gromacs/gmxpreprocess/nm2type.c
index d4b01a884dfae8a5dcdd3b11eda4fff0d509dccb..41882302acdcf05967b850243e6ed6fdc053f8ad 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.c
+++ b/src/gromacs/gmxpreprocess/nm2type.c
@@ -37,26 +37,25 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "nm2type.h"
+
 #include <string.h>
 
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-
-#include "nm2type.h"
-
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
 {

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index 0a1aeb20d41ecd14255f0854778d09539509f2e7..ac9f6ec0837524aa9a7b6b5543e086b8ed87bb2f 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -43,40 +43,37 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "pdb2top.h"
-#include "ter_db.h"
+#include "gromacs/fileio/strdb.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "genhydro.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/topology/index.h"
-#include "fflibutil.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/hizzie.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/specbond.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/xlate.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-
-#include "hizzie.h"
-#include "specbond.h"
-#include "xlate.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char gmx[6];

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index ec4f8927ce5d570c14cde224c8b774b9cb3e429c..8d9de45d32635457a9d0b368bd2e7181862fbe4b 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -36,36 +36,35 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
-#include <math.h>
+#include "pdb2top.h"
+
 #include <ctype.h>
+#include <math.h>
+#include <stdio.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "topio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gen_ad.h"
 #include "gromacs/fileio/filenm.h"
-#include "gen_vsite.h"
-#include "add_par.h"
-#include "toputil.h"
-#include "fflibutil.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gen_vsite.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/pdb2top.h b/src/gromacs/gmxpreprocess/pdb2top.h
index 9b54d001970c8f14555cec8860b1f94540d65c26..cfbc800c879048746709698f1a4deac9228f09b8 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.h
+++ b/src/gromacs/gmxpreprocess/pdb2top.h
@@ -38,11 +38,11 @@
 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
 #define GMX_GMXPREPROCESS_PDB2TOP_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "toputil.h"
-#include "hackblock.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxpreprocess/pgutil.c b/src/gromacs/gmxpreprocess/pgutil.c
index 1cebc523b6ec3661774f6e5c9b808960cc14e610..ff38d066acff9b546424ebe34c47f207541b1566 100644 (file)
--- a/src/gromacs/gmxpreprocess/pgutil.c
+++ b/src/gromacs/gmxpreprocess/pgutil.c
@@ -38,9 +38,11 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/utility/cstringutil.h"
 #include "pgutil.h"
+
 #include <string.h>
+
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 
 #define BUFSIZE 1024

diff --git a/src/gromacs/gmxpreprocess/protonate.c b/src/gromacs/gmxpreprocess/protonate.c
index 5f1d99f6fce8a97de85e82d2696333337f8fbe78..4b73ff2760088291247b6ee7a5381e70f1bbb495 100644 (file)
--- a/src/gromacs/gmxpreprocess/protonate.c
+++ b/src/gromacs/gmxpreprocess/protonate.c
@@ -39,20 +39,20 @@
 #include "protonate.h"
 
 #include <math.h>
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "genhydro.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "hackblock.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_protonate(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxpreprocess/read-conformation.cpp b/src/gromacs/gmxpreprocess/read-conformation.cpp
index b792b95c17a8bdf29221a6e45211270562fc2ae6..72886e8ced652aa4ca544db215276caf13fe3158 100644 (file)
--- a/src/gromacs/gmxpreprocess/read-conformation.cpp
+++ b/src/gromacs/gmxpreprocess/read-conformation.cpp
@@ -37,8 +37,8 @@
 #include "read-conformation.h"
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/readadress.c b/src/gromacs/gmxpreprocess/readadress.c
index bc46c5802e20ea574e65a99184bfe434de89d7d4..a95374cda85b3e7d873a8804f18ac396778b4570 100644 (file)
--- a/src/gromacs/gmxpreprocess/readadress.c
+++ b/src/gromacs/gmxpreprocess/readadress.c
@@ -38,7 +38,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 0322b5b28c490ee4807eb4a3d05f38fd8234d28e..8f55b6c6609358dcc0d19c872e9da8e9fdb006d3 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -36,30 +36,30 @@
  */
 #include "gmxpre.h"
 
+#include "readir.h"
+
 #include <ctype.h>
 #include <limits.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/warninp.h"
-#include "readir.h"
-#include "toputil.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "calc_verletbuf.h"
-
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/readir.h b/src/gromacs/gmxpreprocess/readir.h
index eb93bbfc4580639328bd86b4c3e04419bebaec52..e20453e20042a3cfbd8f2aafb223bfbea18dce0c 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.h
+++ b/src/gromacs/gmxpreprocess/readir.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXPREPROCESS_READIR_H
 #define GMX_GMXPREPROCESS_READIR_H
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/readinp.h"
-#include "grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index 70e484aae63279fb7f477931370eb21cab1119de..2e78022c5b1d32b148f31348616f69ab83af7e1a 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <stdlib.h>
+#include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "readir.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static char pulldim[STRLEN];

diff --git a/src/gromacs/gmxpreprocess/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
index 527aca8764653c0c1207ccc035612c056910e5ba..f6289af803e0604b26d8a4a18f208dcd87f777d6 100644 (file)
--- a/src/gromacs/gmxpreprocess/readrot.c
+++ b/src/gromacs/gmxpreprocess/readrot.c
@@ -36,15 +36,14 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "readir.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"
-
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *RotStr = {"Enforced rotation:"};
 

diff --git a/src/gromacs/gmxpreprocess/resall.c b/src/gromacs/gmxpreprocess/resall.c
index b363023b1d31f0b8e768240af1ea9ccf9b6d1917..fe75e0cc652e8f65294e2c8aab6a8aa960047d47 100644 (file)
--- a/src/gromacs/gmxpreprocess/resall.c
+++ b/src/gromacs/gmxpreprocess/resall.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "resall.h"
+
 #include <ctype.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "resall.h"
-#include "pgutil.h"
-#include "fflibutil.h"
-
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/resall.h b/src/gromacs/gmxpreprocess/resall.h
index c9bd68c60adbc5ca86c548607c6568e5f86f9cbc..487ed643e2a06febc6b4c69f5c069fffd7cd657f 100644 (file)
--- a/src/gromacs/gmxpreprocess/resall.h
+++ b/src/gromacs/gmxpreprocess/resall.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_RESALL_H
 #define GMX_GMXPREPROCESS_RESALL_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "hackblock.h"
-#include "gpp_atomtype.h"
-#include "grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index 421a49a2073b04eade2e6fcd29c9cec934580688..5cfbe5d03ec22cebb258509e0f01b864ba7d099d 100644 (file)
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -40,21 +40,20 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/addconf.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-#include "gromacs/fileio/pdbio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef DEBUG

diff --git a/src/gromacs/gmxpreprocess/sortwater.c b/src/gromacs/gmxpreprocess/sortwater.c
index 43dcda6c5d29e03ce58bf5947f39c100efd2bc9f..73c8b5472d8f7be3eb320460be9a0e554c8d7e96 100644 (file)
--- a/src/gromacs/gmxpreprocess/sortwater.c
+++ b/src/gromacs/gmxpreprocess/sortwater.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "sortwater.h"
+
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "sortwater.h"
-
 #include "gromacs/random/random.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/specbond.c b/src/gromacs/gmxpreprocess/specbond.c
index 208092882bc52b4888eb45e53651cbab7ecca0c4..2d1bfcf261425105a6b0effc306a7b22c4201cbf 100644 (file)
--- a/src/gromacs/gmxpreprocess/specbond.c
+++ b/src/gromacs/gmxpreprocess/specbond.c
@@ -36,19 +36,20 @@
  */
 #include "gmxpre.h"
 
+#include "specbond.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
-#include "specbond.h"
-#include "pdb2top.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
 
 gmx_bool yesno(void)
 {

diff --git a/src/gromacs/gmxpreprocess/specbond.h b/src/gromacs/gmxpreprocess/specbond.h
index cd37ca9af32ddef5aab2746c1c08688bebb1c926..4c8eedc307b62365d1fbb221b286426aad2afa02 100644 (file)
--- a/src/gromacs/gmxpreprocess/specbond.h
+++ b/src/gromacs/gmxpreprocess/specbond.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_SPECBOND_H
 #define GMX_GMXPREPROCESS_SPECBOND_H
 
-#include "pdb2top.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
index 4817b27942da8165a770e76577f416629d8c0a46..df0722c368326e6cb534e58b01efc89cfc981dfb 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.c
+++ b/src/gromacs/gmxpreprocess/ter_db.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
+#include "ter_db.h"
+
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "resall.h"
-#include "h_db.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "ter_db.h"
-#include "toputil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-
-#include "gromacs/fileio/strdb.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* use bonded types definitions in hackblock.h */
 #define ekwRepl ebtsNR+1

diff --git a/src/gromacs/gmxpreprocess/ter_db.h b/src/gromacs/gmxpreprocess/ter_db.h
index 40547627da54ed8b442304a00844f2f8ce1eee07..45477d620705a65421430521529d7b2258db012d 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.h
+++ b/src/gromacs/gmxpreprocess/ter_db.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_TER_DB_H
 #define GMX_GMXPREPROCESS_TER_DB_H
 
-#include "hackblock.h"
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp b/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
index 913208d7b5bebbc98882acca509a717237c35a73..b33d211ed45d555ba3a432c2bc7b8fc7983fcaa5 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
@@ -41,11 +41,13 @@
 
 #include "gmxpre.h"
 
-#include "../insert-molecules.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
+#include "gromacs/gmxpreprocess/insert-molecules.h"
+
 #include "gromacs/utility/futil.h"
 
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+
 namespace
 {
 

diff --git a/src/gromacs/gmxpreprocess/tests/solvate.cpp b/src/gromacs/gmxpreprocess/tests/solvate.cpp
index 947729b78e71e1e2fcb3595689fd1b6662a81440..86be31d27197781e39e41ea3115a4471fc3b84b4 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/tests/solvate.cpp
@@ -41,11 +41,13 @@
 
 #include "gmxpre.h"
 
-#include "../solvate.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
+#include "gromacs/gmxpreprocess/solvate.h"
+
 #include "gromacs/utility/futil.h"
 
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+
 namespace
 {
 

diff --git a/src/gromacs/gmxpreprocess/tomorse.c b/src/gromacs/gmxpreprocess/tomorse.c
index a326f16f0a874239fbc2484d5436abcc9ae24dfa..f1781e90432994261ac8dde60a65d6f2711efe93 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.c
+++ b/src/gromacs/gmxpreprocess/tomorse.c
@@ -37,21 +37,21 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "tomorse.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/cstringutil.h"
-#include "grompp-impl.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
-#include "toputil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gpp_atomtype.h"
-
-#include "tomorse.h"
 
 typedef struct {
     char *ai, *aj;

diff --git a/src/gromacs/gmxpreprocess/tomorse.h b/src/gromacs/gmxpreprocess/tomorse.h
index 39630fbf62d4e337497a8edf01e91c91c04721ad..6a39ea6fd84200e000bbe34358be5c9bd477dcd8 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.h
+++ b/src/gromacs/gmxpreprocess/tomorse.h
@@ -39,6 +39,7 @@
 #define GMX_GMXPREPROCESS_TOMORSE_H
 
 #include <stdio.h>
+
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"

diff --git a/src/gromacs/gmxpreprocess/topdirs.c b/src/gromacs/gmxpreprocess/topdirs.c
index d46b6922a8ab678408183c0b890ce95644f5a271..1c42dfab2d4513603f229a3a1baa4f2b4d2b3c51 100644 (file)
--- a/src/gromacs/gmxpreprocess/topdirs.c
+++ b/src/gromacs/gmxpreprocess/topdirs.c
@@ -36,14 +36,15 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "topdirs.h"
+
 #include <stdarg.h>
+#include <stdio.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "topdirs.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Must correspond to the directive enum in grompp-impl.h */
 static const char *directive_names[d_maxdir+1] = {

diff --git a/src/gromacs/gmxpreprocess/topdirs.h b/src/gromacs/gmxpreprocess/topdirs.h
index f619c8a4ea40f25057425ae0c654d29170951f5f..fa62531eeb70025e794080eab2691cc009a00f9a 100644 (file)
--- a/src/gromacs/gmxpreprocess/topdirs.h
+++ b/src/gromacs/gmxpreprocess/topdirs.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_TOPDIRS_H
 #define GMX_GMXPREPROCESS_TOPDIRS_H
 
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index f7efad094cf21ac20e3ccba791e7af356f8f2f81..ffc95d0596abccbe26cf93d5b5516d1fd1b3e8a4 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "topio.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <errno.h>
@@ -46,34 +48,31 @@
 
 #include <sys/types.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/topshake.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/warninp.h"
-#include "vsite_parm.h"
-
-#include "grompp-impl.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "gpp_nextnb.h"
-#include "topio.h"
-#include "topshake.h"
-#include "gmxcpp.h"
-#include "gpp_bond_atomtype.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define OPENDIR     '[' /* starting sign for directive */
 #define CLOSEDIR    ']' /* ending sign for directive   */

diff --git a/src/gromacs/gmxpreprocess/topio.h b/src/gromacs/gmxpreprocess/topio.h
index 0767cef7289991b428dd834dea397dcd8395b9c8..e03b102aa4dc3da6c8db475d1f2b1a66f4a9c5c9 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.h
+++ b/src/gromacs/gmxpreprocess/topio.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_TOPIO_H
 #define GMX_GMXPREPROCESS_TOPIO_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "readir.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index fdefac9f1401f70fa0288375cd09bcc159bd2125..161940b72e0f2a73267baeab449016d12247b67d 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -36,21 +36,21 @@
  */
 #include "gmxpre.h"
 
+#include "toppush.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "readir.h"
 #include "gromacs/legacyheaders/warninp.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
-
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index 83526df792e9cf3a3b6e983d5039d317b578dbda..1e14c57bc72a8db85f7648838bb51aa85790be03 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
 #define GMX_GMXPREPROCESS_TOPPUSH_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "toputil.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
 #include "gromacs/legacyheaders/warninp.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index 66a1036bdcfe32a71b33a8ffc0df7840fb9fec43..bd2662df2ad09d93914160f2a698f7c199a1dec8 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -37,18 +37,19 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "topshake.h"
+
 #include <ctype.h>
 #include <math.h>
 
-#include "gromacs/math/units.h"
-#include "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "topshake.h"
-#include "toppush.h"
-#include "toputil.h"
-#include "topdirs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void copy_bond (t_params *pr, int to, int from)
 /* copies an entry in a bond list to another position.

diff --git a/src/gromacs/gmxpreprocess/topshake.h b/src/gromacs/gmxpreprocess/topshake.h
index 2844b9f4dde13108dd19725ee4d94cda84c69f55..15e09da6623937ebfd8ad444961a9ac9ab27c17f 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.h
+++ b/src/gromacs/gmxpreprocess/topshake.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_TOPSHAKE_H
 #define GMX_GMXPREPROCESS_TOPSHAKE_H
 
-#include "topio.h"
+#include "gromacs/gmxpreprocess/topio.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/toputil.c b/src/gromacs/gmxpreprocess/toputil.c
index a407b711df95ab1376f662570ddb3a267f630a26..ff567c8ea23070a10f1a68c98e1615f43ea6bab5 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.c
+++ b/src/gromacs/gmxpreprocess/toputil.c
@@ -36,15 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "toputil.h"
+
 #include <assert.h>
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "gpp_atomtype.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/toputil.h b/src/gromacs/gmxpreprocess/toputil.h
index fd4259440bdc27a5cd203aaeafa1c9d3b20e506c..d7d040effe46e3035391c61b73f57dfa608f48ed 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.h
+++ b/src/gromacs/gmxpreprocess/toputil.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_TOPUTIL_H
 #define GMX_GMXPREPROCESS_TOPUTIL_H
 
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index edeab6fe4bb4521ff8ea71c3d2eb4b75260f9012..df9f9160ad7d99b88d00ead8463d296e1a9f796a 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -36,22 +36,23 @@
  */
 #include "gmxpre.h"
 
+#include "vsite_parm.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "vsite_parm.h"
-#include "gromacs/utility/smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     t_iatom a[4];

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.h b/src/gromacs/gmxpreprocess/vsite_parm.h
index c127bbb88f654ce82a7434232dc86fae6fc4fb4c..3001e74bc0f217665a9b0dc1048df76c894e09d8 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.h
+++ b/src/gromacs/gmxpreprocess/vsite_parm.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXPREPROCESS_VSITE_PARM_H
 #define GMX_GMXPREPROCESS_VSITE_PARM_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index f0ae9ad8d8bdcaddfa266c2615d3b98fca20c598..1dacc45c63117bc74cd48636385de6eb25ed1a8e 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -40,24 +40,23 @@
 
 #include <assert.h>
 
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/nm2type.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gen_ad.h"
-#include "gpp_nextnb.h"
-#include "hackblock.h"
-#include "nm2type.h"
-
-#include "gromacs/bonded/bonded.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/symtab.h"

diff --git a/src/gromacs/gmxpreprocess/xlate.c b/src/gromacs/gmxpreprocess/xlate.c
index d8dfc594f89a3b7352a6f78c401658a056dce705..c4d2c7cfe23760334ded99be85c64094a3328b61 100644 (file)
--- a/src/gromacs/gmxpreprocess/xlate.c
+++ b/src/gromacs/gmxpreprocess/xlate.c
@@ -36,15 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "xlate.h"
+
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "fflibutil.h"
-#include "hackblock.h"
-#include "xlate.h"
-
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 7c6585260e25f5c75927454e674357403846071a..7c608c7bd54d528c546de617a3c85a5d809426e5 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -49,11 +49,11 @@
 
 #include "imd.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <windows.h>
 #else

diff --git a/src/gromacs/imd/imd.h b/src/gromacs/imd/imd.h
index f6f26f2c3bd15404dd46e7575b40a568c2982103..01aa585425ac1d3e08e58573692d6cfb8a49d530 100644 (file)
--- a/src/gromacs/imd/imd.h
+++ b/src/gromacs/imd/imd.h
@@ -60,12 +60,12 @@
 #ifndef GMX_IMD_IMD_H
 #define GMX_IMD_IMD_H
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/filenm.h"
-#include "../timing/wallcycle.h"
-
 #include "config.h"
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
+
 #ifdef GMX_NATIVE_WINDOWS
 #include <Windows.h>
 #define NOFLAGS 0

diff --git a/src/gromacs/imd/imdsocket.c b/src/gromacs/imd/imdsocket.c
index e322523845888111cb29d45f7837d1bb891cfa86..ef70405d931d6e5f5219c3c5a5bda7ec8462f012 100644 (file)
--- a/src/gromacs/imd/imdsocket.c
+++ b/src/gromacs/imd/imdsocket.c
@@ -48,15 +48,16 @@
 
 #include "gmxpre.h"
 
+#include "imdsocket.h"
+
 #include "config.h"
 
 #include <errno.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/imd/imd.h"
 #include "gromacs/utility/fatalerror.h"
-#include "imdsocket.h"
-#include "imd.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_NATIVE_WINDOWS
 #ifdef GMX_HAVE_WINSOCK

diff --git a/src/gromacs/imd/imdsocket.h b/src/gromacs/imd/imdsocket.h
index d7f0ce95482b4d4ba3f0938a8f56b0adc2d6dcfc..4effb0c76a91c7a38cfd592ce0669aa69d3b3635 100644 (file)
--- a/src/gromacs/imd/imdsocket.h
+++ b/src/gromacs/imd/imdsocket.h
@@ -60,8 +60,8 @@
   #define GMX_IMD
   #endif
 #else
-#include <sys/socket.h>
 #include <netinet/in.h>
+#include <sys/socket.h>
 #define GMX_IMD
 #endif
 

diff --git a/src/gromacs/legacyheaders/bonded-threading.h b/src/gromacs/legacyheaders/bonded-threading.h
index f1ee5c88a5677405a62b9118701cba7a9983e3f3..e08765fa1f3077eefaf6de831a5930c4b518c04b 100644 (file)
--- a/src/gromacs/legacyheaders/bonded-threading.h
+++ b/src/gromacs/legacyheaders/bonded-threading.h
@@ -38,7 +38,7 @@
 #ifndef GMX_LEGACYHEADERS_BONDED_THREADING_H
 #define GMX_LEGACYHEADERS_BONDED_THREADING_H
 
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/calcgrid.h b/src/gromacs/legacyheaders/calcgrid.h
index 1c6450387ca5a5ce31cfa9be613c91a39bb899f7..251b9e3d57bfdc6f3491a1b9314aca51b1479b90 100644 (file)
--- a/src/gromacs/legacyheaders/calcgrid.h
+++ b/src/gromacs/legacyheaders/calcgrid.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/calcmu.h b/src/gromacs/legacyheaders/calcmu.h
index f72bbfdb042ef2a8f8f8882e4d604224604438d2..c9ed792d7bfa2cdec0185245eecf02b717d583df 100644 (file)
--- a/src/gromacs/legacyheaders/calcmu.h
+++ b/src/gromacs/legacyheaders/calcmu.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/chargegroup.h b/src/gromacs/legacyheaders/chargegroup.h
index 417917fc6597d1799d51d4d9866ee7235e4d464d..26c81b081bdf452592934bf6ffa3f181d5ca47eb 100644 (file)
--- a/src/gromacs/legacyheaders/chargegroup.h
+++ b/src/gromacs/legacyheaders/chargegroup.h
@@ -40,8 +40,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/checkpoint.h b/src/gromacs/legacyheaders/checkpoint.h
index 73ebd2a8f0f8148f0a00dda615b3faf9aa31e91b..78f329dc232d728fbccc0fea5a932ab7b773f766 100644 (file)
--- a/src/gromacs/legacyheaders/checkpoint.h
+++ b/src/gromacs/legacyheaders/checkpoint.h
@@ -39,9 +39,9 @@
 #define _checkpoint_h
 
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/gmxfio.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/coulomb.h b/src/gromacs/legacyheaders/coulomb.h
index 5c55f13f4535182c832efa965fd502f57fcb7ac1..0b1f63040832406eb3cf376ba3c172feb61e410f 100644 (file)
--- a/src/gromacs/legacyheaders/coulomb.h
+++ b/src/gromacs/legacyheaders/coulomb.h
@@ -39,6 +39,7 @@
 #define _coulomb_h
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/legacyheaders/domdec.h b/src/gromacs/legacyheaders/domdec.h
index 2516c5b3284d9d32bfe4ed29d92d8b1d8a295bbf..13b55711e8c385ee03d41139beb3563cc684c4cb 100644 (file)
--- a/src/gromacs/legacyheaders/domdec.h
+++ b/src/gromacs/legacyheaders/domdec.h
@@ -36,11 +36,10 @@
 #ifndef _domdec_h
 #define _domdec_h
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/genborn.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/ebin.h b/src/gromacs/legacyheaders/ebin.h
index 3dd6f42a0537b2fa5d8144e68527a7b115f42cae..f0bd0e79140d77a73e9a6a13572879725a332ee7 100644 (file)
--- a/src/gromacs/legacyheaders/ebin.h
+++ b/src/gromacs/legacyheaders/ebin.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/energy.h"
-#include "../fileio/enxio.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/force.h b/src/gromacs/legacyheaders/force.h
index 2bf5891d27f0f6578a0a2e2210d0cf2100dfcc7a..c93e720824f5949a419153f1c01b6d4baace9b3b 100644 (file)
--- a/src/gromacs/legacyheaders/force.h
+++ b/src/gromacs/legacyheaders/force.h
@@ -39,14 +39,13 @@
 #define _force_h
 
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/genborn.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/gmx_omp_nthreads.h b/src/gromacs/legacyheaders/gmx_omp_nthreads.h
index c5ceef442e2ba1221019c8ff194084abf951033c..1b7380fdb616733b436c40e16168f0f6e00383ba 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_omp_nthreads.h
+++ b/src/gromacs/legacyheaders/gmx_omp_nthreads.h
@@ -38,7 +38,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/gmx_thread_affinity.h b/src/gromacs/legacyheaders/gmx_thread_affinity.h
index dd10f54e568294ba0b10b35212dacff7b9430e6f..d2a2ce2b55de4989ed065cc1fa02c15f788975e8 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_thread_affinity.h
+++ b/src/gromacs/legacyheaders/gmx_thread_affinity.h
@@ -38,7 +38,7 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/types/hw_info.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/gpu_utils.h b/src/gromacs/legacyheaders/gpu_utils.h
index 27a44ee90ede035d772da7e1b0f731281d5e0d73..08f596f404e4976b8a025d67493b840b2ded5d35 100644 (file)
--- a/src/gromacs/legacyheaders/gpu_utils.h
+++ b/src/gromacs/legacyheaders/gpu_utils.h
@@ -40,8 +40,8 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU
 #define FUNC_TERM_INT ;

diff --git a/src/gromacs/legacyheaders/main.h b/src/gromacs/legacyheaders/main.h
index 7dff7326be4751e758e7de2fdaed5c52021ec442..43329b9d9ae560574f877a5838348d7a8ab1b7f6 100644 (file)
--- a/src/gromacs/legacyheaders/main.h
+++ b/src/gromacs/legacyheaders/main.h
@@ -40,9 +40,10 @@
 
 
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/network.h"
-#include "../fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/md_support.h b/src/gromacs/legacyheaders/md_support.h
index 1fd51c4f9f09b4a18dca321cc695357d40b82a56..66f832310eb80c29329a7ff00d1ba0373dadb1eb 100644 (file)
--- a/src/gromacs/legacyheaders/md_support.h
+++ b/src/gromacs/legacyheaders/md_support.h
@@ -38,12 +38,11 @@
 #ifndef _md_support_h
 #define _md_support_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/globsig.h"
 #include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vcm.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/mdatoms.h b/src/gromacs/legacyheaders/mdatoms.h
index 54e4cb89cd4b70c071cecd4966fa15cc87b69196..18d10ffb1f88243b54639e05c890d69d75c1b7e6 100644 (file)
--- a/src/gromacs/legacyheaders/mdatoms.h
+++ b/src/gromacs/legacyheaders/mdatoms.h
@@ -42,8 +42,8 @@
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/mdebin.h b/src/gromacs/legacyheaders/mdebin.h
index 08d7b1f2982e8bb08a135443517fe31bb0589c9e..ef089de0aedffbc9a9d984a41d476ab13d1250d4 100644 (file)
--- a/src/gromacs/legacyheaders/mdebin.h
+++ b/src/gromacs/legacyheaders/mdebin.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/legacyheaders/ebin.h"
-#include "../fileio/enxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/legacyheaders/mdrun.h b/src/gromacs/legacyheaders/mdrun.h
index e05b4ac11cf52ffc0cb6f9fa808396b4dca1d91c..754a3796c3c1b7aed409c92f62fae2acb3f66710 100644 (file)
--- a/src/gromacs/legacyheaders/mdrun.h
+++ b/src/gromacs/legacyheaders/mdrun.h
@@ -40,19 +40,19 @@
 
 #include <stdio.h>
 #include <time.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/types/membedt.h"
 #include "gromacs/legacyheaders/types/globsig.h"
-
-#include "../fileio/filenm.h"
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/network.h b/src/gromacs/legacyheaders/network.h
index 5e5e5f3d855276c3ab6e01a433652d1a97207829..0824c6576a231facc2500b714e8d371fc923cd88 100644 (file)
--- a/src/gromacs/legacyheaders/network.h
+++ b/src/gromacs/legacyheaders/network.h
@@ -45,8 +45,8 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/fatalerror.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/nonbonded.h b/src/gromacs/legacyheaders/nonbonded.h
index e61f1323f043ff9fa56db22c2f0da2c0dd4fd0de..c985396e5914ac0067f9fb6e767ad7a4d0a40d59 100644 (file)
--- a/src/gromacs/legacyheaders/nonbonded.h
+++ b/src/gromacs/legacyheaders/nonbonded.h
@@ -38,10 +38,10 @@
 #ifndef _nonbonded_h
 #define _nonbonded_h
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/ns.h b/src/gromacs/legacyheaders/ns.h
index a9d7202b5553eabf71443dc69edb2ddc787bdb14..26582e5d438b05018cbb36d4c87acbad687812e5 100644 (file)
--- a/src/gromacs/legacyheaders/ns.h
+++ b/src/gromacs/legacyheaders/ns.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/oenv.h b/src/gromacs/legacyheaders/oenv.h
index d622c1b52b25a5904db60e42bd725fef03322162..ade929e0815d51ed514701487a6ebe453b1248c0 100644 (file)
--- a/src/gromacs/legacyheaders/oenv.h
+++ b/src/gromacs/legacyheaders/oenv.h
@@ -38,8 +38,8 @@
 #ifndef _oenv_h
 #define _oenv_h
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/perf_est.h b/src/gromacs/legacyheaders/perf_est.h
index 4e548734fecd302f0d0350cf196d84c9cc3c0567..67b54dc46f044f09d78749e2e2317047bf6821c3 100644 (file)
--- a/src/gromacs/legacyheaders/perf_est.h
+++ b/src/gromacs/legacyheaders/perf_est.h
@@ -38,8 +38,8 @@
 #define _perf_est_h
 
 #include "gromacs/legacyheaders/types/inputrec.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/pmalloc_cuda.h b/src/gromacs/legacyheaders/pmalloc_cuda.h
index 6b1be08a7fba25b4387b074a32b634e122f9f695..d45890802c8bc1ec013649385aee67288af57ca4 100644 (file)
--- a/src/gromacs/legacyheaders/pmalloc_cuda.h
+++ b/src/gromacs/legacyheaders/pmalloc_cuda.h
@@ -39,6 +39,7 @@
 #include "config.h"
 
 #include <stdlib.h>
+
 #include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU

diff --git a/src/gromacs/legacyheaders/pme.h b/src/gromacs/legacyheaders/pme.h
index 4001f52961144468513073f870cdaaf209d99e73..f71f6f51b2dd0df4a109c31146cad028484994f3 100644 (file)
--- a/src/gromacs/legacyheaders/pme.h
+++ b/src/gromacs/legacyheaders/pme.h
@@ -39,11 +39,12 @@
 #define _pme_h
 
 #include <stdio.h>
+
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../math/gmxcomplex.h"
-#include "../timing/wallcycle.h"
-#include "../timing/walltime_accounting.h"
-#include "../legacyheaders/network.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/qmmm.h b/src/gromacs/legacyheaders/qmmm.h
index 3fc8e87f12b8c631cb3876e4ef834b534d1e0cc7..d3b5839f86c3b81335118a570f94db75137843cd 100644 (file)
--- a/src/gromacs/legacyheaders/qmmm.h
+++ b/src/gromacs/legacyheaders/qmmm.h
@@ -38,9 +38,9 @@
 #ifndef _QMMM_h
 #define _QMMM_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/rbin.h b/src/gromacs/legacyheaders/rbin.h
index ec2cd30dc6be5e0db5419d735d5dd8d3bf33c5bc..fb0f7d6433847295410f87dcec78351f99b82d02 100644 (file)
--- a/src/gromacs/legacyheaders/rbin.h
+++ b/src/gromacs/legacyheaders/rbin.h
@@ -38,7 +38,7 @@
 #ifndef _rbin_h
 #define _rbin_h
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/readinp.h b/src/gromacs/legacyheaders/readinp.h
index 5d5044fa076b7b6c695479200962c8bc5a70b177..29b7a65baede5abd32f87c38f36ba5c9539f34d5 100644 (file)
--- a/src/gromacs/legacyheaders/readinp.h
+++ b/src/gromacs/legacyheaders/readinp.h
@@ -40,8 +40,8 @@
 
 #include <string.h>
 
-#include "../utility/basedefinitions.h"
 #include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/shellfc.h b/src/gromacs/legacyheaders/shellfc.h
index d16913544e77e59f4af67a9f679e1939c4e2b0e9..47f0d994c9ac0bcc0268340c141f25d3e717cae6 100644 (file)
--- a/src/gromacs/legacyheaders/shellfc.h
+++ b/src/gromacs/legacyheaders/shellfc.h
@@ -35,10 +35,9 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-#include "../timing/wallcycle.h"
-
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/sighandler.h b/src/gromacs/legacyheaders/sighandler.h
index 78edc547a9cf1d6da18aecf65cb09a6ece2a99cd..b2531a67e97960e46bed9624b21b2b0006de4e7f 100644 (file)
--- a/src/gromacs/legacyheaders/sighandler.h
+++ b/src/gromacs/legacyheaders/sighandler.h
@@ -40,7 +40,7 @@
 
 #include <signal.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/sim_util.h b/src/gromacs/legacyheaders/sim_util.h
index b7f94dea7fd5af1d40ded346bd7c75288d89eb1e..b1c89b790a9c63c410ff1869e5613b51925a4ac0 100644 (file)
--- a/src/gromacs/legacyheaders/sim_util.h
+++ b/src/gromacs/legacyheaders/sim_util.h
@@ -38,14 +38,14 @@
 #ifndef _sim_util_h
 #define _sim_util_h
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/mdoutf.h"
 #include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vcm.h"
-#include "../fileio/enxio.h"
-#include "../fileio/mdoutf.h"
-#include "../timing/wallcycle.h"
-#include "../timing/walltime_accounting.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/splitter.h b/src/gromacs/legacyheaders/splitter.h
index 2e6bc8ec0f84f6594464f8effed65aeef64b45c9..7db0fcf5ac7980f3fef758b988dd57e844193bd5 100644 (file)
--- a/src/gromacs/legacyheaders/splitter.h
+++ b/src/gromacs/legacyheaders/splitter.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/tables.h b/src/gromacs/legacyheaders/tables.h
index 56afdaa01d55726401f06a0a1c37f3eb773414e9..a33250f4463462ace5b594368b21e509a18644cb 100644 (file)
--- a/src/gromacs/legacyheaders/tables.h
+++ b/src/gromacs/legacyheaders/tables.h
@@ -35,8 +35,8 @@
 
 #ifndef _tables_h
 #define _tables_h
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/tgroup.h b/src/gromacs/legacyheaders/tgroup.h
index 5dacda4be951a4641039abe91a9b7288a99e82af..64cc730fae1f95242f0497baf5e5ac1aaf8ae187 100644 (file)
--- a/src/gromacs/legacyheaders/tgroup.h
+++ b/src/gromacs/legacyheaders/tgroup.h
@@ -38,8 +38,8 @@
 #ifndef _tgroup_h
 #define _tgroup_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/txtdump.h b/src/gromacs/legacyheaders/txtdump.h
index 75116f7a5a6073e6d74ad89e65b046eb9ecbaca1..c8a3a086b83b11421b89daa28736982812499b1c 100644 (file)
--- a/src/gromacs/legacyheaders/txtdump.h
+++ b/src/gromacs/legacyheaders/txtdump.h
@@ -40,8 +40,9 @@
 
 
 #include <stdio.h>
+
+#include "gromacs/fileio/tpxio.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/tpxio.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h
index aa2c698936ffea5389e048b2b03d05411305d53c..ad79e254bdc3ddcdbf1f9f2d7d84ccbc180cc382 100644 (file)
--- a/src/gromacs/legacyheaders/typedefs.h
+++ b/src/gromacs/legacyheaders/typedefs.h
@@ -44,25 +44,25 @@
 
 #include <sys/types.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/types/enums.h"
-#include "../fileio/trx.h"
-#include "../topology/topology.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
 #include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/legacyheaders/types/nsgrid.h"
-#include "gromacs/legacyheaders/types/forcerec.h"
-#include "gromacs/legacyheaders/types/fcdata.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
-#include "gromacs/legacyheaders/types/ifunc.h"
-#include "gromacs/legacyheaders/types/group.h"
-#include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/legacyheaders/types/shellfc.h"
-#include "gromacs/legacyheaders/types/constr.h"
 #include "gromacs/legacyheaders/types/oenv.h"
-#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/topology/topology.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/commrec.h b/src/gromacs/legacyheaders/types/commrec.h
index 4fbb9bb8825dd2417409d7f8f5c34995a0ea256c..4486c847b6c9ee1923c96fe49c49600628132bba 100644 (file)
--- a/src/gromacs/legacyheaders/types/commrec.h
+++ b/src/gromacs/legacyheaders/types/commrec.h
@@ -37,8 +37,8 @@
 #ifndef _commrec_h
 #define _commrec_h
 
-#include "../../utility/gmxmpi.h"
-#include "../typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/gmxmpi.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/forcerec.h b/src/gromacs/legacyheaders/types/forcerec.h
index 07fc2be29f521e5b502136e28dc0df4c88aff97a..f3f1302d5972ab4ed06a9533ea28a7aa6f6397b4 100644 (file)
--- a/src/gromacs/legacyheaders/types/forcerec.h
+++ b/src/gromacs/legacyheaders/types/forcerec.h
@@ -39,12 +39,12 @@
 #define GMX_LEGACYHEADERS_TYPES_FORCEREC_H
 
 #include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/ns.h"
 #include "gromacs/legacyheaders/types/genborn.h"
-#include "gromacs/legacyheaders/types/qmmmrec.h"
-#include "../../topology/idef.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/ns.h"
+#include "gromacs/legacyheaders/types/qmmmrec.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/hw_info.h b/src/gromacs/legacyheaders/types/hw_info.h
index 1ad1a771a1e97d064c98b75dc7969004bb9dfc7b..13715add38aea0a6a84b01f3bcbcfe22e8dac2f5 100644 (file)
--- a/src/gromacs/legacyheaders/types/hw_info.h
+++ b/src/gromacs/legacyheaders/types/hw_info.h
@@ -36,9 +36,9 @@
 #ifndef HWINFO_H
 #define HWINFO_H
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../gmx_cpuid.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/ifunc.h b/src/gromacs/legacyheaders/types/ifunc.h
index 5b72be9154d6f1e84fa9972ada058213c5a76771..25d13c6f58e4544ab69c4e6acfc9e4eff0123d93 100644 (file)
--- a/src/gromacs/legacyheaders/types/ifunc.h
+++ b/src/gromacs/legacyheaders/types/ifunc.h
@@ -39,9 +39,9 @@
 #ifndef _ifunc_h
 #define _ifunc_h
 
-#include "../../topology/idef.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/inputrec.h b/src/gromacs/legacyheaders/types/inputrec.h
index d6f7433ef83644899c641fb2b909dffa8ced89e5..26af01e0efe4865b2dd13aba0d38ee38e05120dd 100644 (file)
--- a/src/gromacs/legacyheaders/types/inputrec.h
+++ b/src/gromacs/legacyheaders/types/inputrec.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/enums.h"
-#include "../../swap/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/ns.h b/src/gromacs/legacyheaders/types/ns.h
index bc69cad31d298385950a53fd001f3845044dbb33..e141407525bdb105ca80a144d4d046fbe0e0e217 100644 (file)
--- a/src/gromacs/legacyheaders/types/ns.h
+++ b/src/gromacs/legacyheaders/types/ns.h
@@ -38,8 +38,8 @@
 #ifndef GMX_LEGACYHEADERS_TYPES_NS_H
 #define GMX_LEGACYHEADERS_TYPES_NS_H
 
-#include "gromacs/legacyheaders/types/nsgrid.h"
 #include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/types/rgb.h b/src/gromacs/legacyheaders/types/rgb.h
index 60436a740fb9ea714753680a82396e79fa4d1640..f754da9231ee1922622783a27253a83beee1cc0e 100644 (file)
--- a/src/gromacs/legacyheaders/types/rgb.h
+++ b/src/gromacs/legacyheaders/types/rgb.h
@@ -37,7 +37,7 @@
 #ifndef GMX_LEGACYHEADERS_TYPES_RGB_H
 #define GMX_LEGACYHEADERS_TYPES_RGB_H
 
-#include "../../utility/real.h"
+#include "gromacs/utility/real.h"
 
 typedef struct {
     real r, g, b;

diff --git a/src/gromacs/legacyheaders/types/simple.h b/src/gromacs/legacyheaders/types/simple.h
index b648539ac8d5363edc5b5ec968b45ca76e354f51..ec8e23a860a1793dc1b7906a330dbccf41e952b5 100644 (file)
--- a/src/gromacs/legacyheaders/types/simple.h
+++ b/src/gromacs/legacyheaders/types/simple.h
@@ -37,9 +37,9 @@
 #ifndef _simple_h
 #define _simple_h
 
-#include "../../math/vectypes.h"
-#include "../../utility/basedefinitions.h"
-#include "../../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 typedef int         atom_id;      /* To indicate an atoms id         */
 #define NO_ATID     (atom_id)(~0) /* Use this to indicate invalid atid */

diff --git a/src/gromacs/legacyheaders/types/state.h b/src/gromacs/legacyheaders/types/state.h
index 76c2c1cc64b35436efa9b2b67c32fc2b77229b3c..05b9135fe2610c2e6325998eef62e1fe4090db80 100644 (file)
--- a/src/gromacs/legacyheaders/types/state.h
+++ b/src/gromacs/legacyheaders/types/state.h
@@ -39,7 +39,7 @@
 
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "../../swap/enums.h"
+#include "gromacs/swap/enums.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/legacyheaders/update.h
index 55bfebdc2d3f06eb2dee3015e9c5df8345dd11d4..ce3e00d722eae19631d8c222c2613149385cdec5 100644 (file)
--- a/src/gromacs/legacyheaders/update.h
+++ b/src/gromacs/legacyheaders/update.h
@@ -38,11 +38,10 @@
 #ifndef _update_h
 #define _update_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/network.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/vcm.h b/src/gromacs/legacyheaders/vcm.h
index 0486b41f729f717056762e44ebee46c208788756..aaab02a8064f1da9e803286123fcfbde1c9f5367 100644 (file)
--- a/src/gromacs/legacyheaders/vcm.h
+++ b/src/gromacs/legacyheaders/vcm.h
@@ -42,9 +42,9 @@
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/viewit.h b/src/gromacs/legacyheaders/viewit.h
index af7fd882c0b6af8db967598e0005d9b94b996244..e63616706a6cbab38da29270002b5eabe3ee7d2a 100644 (file)
--- a/src/gromacs/legacyheaders/viewit.h
+++ b/src/gromacs/legacyheaders/viewit.h
@@ -38,8 +38,8 @@
 #ifndef _viewit_h
 #define _viewit_h
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/types/oenv.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/vsite.h b/src/gromacs/legacyheaders/vsite.h
index 79b6a839d662c65d9bcd6bd7fffedf98d62a2525..6cbecbe391848c82ca8ece2979f755eff43458da 100644 (file)
--- a/src/gromacs/legacyheaders/vsite.h
+++ b/src/gromacs/legacyheaders/vsite.h
@@ -41,7 +41,7 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../pbcutil/ishift.h"
+#include "gromacs/pbcutil/ishift.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/warninp.h b/src/gromacs/legacyheaders/warninp.h
index da485eda87bdc9d2a8f76abe837be44b63823833..cd3f32c84aa2ed2ec4a11d01cdb04dde8556b288 100644 (file)
--- a/src/gromacs/legacyheaders/warninp.h
+++ b/src/gromacs/legacyheaders/warninp.h
@@ -38,7 +38,7 @@
 #ifndef _warninp_h
 #define _warninp_h
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/linearalgebra/eigensolver.c b/src/gromacs/linearalgebra/eigensolver.c
index 37e6bc702215ece91a825637f60b4eedabe56297..7d3f0d875492d0510704d645a0c41d1dace2e168 100644 (file)
--- a/src/gromacs/linearalgebra/eigensolver.c
+++ b/src/gromacs/linearalgebra/eigensolver.c
@@ -43,8 +43,8 @@
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gmx_lapack.h"
 #include "gmx_arpack.h"
+#include "gmx_lapack.h"
 
 void
 eigensolver(real *   a,

diff --git a/src/gromacs/linearalgebra/eigensolver.h b/src/gromacs/linearalgebra/eigensolver.h
index 0786bf55ceb88a44e6eaa2b81959153f6e548ccb..0c2b97d92d0cc43330f681e47a4bc0ccc214be91 100644 (file)
--- a/src/gromacs/linearalgebra/eigensolver.h
+++ b/src/gromacs/linearalgebra/eigensolver.h
@@ -37,9 +37,8 @@
 #ifndef GMX_LINEARALGEBRA_EIGENSOLVER_H
 #define GMX_LINEARALGEBRA_EIGENSOLVER_H
 
-#include "../utility/real.h"
-
-#include "sparsematrix.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/linearalgebra/gmx_arpack.c b/src/gromacs/linearalgebra/gmx_arpack.c
index b7a424a733cebae30c5307cde31d0a2fa31fc7d2..287f0da282b4839c90b2ed69ee27114b5326c2a8 100644 (file)
--- a/src/gromacs/linearalgebra/gmx_arpack.c
+++ b/src/gromacs/linearalgebra/gmx_arpack.c
@@ -35,13 +35,14 @@
  */
 #include "gmxpre.h"
 
+#include "gmx_arpack.h"
+
 #include <math.h>
 #include <string.h>
 
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-#include "gmx_arpack.h"
 #include "gmx_blas.h"
 #include "gmx_lapack.h"
 

diff --git a/src/gromacs/linearalgebra/sparsematrix.c b/src/gromacs/linearalgebra/sparsematrix.c
index 34f5fd44434b9763831c1ffd1e761358088d7dde..5b2405c3de99bcefac6c790027f0cd23cfd49e39 100644 (file)
--- a/src/gromacs/linearalgebra/sparsematrix.c
+++ b/src/gromacs/linearalgebra/sparsematrix.c
@@ -39,8 +39,8 @@
 #include "sparsematrix.h"
 
 #include <assert.h>
-#include <stdlib.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/linearalgebra/sparsematrix.h b/src/gromacs/linearalgebra/sparsematrix.h
index d7b08f6dfb5e36460c0093454088d1691e20ac8f..04731f0181fce3403d000db382478eeba3dc069c 100644 (file)
--- a/src/gromacs/linearalgebra/sparsematrix.h
+++ b/src/gromacs/linearalgebra/sparsematrix.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/3dtransforms.cpp b/src/gromacs/math/3dtransforms.cpp
index b2247bdbfb690dac3c5a531ca079ea010b77b7ef..41e80d614f23ebc13522a4fabbca3ed0b594cbd4 100644 (file)
--- a/src/gromacs/math/3dtransforms.cpp
+++ b/src/gromacs/math/3dtransforms.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/math/3dtransforms.h"
+#include "3dtransforms.h"
 
 #include <math.h>
 #include <stdio.h>

diff --git a/src/gromacs/math/3dtransforms.h b/src/gromacs/math/3dtransforms.h
index 4bcba5c0fb0fd5daa1c9021e40d4635e4210d152..40516c60c6aaf73762d8657b3e863bb1500a8a91 100644 (file)
--- a/src/gromacs/math/3dtransforms.h
+++ b/src/gromacs/math/3dtransforms.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../utility/real.h"
-#include "vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/do_fit.h b/src/gromacs/math/do_fit.h
index f74bf1e89576fb160677b266fdb534764dd7aa9d..7ccb652f19064e30d8cd37178eeb026dadddb403 100644 (file)
--- a/src/gromacs/math/do_fit.h
+++ b/src/gromacs/math/do_fit.h
@@ -37,10 +37,9 @@
 #ifndef GMX_MATH_DO_FIT_H
 #define GMX_MATH_DO_FIT_H
 
-#include "../legacyheaders/types/simple.h"
-#include "../utility/real.h"
-
-#include "vectypes.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/gmxcomplex.h b/src/gromacs/math/gmxcomplex.h
index 111ca37af1ae8418e73311ace51020997bb1d84e..8fa0c8ad6a8570b0fc45cfcbac2d6aa201908e8f 100644 (file)
--- a/src/gromacs/math/gmxcomplex.h
+++ b/src/gromacs/math/gmxcomplex.h
@@ -39,9 +39,8 @@
 
 #include <math.h>
 
-#include "../utility/real.h"
-
-#include "vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 typedef struct {
     real re, im;

diff --git a/src/gromacs/math/units.h b/src/gromacs/math/units.h
index 4859f52e377973711f1df52bd33a891762b2a3fd..6afd10f2a9b386781640cd0bf94c0f535e9a825e 100644 (file)
--- a/src/gromacs/math/units.h
+++ b/src/gromacs/math/units.h
@@ -43,7 +43,7 @@
  * be anywhere else in the code.
  */
 
-#include "utilities.h"
+#include "gromacs/math/utilities.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/utilities.c b/src/gromacs/math/utilities.c
index c2df23ec2ee333d4cadb77154b0205d4c0e56439..03b7134427da15d9a9509925dacebdf899ed1c9a 100644 (file)
--- a/src/gromacs/math/utilities.c
+++ b/src/gromacs/math/utilities.c
@@ -38,12 +38,12 @@
 
 #include "utilities.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <limits.h>
 #include <math.h>
 
-#include "config.h"
-
 #ifdef HAVE__FINITE
 #include <float.h>
 #endif

diff --git a/src/gromacs/math/utilities.h b/src/gromacs/math/utilities.h
index 3ab1061140452170032ae84481e87c451d9b67b4..2932220068bf53b5d43731c35882630a0f84d4ae 100644 (file)
--- a/src/gromacs/math/utilities.h
+++ b/src/gromacs/math/utilities.h
@@ -40,8 +40,8 @@
 #include <limits.h>
 #include <math.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/vec.h b/src/gromacs/math/vec.h
index 2b2dcbc513c4d5eec5ce8f860bf8e57d47dbfb3f..d5ee22cbe1b3fead8a6a22449034d044fb1d47eb 100644 (file)
--- a/src/gromacs/math/vec.h
+++ b/src/gromacs/math/vec.h
@@ -115,13 +115,12 @@
 
 #include <math.h>
 
-#include "units.h"
-#include "utilities.h"
-#include "vectypes.h"
-
-#include "../utility/basedefinitions.h"
-#include "../utility/fatalerror.h"
-#include "../utility/real.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/math/vectypes.h b/src/gromacs/math/vectypes.h
index fe9dd68194e4caa41d11067dde6a84e5d3113f71..ebb12dc512f3080576d7f2a18fbef834253ce02d 100644 (file)
--- a/src/gromacs/math/vectypes.h
+++ b/src/gromacs/math/vectypes.h
@@ -37,7 +37,7 @@
 #ifndef GMX_MATH_VECTYPES_H
 #define GMX_MATH_VECTYPES_H
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 #define XX      0 /* Defines for indexing in */
 #define YY      1 /* vectors                 */

diff --git a/src/gromacs/mdlib/adress.c b/src/gromacs/mdlib/adress.c
index dce59d513de878aa34169dc14bfc0564b4b0dc81..9e9db2908984f30cd6a842a4780d2979b194382e 100644 (file)
--- a/src/gromacs/mdlib/adress.c
+++ b/src/gromacs/mdlib/adress.c
@@ -37,12 +37,12 @@
 #include "gmxpre.h"
 
 #include "adress.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/types/simple.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 
 real

diff --git a/src/gromacs/mdlib/adress.h b/src/gromacs/mdlib/adress.h
index 7d3e9332f9a9be46b4675210c79b8321834b497c..a25514d8b18e6c0b70129568f550e7203fa28a20 100644 (file)
--- a/src/gromacs/mdlib/adress.h
+++ b/src/gromacs/mdlib/adress.h
@@ -39,8 +39,8 @@
 #ifndef _adress_h_
 #define _adress_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/mdlib/calcmu.c b/src/gromacs/mdlib/calcmu.c
index 618b9cf0a26e4114117134aa39930e4e4e06fb62..7f2d383ca15b3fd250fd40777e008b5bab9a2ede 100644 (file)
--- a/src/gromacs/mdlib/calcmu.c
+++ b/src/gromacs/mdlib/calcmu.c
@@ -37,15 +37,16 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/calcmu.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/math/vec.h"
 
 void calc_mu(int start, int homenr, rvec x[], real q[], real qB[],
              int nChargePerturbed,

diff --git a/src/gromacs/mdlib/calcvir.c b/src/gromacs/mdlib/calcvir.c
index 19d27411a11e0b6acc5d9c9fd7bf130e1c5a4f13..0f6ab60aa02fe2f2cd0730cd32f0d01545c48ce8 100644 (file)
--- a/src/gromacs/mdlib/calcvir.c
+++ b/src/gromacs/mdlib/calcvir.c
@@ -39,7 +39,6 @@
 
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vectypes.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index 2b45442554d1b2a51e4cbfd0c84726bfe0059ada..3423b0811aa733c4d664c7a781237e268337848c 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -40,20 +40,19 @@
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/constr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index 7b9addc389e06f2ba2280bef92059f0a2e17fee2..fb075d4648bcb71f57d959400cd69a7f60ed817b 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -36,31 +36,31 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/constr.h"
+
 #include <assert.h>
 #include <stdlib.h>
 
+#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/splitter.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/coupling.c b/src/gromacs/mdlib/coupling.c
index 7583da13815a4d61edabc6a83c2da295969e404a..41806dc44b4338b324cf84d733cc81e2527d4505 100644 (file)
--- a/src/gromacs/mdlib/coupling.c
+++ b/src/gromacs/mdlib/coupling.c
@@ -38,20 +38,19 @@
 
 #include <assert.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/random/random.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define NTROTTERPARTS 3
 

diff --git a/src/gromacs/mdlib/csettle.c b/src/gromacs/mdlib/csettle.c
index 44920009a9adeed85934b49ee2de1f90e221af2c..bfd68b0aff344e7cbbf663297e2e5839f818e67a 100644 (file)
--- a/src/gromacs/mdlib/csettle.c
+++ b/src/gromacs/mdlib/csettle.c
@@ -40,7 +40,6 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/constr.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 27d2bcb14a76e8191b4341857b80396afae1c51e..bad4092e3ebe4060c7721a4a54984436a5f8098a 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -35,52 +35,52 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/domdec.h"
+
 #include "config.h"
 
-#include <stdio.h>
-#include <time.h>
+#include <assert.h>
 #include <math.h>
-#include <string.h>
+#include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
+#include <string.h>
+#include <time.h>
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
 #include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/domdec_network.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/bonded-threading.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/gpu_utils.h"
-
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/qsort_threadsafe.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/domdec_box.c b/src/gromacs/mdlib/domdec_box.c
index 89fc97c82084bbc2411792f3c92cf9cfda3d2d17..7c9c4d088fed49e039482c8890c498c881a85869 100644 (file)
--- a/src/gromacs/mdlib/domdec_box.c
+++ b/src/gromacs/mdlib/domdec_box.c
@@ -35,15 +35,14 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 
 static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,

diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index e83c16930ef29fae671a8d06f30309959cfb0e56..e538a6a5049a1a42de32e63849088b85bc15534e 100644 (file)
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -37,18 +37,17 @@
 
 #include <assert.h>
 
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_hash.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/domdec_network.c b/src/gromacs/mdlib/domdec_network.c
index 8c1ef5153d1e917cc9707bc400ed8ff9d00883b2..eec664a5d028eda9623a889928bd42bd89a4dbec 100644 (file)
--- a/src/gromacs/mdlib/domdec_network.c
+++ b/src/gromacs/mdlib/domdec_network.c
@@ -35,12 +35,13 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/domdec_network.h"
+
 #include "config.h"
 
 #include <string.h>
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
 
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/gmxmpi.h"
 
 

diff --git a/src/gromacs/mdlib/domdec_setup.c b/src/gromacs/mdlib/domdec_setup.c
index 5caa68a9b58508750b040a2e4140d07cb00c1d48..0903c32d14cc479058ac32e7a36aa7c07ffa9f0d 100644 (file)
--- a/src/gromacs/mdlib/domdec_setup.c
+++ b/src/gromacs/mdlib/domdec_setup.c
@@ -35,16 +35,17 @@
 
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <assert.h>
+#include <stdio.h>
+
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Margin for setting up the DD grid */
 #define DD_GRID_MARGIN_PRES_SCALE 1.05

diff --git a/src/gromacs/mdlib/domdec_top.c b/src/gromacs/mdlib/domdec_top.c
index 8360e45540e56cac3cea945970dfe39d4d3504ac..cf45ba3ff4f0f34b4324ec4c10c1fa8c7d545ca3 100644 (file)
--- a/src/gromacs/mdlib/domdec_top.c
+++ b/src/gromacs/mdlib/domdec_top.c
@@ -37,18 +37,17 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/ebin.c b/src/gromacs/mdlib/ebin.c
index 33a0742130c8aaf96893ad22a087d43c134bf7f9..8056f1f9bf252e0cec24df9997742506017fc105 100644 (file)
--- a/src/gromacs/mdlib/ebin.c
+++ b/src/gromacs/mdlib/ebin.c
@@ -37,15 +37,17 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/ebin.h"
+
 #include <math.h>
 #include <string.h>
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 t_ebin *mk_ebin(void)
 {

diff --git a/src/gromacs/mdlib/ewald.c b/src/gromacs/mdlib/ewald.c
index bcf1865df33e118fe24bc5d3f14785ac031912ca..97d0962f3993610753dd47a181115aae8ba6be44 100644 (file)
--- a/src/gromacs/mdlib/ewald.c
+++ b/src/gromacs/mdlib/ewald.c
@@ -40,17 +40,16 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/futil.h"
-#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TOL 2e-5
 

diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index be1ea75c670a83719bfb7c59ccfcb400ab289513..4996f51371992bc647458d34e5183dcb3405804c 100644 (file)
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -37,36 +37,34 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/calcmu.h"
 #include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/xtcio.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 static void init_df_history_weights(df_history_t *dfhist, t_expanded *expand, int nlim)
 {

diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 03f4d9efd8b5618f4178d747f5d892f838e73f0c..a4b3f65ec1283c4204c77db6a45d06899812c6a0 100644 (file)
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/force.h"
+
 #include "config.h"
 
 #include <assert.h>
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index 5be156dd7c4dcd1c77d95855d42220e7bbb7a46e..68edaad1c1d50322aa00e3fd33f83625bd8ba092 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -42,46 +42,43 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/tables.h"
-#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/pmalloc_cuda.h"
 #include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/mtop_util.h"
-#include "nbnxn_simd.h"
-#include "nbnxn_search.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_consts.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-#include "gromacs/legacyheaders/inputrec.h"
-
+#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "gromacs/legacyheaders/gpu_utils.h"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/legacyheaders/pmalloc_cuda.h"
-#include "nb_verlet.h"
-
 t_forcerec *mk_forcerec(void)
 {
     t_forcerec *fr;

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index f3a8973262879fa4a565647b6a3b699a62402625..c26de6a12701d0c728dd6ddf89865701c6efea14 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -37,39 +37,39 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/genborn.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/nrnb.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
 #  ifdef GMX_DOUBLE
-#    include "genborn_sse2_double.h"
-#    include "genborn_allvsall_sse2_double.h"
+#    include "gromacs/mdlib/genborn_allvsall_sse2_double.h"
+#    include "gromacs/mdlib/genborn_sse2_double.h"
 #  else
-#    include "genborn_sse2_single.h"
-#    include "genborn_allvsall_sse2_single.h"
+#    include "gromacs/mdlib/genborn_allvsall_sse2_single.h"
+#    include "gromacs/mdlib/genborn_sse2_single.h"
 #  endif /* GMX_DOUBLE */
 #endif   /* SSE or AVX present */
 
-#include "genborn_allvsall.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
 
 /*#define DISABLE_SSE*/
 

diff --git a/src/gromacs/mdlib/genborn_allvsall.c b/src/gromacs/mdlib/genborn_allvsall.c
index b294cbbf5ebd4b6d116a211a403f34d1b91ed3c0..a18f2e1ac5cbc267a47a4ec97a3bd0b1f1ff1a11 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.c
+++ b/src/gromacs/mdlib/genborn_allvsall.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
+#include "genborn_allvsall.h"
 
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+#include <math.h>
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 
 typedef struct

diff --git a/src/gromacs/mdlib/genborn_allvsall.h b/src/gromacs/mdlib/genborn_allvsall.h
index 1f91757d1638085eda9130c2ed4d9796b548968d..83492bdef1e65dad07c950d0fd27d9d93a8f3729 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.h
+++ b/src/gromacs/mdlib/genborn_allvsall.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_H
 #define _GENBORN_ALLVSALL_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii(t_forcerec *           fr,

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
index 4816c101337fd7aacb534e747e6f3077fa2e69c0..58475254654e5e667a84df8a6caaa915f8221d9b 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
@@ -37,15 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.h b/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
index 045f5eb8a802b58d31e26506b9a41b4c1f5d4c1c..3629475dc342ce68754bc04950e7fe593a088bf2 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_SSE2_DOUBLE_H
 #define _GENBORN_ALLVSALL_SSE2_DOUBLE_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii_sse2_double(t_forcerec *           fr,

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
index b574baea47a38f456efdb791d614af88dd8ebaeb..8c3ce47c99fbb18cf09bbc58678599efa3c1b575 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
@@ -37,15 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
+#include "gromacs/utility/smalloc.h"
 
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
 

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.h b/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
index 784b127a40a941228a8211a39f7980e3f6fe803e..d1e908a985c73e2f6614fc9e3520502498fb3625 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_SSE2_SINGLE_H
 #define _GENBORN_ALLVSALL_SSE2_SINGLE_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii_sse2_single(t_forcerec *           fr,

diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index 54eca2fe79e0fc967ad1d2b94d2b1493e1cabb36..df68d0508e00b64831721128774c2cfef50f84c2 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -39,27 +39,25 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/genborn.h"
-
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Only compile this file if SSE2 intrinsics are available */
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
-#include <gmx_sse2_double.h>
-#include <emmintrin.h>
-
 #include "genborn_sse2_double.h"
 
+#include <emmintrin.h>
+#include <gmx_sse2_double.h>
+
 int
 calc_gb_rad_still_sse2_double(t_commrec *cr, t_forcerec *fr,
                               int natoms, gmx_localtop_t *top,

diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index bd5d6097dd7bc5882ae59c6e15a648e032004708..7c847473a199587a5b62783ddea37d7000df67d4 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -39,29 +39,27 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/genborn.h"
-
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Only compile this file if SSE intrinsics are available */
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
 
-#include <gmx_sse2_single.h>
-#include <emmintrin.h>
-
 #include "genborn_sse2_single.h"
 
+#include <emmintrin.h>
+#include <gmx_sse2_single.h>
+
 
 int
 calc_gb_rad_still_sse2_single(t_commrec *cr, t_forcerec *fr,

diff --git a/src/gromacs/mdlib/groupcoord.cpp b/src/gromacs/mdlib/groupcoord.cpp
index 17d3f713b1e8aabadd9fe817f3569da95ae96abd..b02f852374416c8ab629f037aa3e2734c49cca8c 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.cpp
+++ b/src/gromacs/mdlib/groupcoord.cpp
@@ -37,11 +37,12 @@
 #include "gmxpre.h"
 
 #include "groupcoord.h"
+
+#include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
 
 #define MIN(a, b) (((a) < (b)) ? (a) : (b))
 

diff --git a/src/gromacs/mdlib/groupcoord.h b/src/gromacs/mdlib/groupcoord.h
index 4791aec83c503549314de7799a3ed7e81d017a44..686ce17517e2a1cc82c89801570fcd4383fc1158 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.h
+++ b/src/gromacs/mdlib/groupcoord.h
@@ -48,6 +48,7 @@
  */
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 

diff --git a/src/gromacs/mdlib/init.c b/src/gromacs/mdlib/init.c
index 6b44531834f143945dda4ed1544fd67d3cda085f..21549e2aa7eaa23d433feb168dd5a0f589366081 100644 (file)
--- a/src/gromacs/mdlib/init.c
+++ b/src/gromacs/mdlib/init.c
@@ -37,18 +37,19 @@
 #include "gmxpre.h"
 
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define BUFSIZE 256
 

diff --git a/src/gromacs/mdlib/iteratedconstraints.c b/src/gromacs/mdlib/iteratedconstraints.c
index a53633db6f00b61ae8b0ef9a01719b74204aa128..7899fdd12cf56235ad0901d616604dc95c0c7580 100644 (file)
--- a/src/gromacs/mdlib/iteratedconstraints.c
+++ b/src/gromacs/mdlib/iteratedconstraints.c
@@ -37,12 +37,13 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/md_support.h"
+
 #include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/iteratedconstraints.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef GMX_DOUBLE
 #define CONVERGEITER  0.000000001

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index 9e1abb9f1fead57be0c7fc3fef8248b2a09832e4..52b05bdd88feff17835a7ab1c2cc4692cb7b1840 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -37,22 +37,22 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/md_support.h"
+
 #include <algorithm>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/mdatom.c b/src/gromacs/mdlib/mdatom.c
index ea59275ec10e2143156eaaf95a5ab72b11285dfc..01c5c55bd6140a5453f8ee24eac3a13f80e0e70a 100644 (file)
--- a/src/gromacs/mdlib/mdatom.c
+++ b/src/gromacs/mdlib/mdatom.c
@@ -38,12 +38,12 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/utility/smalloc.h"
 
 #define ALMOST_ZERO 1e-30
 

diff --git a/src/gromacs/mdlib/mdebin.c b/src/gromacs/mdlib/mdebin.c
index 84f24ac4380c9883748b43785edce1ef277c4d83..84b1db0f3d12f3329f77a1eadbdab3da1d902420 100644 (file)
--- a/src/gromacs/mdlib/mdebin.c
+++ b/src/gromacs/mdlib/mdebin.c
@@ -36,28 +36,28 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/mdebin.h"
+
 #include <float.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/math/units.h"
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "mdebin_bar.h"
-
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdebin_bar.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/smalloc.h"
 
 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };

diff --git a/src/gromacs/mdlib/mdebin_bar.c b/src/gromacs/mdlib/mdebin_bar.c
index a6bf3745ca354c50f41a3d657e99e7c63b83db2b..e351275864fe06b0e57b0059d7084235b07b6086 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.c
+++ b/src/gromacs/mdlib/mdebin_bar.c
@@ -36,16 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
+#include "mdebin_bar.h"
+
 #include <float.h>
 #include <math.h>
+#include <string.h>
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "mdebin_bar.h"
 
 /* reset the delta_h list to prepare it for new values */
 static void mde_delta_h_reset(t_mde_delta_h *dh)

diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 00ebe44ee04fea0610379397400e26edb0ab2774..234bcbdd8fc68df3abae1445a5c266ba73d8a294 100644 (file)
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -42,35 +42,32 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/bonded-threading.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/md_logging.h"
-
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/mtxio.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/math/vec.h"
@@ -78,6 +75,7 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/nb_verlet.h b/src/gromacs/mdlib/nb_verlet.h
index 78c4f691dac30a80b052ad245e23583f6004a969..8fa19d0042bd8e3fe2cb1186fcb76f8051aadd35 100644 (file)
--- a/src/gromacs/mdlib/nb_verlet.h
+++ b/src/gromacs/mdlib/nb_verlet.h
@@ -36,8 +36,8 @@
 #ifndef NB_VERLET_H
 #define NB_VERLET_H
 
-#include "nbnxn_pairlist.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.c b/src/gromacs/mdlib/nbnxn_atomdata.c
index dd0e53d9c238c58247fbadba7775964253c55069..ca0f4999bc7fb28600001e0ff32914f15114f9ec 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.c
+++ b/src/gromacs/mdlib/nbnxn_atomdata.c
@@ -35,6 +35,8 @@
 
 #include "gmxpre.h"
 
+#include "nbnxn_atomdata.h"
+
 #include "config.h"
 
 #include <assert.h>
@@ -42,16 +44,15 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "nbnxn_consts.h"
-#include "nbnxn_internal.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "thread_mpi/atomic.h"
 
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
index 301627d872629cbe009bccfe6a6df9146113574e..799425edab3121ddcd2a131f0a92621ee6482bfc 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
@@ -36,11 +36,11 @@
 
 #include "nbnxn_cuda.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <stdlib.h>
 
-#include "config.h"
-
 #if defined(_MSVC)
 #include <limits>
 #endif
@@ -58,10 +58,11 @@
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/cstringutil.h"
 
+#include "nbnxn_cuda_types.h"
+
 #if defined TEXOBJ_SUPPORTED && __CUDA_ARCH__ >= 300
 #define USE_TEXOBJ
 #endif

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
index 6ccce27efdc3dcb939baae70da00f22e1151c629..174a9054af9f902254ba00f56653e72f0cda62ad 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
@@ -35,11 +35,11 @@
 #ifndef NBNXN_CUDA_H
 #define NBNXN_CUDA_H
 
+#include "config.h"
+
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
 #include "gromacs/legacyheaders/types/simple.h"
 
-#include "config.h"
-
 #ifdef GMX_GPU
 #define FUNC_TERM ;
 #else

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
index fead7a37b4933986dd3036dda1added372f3310a..f0e6fa8561d6e4e00aa6bf115a26cea55d632df4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
@@ -34,36 +34,36 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_cuda_data_mgmt.h"
+
 #include "config.h"
 
 #include <assert.h>
 #include <stdarg.h>
-#include <stdlib.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include <cuda.h>
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
+#include "gromacs/legacyheaders/pmalloc_cuda.h"
 #include "gromacs/legacyheaders/tables.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
-#include "../nbnxn_consts.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-
-#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/legacyheaders/pmalloc_cuda.h"
-#include "gromacs/legacyheaders/gpu_utils.h"
-
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "nbnxn_cuda_types.h"
+
 static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
 
 /* This is a heuristically determined parameter for the Fermi architecture for

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
index b3c34e9a446f10ab32cc6e823d4653d0f130faad..00cac2ee453c23bddb0e46452aa338140e608b2b 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
@@ -36,12 +36,12 @@
 #ifndef NBNXN_CUDA_DATA_MGMT_H
 #define NBNXN_CUDA_DATA_MGMT_H
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/types/hw_info.h"
 #include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "gromacs/legacyheaders/types/hw_info.h"
-
-#include "config.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU
 #define FUNC_TERM ;

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
index 7ea591db30fe37f39cd39005c258b793e3f4ae53..ac8a530f2c795d19674f0ef44e95a8fd47209a19 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
@@ -38,7 +38,7 @@
  * code that is in double precision.
  */
 
-#include "../../gmxlib/cuda_tools/vectype_ops.cuh"
+#include "gromacs/gmxlib/cuda_tools/vectype_ops.cuh"
 
 #ifndef NBNXN_CUDA_KERNEL_UTILS_CUH
 #define NBNXN_CUDA_KERNEL_UTILS_CUH

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
index 897b956a74c63ec8a76948a911a6ff7ee5124863..c468306899094a050f87816c90cb0fe4087de5a0 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
@@ -52,30 +52,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -88,30 +88,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -124,30 +124,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -161,30 +161,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -197,30 +197,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -233,30 +233,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
index 367a59c75f712fb03edec238896b01e579fef63a..fe186eda89183700e31279017dc61636c1ce662a 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
@@ -46,10 +46,10 @@
 #ifndef NBNXN_CUDA_TYPES_H
 #define NBNXN_CUDA_TYPES_H
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/legacyheaders/types/interaction_const.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 /* CUDA versions from 5.0 above support texture objects. */
 #if CUDA_VERSION >= 5000

diff --git a/src/gromacs/mdlib/nbnxn_internal.h b/src/gromacs/mdlib/nbnxn_internal.h
index 5d5844cb226bd69ed37b454fe04c4387880502ea..909a4b07bb99b5d373df13ea613ba1bfee404f6e 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_internal.h
+++ b/src/gromacs/mdlib/nbnxn_internal.h
@@ -36,11 +36,11 @@
 #ifndef _nbnxn_internal_h
 #define _nbnxn_internal_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nbnxn_simd.h"
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/timing/cyclecounter.h"
 
 
 /* Bounding box calculations are (currently) always in single precision, so

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
index ba8f2f0140433ba4c04745cb972073274c5fe5fd..2fded68209937ef2b29ca72c1e4548d9461dc353 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
@@ -34,10 +34,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/ishift.h"
-
 #include "nbnxn_kernel_common.h"
 
+#include "gromacs/pbcutil/ishift.h"
+
 static void
 clear_f_all(const nbnxn_atomdata_t *nbat, real *f)
 {

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
index 01de457ba720d06ed676e88459304b8391b71531..9432b2f3119546932bf371d2805ec4e9343740e6 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -37,7 +37,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -48,9 +47,10 @@
 {2}
 #define GMX_SIMD_J_UNROLL_SIZE {3}
 #include "{4}"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
index 1256eb6a6d1614eec31d0e9b575cc2a96ac05668..22ada3b193bd4770efa13ada39efbffa3742c36e 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
@@ -33,7 +33,6 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
index 30cfb49890ca3ef152b8098efa83dffeb2612766..5e8ac7ca2abd538f80614883b54427f65d2c016d 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
@@ -34,22 +34,21 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_kernel_gpu_ref.h"
+
 #include "config.h"
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/force.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/ishift.h"
-
-#include "nbnxn_kernel_gpu_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
 
 #define NCL_PER_SUPERCL         (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
 #define CL_SIZE                 (NBNXN_GPU_CLUSTER_SIZE)

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
index efcafd3f1d857ecb2325586405780198d63bde74..3db03bbec59c7f76f080ef9322b77f3cf2ac3cdc 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
@@ -34,24 +34,23 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_kernel_ref.h"
+
 #include "config.h"
 
-#include <math.h>
 #include <assert.h>
+#include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nbnxn_kernel_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
-#include "gromacs/mdlib/nb_verlet.h"
-
 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  */
 
@@ -74,21 +73,21 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Analytical reaction-field kernels */
 #define CALC_COUL_RF
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
@@ -98,42 +97,42 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Tabulated exclusion interaction electrostatics kernels */
 #define CALC_COUL_TAB
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
 /* Twin-range cut-off kernels */
 #define VDW_CUTOFF_CHECK
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
index 91447143a8a48c7645c339a9cfa2157c2f55614b..099a9079a41eaaa22b6a9bb37019aac074534ac5 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
@@ -39,16 +39,16 @@
  */
 
 /* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 
 /* Include the force+energy kernels */
 #define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 #undef CALC_ENERGIES
 
 /* Include the force+energygroups kernels */
 #define CALC_ENERGIES
 #define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 #undef ENERGY_GROUPS
 #undef CALC_ENERGIES

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
index cc6fb229b9911b41cd996f0e15ee0103ff9a4445..e0cfcef8bd01be56ef8ab4a4f7278497c26f21bf 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
@@ -332,19 +332,19 @@ NBK_FUNC_NAME(_VgrpF)
             {
 #define CALC_COULOMB
 #define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef HALF_LJ
 #undef CALC_COULOMB
             }
             else if (do_coul)
             {
 #define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef CALC_COULOMB
             }
             else
             {
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
             }
 #undef CHECK_EXCLS
             cjind++;
@@ -356,19 +356,19 @@ NBK_FUNC_NAME(_VgrpF)
             {
 #define CALC_COULOMB
 #define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef HALF_LJ
 #undef CALC_COULOMB
             }
             else if (do_coul)
             {
 #define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef CALC_COULOMB
             }
             else
             {
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
             }
         }
         ninner += cjind1 - cjind0;

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
index 5d081738f85d0359fa21ece0c35ce7eb69a8b11c..b5167b1fa85c0891ce1d677dab2000229447a628 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
@@ -35,10 +35,10 @@
 #ifndef _nbnxn_kernel_simd_utils_h_
 #define _nbnxn_kernel_simd_utils_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-
 #include "config.h"
 
+#include "gromacs/legacyheaders/types/simple.h"
+
 /*! \brief Provides hardware-specific utility routines for the SIMD kernels.
  *
  * Defines all functions, typedefs, constants and macros that have
@@ -65,7 +65,7 @@ prepare_table_load_buffer(const int gmx_unused *array)
     return NULL;
 }
 
-#include "nbnxn_kernel_simd_utils_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ref.h"
 
 #else /* GMX_SIMD_REFERENCE */
 
@@ -96,17 +96,17 @@ prepare_table_load_buffer(int gmx_unused *array)
 
 #ifdef GMX_DOUBLE
 #if GMX_SIMD_REAL_WIDTH == 2
-#include "nbnxn_kernel_simd_utils_x86_128d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128d.h"
 #else
-#include "nbnxn_kernel_simd_utils_x86_256d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256d.h"
 #endif
 #else /* GMX_DOUBLE */
 /* In single precision aligned FDV0 table loads are optimal */
 #define TAB_FDV0
 #if GMX_SIMD_REAL_WIDTH == 4
-#include "nbnxn_kernel_simd_utils_x86_128s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h"
 #else
-#include "nbnxn_kernel_simd_utils_x86_256s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256s.h"
 #endif
 #endif /* GMX_DOUBLE */
 
@@ -125,11 +125,11 @@ static const int nbfp_stride = GMX_SIMD_REAL_WIDTH;
 #endif
 
 #ifdef GMX_SIMD_IBM_QPX
-#include "nbnxn_kernel_simd_utils_ibm_qpx.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ibm_qpx.h"
 #endif /* GMX_SIMD_IBM_QPX */
 
 #ifdef __MIC__
-#include "nbnxn_kernel_simd_utils_x86_mic.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_mic.h"
 #endif
 
 #endif /* GMX_TARGET_X86 && !__MIC__ */

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
index 17d1186c48b118393e13fa11a559faefc7c8542f..589dafa32036cb80d9aeccc4125d396eec54e356 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
@@ -35,10 +35,10 @@
 #ifndef _nbnxn_kernel_simd_utils_x86_128s_h_
 #define _nbnxn_kernel_simd_utils_x86_128s_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-
 #include "config.h"
 
+#include "gromacs/legacyheaders/types/simple.h"
+
 /* This files contains all functions/macros for the SIMD kernels
  * which have explicit dependencies on the j-cluster size and/or SIMD-width.
  * The functionality which depends on the j-cluster size is:

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
index 37ca75a469a0f302f96b23f5270b5df5939f0b2a..ed1456873bcf373c6844295b7b286eb79e8a5577 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -42,7 +42,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -57,9 +56,10 @@
 
 #define GMX_SIMD_J_UNROLL_SIZE 2
 #include "nbnxn_kernel_simd_2xnn.h"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
index 4e8235e1acbc46c06ee4cfd42f0f557fac59aa1e..f554134cbe35aba9f63b26ac86c66ec8d0f49ea2 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
@@ -38,7 +38,6 @@
  */
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
index a87ca0eb169f9d344beb90311960b78106c8026c..3f3abe8308823e358e44e24d2f246bcefd93e7a9 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
@@ -32,11 +32,11 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
 #ifdef CALC_COUL_EWALD
 #include "gromacs/math/utilities.h"
 #endif
@@ -51,7 +51,7 @@
 /* The stride of all the atom data arrays is equal to half the SIMD width */
 #define STRIDE     UNROLLJ
 
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 static gmx_inline void gmx_simdcall
 gmx_load_simd_2xnn_interactions(int                  excl,

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
index 590c09547df299ca20279ee02be9f82a5f4863a5..21a63ab4aa7b6fcdd899101711d8c75690025dd6 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
@@ -603,13 +603,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
 #undef HALF_LJ
 #undef CALC_COULOMB
@@ -621,13 +621,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
 #undef CALC_COULOMB
         }
@@ -637,13 +637,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
         }
 #undef CALC_LJ

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
index be21910a622a63a5b73a643b52fc973fb4889941..d17ba1e7bdbb1c328aa810bf3e268ed1c98d62fb 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -42,7 +42,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -56,9 +55,10 @@
 
 #define GMX_SIMD_J_UNROLL_SIZE 1
 #include "nbnxn_kernel_simd_4xn.h"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
index c75d58a002d16499ae4a8c07d14f2f91a4ff74cc..87c96994e808b529009e8d069dac905313313950 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
@@ -38,7 +38,6 @@
  */
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
index 9216457430e57b278fdd7818fc5202fa2cd03bda..146c95855be950c76df0f85aa910b34dd6994de0 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
@@ -32,11 +32,11 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
 #ifdef CALC_COUL_EWALD
 #include "gromacs/math/utilities.h"
 #endif
@@ -57,7 +57,7 @@
 #define STRIDE     (UNROLLI)
 #endif
 
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 static gmx_inline void gmx_simdcall
 gmx_load_simd_4xn_interactions(int gmx_unused             excl,

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
index ffe53d5cd709cc26c50e69c3528a025feccae313..15bdf6ca91455228ba6318e24498597c516e4565 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
@@ -627,13 +627,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
 #undef HALF_LJ
 #undef CALC_COULOMB
@@ -645,13 +645,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
 #undef CALC_COULOMB
         }
@@ -661,13 +661,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
         }
 #undef CALC_LJ

diff --git a/src/gromacs/mdlib/nbnxn_pairlist.h b/src/gromacs/mdlib/nbnxn_pairlist.h
index fa03d2681b4e256dbb6d23435e13e0fd6f6c32fc..3f441ad16c21d3c20c8fd2a21f664b513244ca72 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_pairlist.h
+++ b/src/gromacs/mdlib/nbnxn_pairlist.h
@@ -37,6 +37,7 @@
 #define _nbnxn_pairlist_h
 
 #include "thread_mpi/atomic.h"
+
 #include "gromacs/legacyheaders/types/nblist.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 6c1e301a0719ba0ada67042d4639c4e22487d7aa..f13de8c7db485633350dd28414c1d23bb53eb237 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -37,6 +37,8 @@
 
 #include "nbnxn_search.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <string.h>
@@ -55,8 +57,6 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 /* nbnxn_internal.h included gromacs/simd/macros.h */
 #include "gromacs/mdlib/nbnxn_internal.h"
 #ifdef GMX_SIMD

diff --git a/src/gromacs/mdlib/nbnxn_search.h b/src/gromacs/mdlib/nbnxn_search.h
index 7c7def3ff4a882597fea976d25e2cf7497096296..8e644bf21a7f95b1547f773f18646709211766a4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.h
+++ b/src/gromacs/mdlib/nbnxn_search.h
@@ -37,7 +37,7 @@
 #define _nbnxn_search_h
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h b/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
index 59760f4b94fd18072ab50e6e15c045a19e306666..2ff7bc991e32ad57953e57a7c25d98d9c5ebc0e4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
+++ b/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
@@ -34,7 +34,7 @@
  */
 
 /* Get the half-width SIMD stuff from the kernel utils files */
-#include "nbnxn_kernels/nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 
 #if GMX_SIMD_REAL_WIDTH >= 2*NBNXN_CPU_CLUSTER_I_SIZE

diff --git a/src/gromacs/mdlib/nlistheuristics.c b/src/gromacs/mdlib/nlistheuristics.c
index abe58155557bd5d76d928d9372b27cfa5db0871b..44f789e7bb5bb6b1d25f1ec67da7e5c2f3f85184 100644 (file)
--- a/src/gromacs/mdlib/nlistheuristics.c
+++ b/src/gromacs/mdlib/nlistheuristics.c
@@ -38,7 +38,6 @@
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/nlistheuristics.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 8eb8a70d62ce8ee6fce1f984f2114c002187ef78..9145929c475b11a0d5bda33347479803215ca818 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -36,32 +36,32 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/ns.h"
+
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/topology/mtop_util.h"
-
-#include "gromacs/legacyheaders/domdec.h"
-#include "adress.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "adress.h"
+
 /*
  *    E X C L U S I O N   H A N D L I N G
  */

diff --git a/src/gromacs/mdlib/nsgrid.c b/src/gromacs/mdlib/nsgrid.c
index 8ad27efc6cad5902023bceb3adebcac38d9adfa1..0f0120e0e1a155c36eb8b4365b23f3102495b690 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.c
+++ b/src/gromacs/mdlib/nsgrid.c
@@ -37,21 +37,22 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nsgrid.h"
+
+#include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include <stdio.h>
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/utility/smalloc.h"
 
 /***********************************
  *         Grid Routines

diff --git a/src/gromacs/mdlib/perf_est.c b/src/gromacs/mdlib/perf_est.c
index 29010b067ad9b6315ad3bced7cf112e26dd7892d..837113f2aec7e4791b259112854434e2c054ca28 100644 (file)
--- a/src/gromacs/mdlib/perf_est.c
+++ b/src/gromacs/mdlib/perf_est.c
@@ -36,17 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/perf_est.h"
+
 #include <math.h>
 
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "nbnxn_search.h"
-#include "nbnxn_consts.h"
-
 /* Computational cost of bonded, non-bonded and PME calculations.
  * This will be machine dependent.
  * The numbers here are accurate for Intel Core2 and AMD Athlon 64

diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index 284480184ee23bb6751068cefea47cda31f4db0a..67a12ab58db8d0a8f5b4dc4a2f53f75214da1568 100644 (file)
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -59,6 +59,8 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/pme.h"
+
 #include "config.h"
 
 #include <assert.h>
@@ -67,27 +69,25 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/fft/parallel_3dfft.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/timing/cyclecounter.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Include the SIMD macro file and then check for support */
 #include "gromacs/simd/simd.h"
@@ -1436,7 +1436,7 @@ static void spread_coefficients_bsplines_thread(pmegrid_t                    *pm
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_BSPLINE(4);
 #endif
@@ -1445,7 +1445,7 @@ static void spread_coefficients_bsplines_thread(pmegrid_t                    *pm
 #ifdef PME_SIMD4_SPREAD_GATHER
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_BSPLINE(5);
 #endif
@@ -2599,7 +2599,7 @@ static void gather_f_bsplines(gmx_pme_t pme, real *grid,
 #define PME_GATHER_F_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_FSPLINE(4);
 #endif
@@ -2608,7 +2608,7 @@ static void gather_f_bsplines(gmx_pme_t pme, real *grid,
 #ifdef PME_SIMD4_SPREAD_GATHER
 #define PME_GATHER_F_SIMD4_ALIGNED
 #define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_FSPLINE(5);
 #endif

diff --git a/src/gromacs/mdlib/pme_pp.c b/src/gromacs/mdlib/pme_pp.c
index 6ed1d563fba876f9b2d3536c3fac6732660aefe9..f00d242ae766acdc1b170c774f329b0046818485 100644 (file)
--- a/src/gromacs/mdlib/pme_pp.c
+++ b/src/gromacs/mdlib/pme_pp.c
@@ -39,21 +39,20 @@
 
 #include "config.h"
 
-
+#include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include <math.h>
+
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/sighandler.h"
-
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 enum {
     eCommType_ChargeA, eCommType_ChargeB, eCommType_SQRTC6A, eCommType_SQRTC6B,

diff --git a/src/gromacs/mdlib/qm_gamess.c b/src/gromacs/mdlib/qm_gamess.c
index 9fcaed86dc8ac4bf0d2f8a214d4caa1e547c08d1..d913f7f48925abd33818aa8e90317dac5d590b2a 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.c
+++ b/src/gromacs/mdlib/qm_gamess.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* QMMM sub routines */

diff --git a/src/gromacs/mdlib/qm_gaussian.c b/src/gromacs/mdlib/qm_gaussian.c
index 1092a65046a32889568fac6f839a1c82d61421f1..6339b94f8a4b00b4bcf83813d0be7046a5194277 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.c
+++ b/src/gromacs/mdlib/qm_gaussian.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* TODO: this should be made thread-safe */

diff --git a/src/gromacs/mdlib/qm_mopac.c b/src/gromacs/mdlib/qm_mopac.c
index 7f1bea8a83fed90daa6c1af114d7b43defe4b3ae..6eb689cd3ea5d5f4002da26408af314e9154625c 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.c
+++ b/src/gromacs/mdlib/qm_mopac.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* mopac interface routines */

diff --git a/src/gromacs/mdlib/qm_orca.c b/src/gromacs/mdlib/qm_orca.c
index f5f85e4f8d0743a38723ede0f29b228edead895b..11ddfd325b901c82b2b25aa211aa228f59c9546b 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.c
+++ b/src/gromacs/mdlib/qm_orca.c
@@ -41,20 +41,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* ORCA interface routines */
 

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index ccb566ae9ca7209477b1c2c49953220e9181dec9..bb83405a5548e083d481bcf88616aed3c422a2b5 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/qmmm.h"
+
 #include "config.h"
 
 #include <math.h>
@@ -43,25 +45,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/topology/mtop_util.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/rf_util.c b/src/gromacs/mdlib/rf_util.c
index ee68bd8ee0fef524bebb043a0ad68fcef87db791..a4703cca24ebd8af1d5be38ae523119e038dd3f0 100644 (file)
--- a/src/gromacs/mdlib/rf_util.c
+++ b/src/gromacs/mdlib/rf_util.c
@@ -36,16 +36,15 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
 
 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
                         const t_mdatoms *mdatoms, const t_blocka *excl,

diff --git a/src/gromacs/mdlib/shakef.c b/src/gromacs/mdlib/shakef.c
index fba6074500e56346dc0b68343ca39efb5d1c7f62..7ee7dbe2a82715ffc47cfb04b0592e79581f0749 100644 (file)
--- a/src/gromacs/mdlib/shakef.c
+++ b/src/gromacs/mdlib/shakef.c
@@ -38,12 +38,12 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct gmx_shakedata
 {

diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index ad3f4d5c6ef37b4340042402e07d45e4f8efa456..ce00047a385e027f53baf857f9d1c25cd3b244df 100644 (file)
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/shellfc.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 4090760008135c7cce14eacd163c55c11f2108a5..886f6acdd3b8e3b18f1d7b65e86d0a04409e24bd 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -38,13 +38,13 @@
 
 #include "gromacs/legacyheaders/sim_util.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
@@ -78,7 +78,6 @@
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdlib/adress.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"
 #include "gromacs/mdlib/nbnxn_search.h"
@@ -99,6 +98,8 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "adress.h"
+
 void print_time(FILE                     *out,
                 gmx_walltime_accounting_t walltime_accounting,
                 gmx_int64_t               step,

diff --git a/src/gromacs/mdlib/stat.c b/src/gromacs/mdlib/stat.c
index e0d2ee19c60aef83fb58f280b28ab7ef5711709b..280237f2150348287bc9667cbf550c0c13a65005 100644 (file)
--- a/src/gromacs/mdlib/stat.c
+++ b/src/gromacs/mdlib/stat.c
@@ -36,32 +36,32 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/rbin.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/fileio/xtcio.h"
+#include <string.h>
+
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trnio.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/rbin.h"
 #include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct gmx_global_stat
 {

diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c
index 5f5d9d58fdb01c9d22a69032c3c4e4bbdee3dc82..1c3389e493ed94f5a8b989ddec150101a54b4895 100644 (file)
--- a/src/gromacs/mdlib/tables.c
+++ b/src/gromacs/mdlib/tables.c
@@ -36,21 +36,23 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/tables.h"
+
 #include <math.h>
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* All the possible (implemented) table functions */
 enum {

diff --git a/src/gromacs/mdlib/tgroup.c b/src/gromacs/mdlib/tgroup.c
index db9a9bb988f3efd6435ef1fb279d5a0b7b227619..1baec82abd2d0075fe51910e871d8fb50f309b88 100644 (file)
--- a/src/gromacs/mdlib/tgroup.c
+++ b/src/gromacs/mdlib/tgroup.c
@@ -37,17 +37,19 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/tgroup.h"
+
 #include <math.h>
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
 {

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 39ebeaf2377b59f020d9f251ec39791feca4c1bd..7da23c74c3e055bb264fdf343c0a0bace19bf8f6 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -41,40 +41,38 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
 #include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/units.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void global_max(t_commrec *cr, int *n)
 {

diff --git a/src/gromacs/mdlib/update.c b/src/gromacs/mdlib/update.c
index 68c30a18e21851d06d9afc369f04dfbe2f17e311..3be84a8a93c697047beff45cb75b6ffa8d861312 100644 (file)
--- a/src/gromacs/mdlib/update.c
+++ b/src/gromacs/mdlib/update.c
@@ -36,31 +36,31 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "gromacs/legacyheaders/update.h"
+
 #include <math.h>
+#include <stdio.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/legacyheaders/constr.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"

diff --git a/src/gromacs/mdlib/vcm.c b/src/gromacs/mdlib/vcm.c
index c6d3b2a3102dd7b504889ad00b0b8703cfe06a58..31c2cf2c949a74b48cc44085341788fdf2dadf07 100644 (file)
--- a/src/gromacs/mdlib/vcm.c
+++ b/src/gromacs/mdlib/vcm.c
@@ -37,14 +37,15 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
 
 t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir)
 {

diff --git a/src/gromacs/mdlib/vsite.c b/src/gromacs/mdlib/vsite.c
index a9df773ec2d081f7718e60f61ce4c9f4615b72e3..984426f3192584e255eb9ddcd0110f13c70cb671 100644 (file)
--- a/src/gromacs/mdlib/vsite.c
+++ b/src/gromacs/mdlib/vsite.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/vsite.h"
+
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/wall.c b/src/gromacs/mdlib/wall.c
index 38f26e3c1c1d466469b30d6942b7659ab68ca3fb..bdc5c90e404b06e96cd38a06e86a28b205c7f669 100644 (file)
--- a/src/gromacs/mdlib/wall.c
+++ b/src/gromacs/mdlib/wall.c
@@ -40,14 +40,13 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/vec.h"
-
-#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/wnblist.c b/src/gromacs/mdlib/wnblist.c
index 62aa867b6bad484d26b477f9c9420dbc48a5b14c..afcef8db519f5a75b9ef912d22547038395c42ae 100644 (file)
--- a/src/gromacs/mdlib/wnblist.c
+++ b/src/gromacs/mdlib/wnblist.c
@@ -39,17 +39,18 @@
 
 #include <stdio.h>
 #include <string.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 #define header "Neighborlist:"
 

diff --git a/src/gromacs/onlinehelp/helpformat.h b/src/gromacs/onlinehelp/helpformat.h
index 6891adfb0845bdd56c32cb4822110f2b4d673146..98df196f449113da271fa0fb42a2efce466da753 100644 (file)
--- a/src/gromacs/onlinehelp/helpformat.h
+++ b/src/gromacs/onlinehelp/helpformat.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/onlinehelp/helpmanager.h b/src/gromacs/onlinehelp/helpmanager.h
index 122d72242e5dd67f52e853c547e6b7ef7ec050cd..4418edf871f2afd6918878e826e6f84cfaa9ec7d 100644 (file)
--- a/src/gromacs/onlinehelp/helpmanager.h
+++ b/src/gromacs/onlinehelp/helpmanager.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/onlinehelp/helptopic.h b/src/gromacs/onlinehelp/helptopic.h
index f67bc8e993b17702412700a44210bcda92154e9c..bff75e3876e669792dce18b654cd4c71b0472edb 100644 (file)
--- a/src/gromacs/onlinehelp/helptopic.h
+++ b/src/gromacs/onlinehelp/helptopic.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,11 +44,10 @@
 #ifndef GMX_ONLINEHELP_HELPTOPIC_H
 #define GMX_ONLINEHELP_HELPTOPIC_H
 
-#include "../utility/common.h"
-#include "../utility/stringutil.h"
-#include "../utility/uniqueptr.h"
-
-#include "helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/onlinehelp/helptopicinterface.h b/src/gromacs/onlinehelp/helptopicinterface.h
index e3f0c92d44ef5ba5f22059e0e0614ee9446c76d5..2a6479ed273adfc8b2664fa89ea0a005f098a77e 100644 (file)
--- a/src/gromacs/onlinehelp/helptopicinterface.h
+++ b/src/gromacs/onlinehelp/helptopicinterface.h
@@ -56,7 +56,7 @@
 #ifndef GMX_ONLINEHELP_HELPTOPICINTERFACE_H
 #define GMX_ONLINEHELP_HELPTOPICINTERFACE_H
 
-#include "../utility/uniqueptr.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/onlinehelp/helpwritercontext.h b/src/gromacs/onlinehelp/helpwritercontext.h
index 157ea00b8a584877bf46b8cf38646943392558df..8bbc2b63e8f6d0a3af17e936a2b25b4ab080517d 100644 (file)
--- a/src/gromacs/onlinehelp/helpwritercontext.h
+++ b/src/gromacs/onlinehelp/helpwritercontext.h
@@ -46,7 +46,7 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/onlinehelp/tests/helpformat.cpp b/src/gromacs/onlinehelp/tests/helpformat.cpp
index f74a80da347a445c90575d307603f380d08bc209..797593e6b899116ce3be98d93d914d508c279996 100644 (file)
--- a/src/gromacs/onlinehelp/tests/helpformat.cpp
+++ b/src/gromacs/onlinehelp/tests/helpformat.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/onlinehelp/helpformat.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/stringtest.h"
 
 namespace

diff --git a/src/gromacs/options.h b/src/gromacs/options.h
index 4b11e1f7c06f3e829a6ecc73adf5c3d2aba27d28..a6bc7e8362f7b94f4c5fa3077638f096e2411317 100644 (file)
--- a/src/gromacs/options.h
+++ b/src/gromacs/options.h
@@ -146,10 +146,10 @@
 #ifndef GMX_OPTIONS_H
 #define GMX_OPTIONS_H
 
-#include "fileio/filenm.h"
-#include "options/basicoptions.h"
-#include "options/filenameoption.h"
-#include "options/filenameoptionmanager.h"
-#include "options/options.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/options.h"
 
 #endif

diff --git a/src/gromacs/options/abstractoption.cpp b/src/gromacs/options/abstractoption.cpp
index c81d0e2a56ae05bd6e1074b7f60f1700f2c1b676..a71ed24353a6867c35c2aceee5935a32e7c19c49 100644 (file)
--- a/src/gromacs/options/abstractoption.cpp
+++ b/src/gromacs/options/abstractoption.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/abstractoption.h"
+#include "abstractoption.h"
 
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/optionflags.h"

diff --git a/src/gromacs/options/abstractoption.h b/src/gromacs/options/abstractoption.h
index 1152081eca90101c5364fd9c271bc40f9bf3cdb2..2793f2f0faa3e19a5fd99cc73b6937bbbab2a5da 100644 (file)
--- a/src/gromacs/options/abstractoption.h
+++ b/src/gromacs/options/abstractoption.h
@@ -57,9 +57,8 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/abstractoptionstorage.h b/src/gromacs/options/abstractoptionstorage.h
index 9cb9ff543e6e66ade451124b3f1a70c492381e67..9081d03898e1dbf8d7a11a88f278c45b30840e8f 100644 (file)
--- a/src/gromacs/options/abstractoptionstorage.h
+++ b/src/gromacs/options/abstractoptionstorage.h
@@ -45,9 +45,8 @@
 
 #include <string>
 
-#include "../utility/common.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/basicoptions.cpp b/src/gromacs/options/basicoptions.cpp
index 8dff27360da2a41ccdeabc470018b69d93cf0a56..412455560756b6325fa1fc173be892f898e05d84 100644 (file)
--- a/src/gromacs/options/basicoptions.cpp
+++ b/src/gromacs/options/basicoptions.cpp
@@ -42,7 +42,6 @@
 #include "gmxpre.h"
 
 #include "basicoptions.h"
-#include "basicoptionstorage.h"
 
 #include <cerrno>
 #include <cstdio>
@@ -56,6 +55,8 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "basicoptionstorage.h"
+
 namespace
 {
 

diff --git a/src/gromacs/options/basicoptions.h b/src/gromacs/options/basicoptions.h
index 67f14e31d9414018c57e06deef57e00da2c586fe..4d58fcf241d53da5f9a4c9a343ee8837afc68642 100644 (file)
--- a/src/gromacs/options/basicoptions.h
+++ b/src/gromacs/options/basicoptions.h
@@ -48,10 +48,9 @@
 
 #include <string>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/basicoptionstorage.h b/src/gromacs/options/basicoptionstorage.h
index 823ec97beb3e4ddca7ab0a5301c82c80c01a7b20..59ab9f16fc86a54925b935acb11a22348eb1d578 100644 (file)
--- a/src/gromacs/options/basicoptionstorage.h
+++ b/src/gromacs/options/basicoptionstorage.h
@@ -45,8 +45,8 @@
 #include <string>
 #include <vector>
 
-#include "basicoptions.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/optionstoragetemplate.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/filenameoption.cpp b/src/gromacs/options/filenameoption.cpp
index 171c668a5afbf964de4f5056bb1f39f40408ef99..1f136417867b10d02b56cd975675f40acc25a886 100644 (file)
--- a/src/gromacs/options/filenameoption.cpp
+++ b/src/gromacs/options/filenameoption.cpp
@@ -42,7 +42,6 @@
 #include "gmxpre.h"
 
 #include "filenameoption.h"
-#include "filenameoptionstorage.h"
 
 #include <cstring>
 
@@ -57,6 +56,8 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "filenameoptionstorage.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/options/filenameoption.h b/src/gromacs/options/filenameoption.h
index 479a35834acb5e878f86fd8d53de7d8a4f075d92..2c1536fc8c683a6c54a48c6f2a42b4a743beaac7 100644 (file)
--- a/src/gromacs/options/filenameoption.h
+++ b/src/gromacs/options/filenameoption.h
@@ -46,8 +46,8 @@
 #include <string>
 #include <vector>
 
-#include "abstractoption.h"
-#include "optionfiletype.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionfiletype.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/filenameoptionmanager.h b/src/gromacs/options/filenameoptionmanager.h
index 1c492e19709a391e4e680e852c948b158bef1870..0fd50ceec80a86631e466e349e55e42a0c91d176 100644 (file)
--- a/src/gromacs/options/filenameoptionmanager.h
+++ b/src/gromacs/options/filenameoptionmanager.h
@@ -45,9 +45,8 @@
 
 #include <string>
 
-#include "options.h"
-
-#include "../utility/common.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/filenameoptionstorage.h b/src/gromacs/options/filenameoptionstorage.h
index 84a0f8fc21bca37caf331aab38e6d283b33ba722..7628a379d1a0f90e7baa7afa74f38cbc8699c04d 100644 (file)
--- a/src/gromacs/options/filenameoptionstorage.h
+++ b/src/gromacs/options/filenameoptionstorage.h
@@ -45,9 +45,9 @@
 #include <string>
 #include <vector>
 
-#include "filenameoption.h"
-#include "optionfiletype.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/optionfiletype.h"
+#include "gromacs/options/optionstoragetemplate.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/optionflags.h b/src/gromacs/options/optionflags.h
index 5a4ff6399b42411315ade14685c8a8c1b772a21d..9157ecba9dabaf72dfc55cb5134a2954dff33fe9 100644 (file)
--- a/src/gromacs/options/optionflags.h
+++ b/src/gromacs/options/optionflags.h
@@ -46,7 +46,7 @@
 #ifndef GMX_OPTIONS_OPTIONFLAGS_H
 #define GMX_OPTIONS_OPTIONFLAGS_H
 
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/options-impl.h b/src/gromacs/options/options-impl.h
index ce23aad95212ad4e71fe5a038940c4162305a041..3fba6da02ad8efc80378ae11bceb42d12fa4fd30 100644 (file)
--- a/src/gromacs/options/options-impl.h
+++ b/src/gromacs/options/options-impl.h
@@ -45,9 +45,9 @@
 #include <string>
 #include <vector>
 
-#include "abstractoption.h"
-#include "optionmanagercontainer.h"
-#include "options.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionmanagercontainer.h"
+#include "gromacs/options/options.h"
 #include "gromacs/utility/uniqueptr.h"
 
 namespace gmx

diff --git a/src/gromacs/options/options.cpp b/src/gromacs/options/options.cpp
index 9aa05a27ffeb9bc6f8f46f9d09109584b3f1bb34..aec42fc98ffc71d58cb297f04513c0f237b1dab4 100644 (file)
--- a/src/gromacs/options/options.cpp
+++ b/src/gromacs/options/options.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/options.h"
+#include "options.h"
 
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/abstractoptionstorage.h"

diff --git a/src/gromacs/options/options.h b/src/gromacs/options/options.h
index 7623086796c57ac63347d1afcafec2dc2fea5a22..6c6c51fcfd0b6aa08cb78a13c0faebeaf00137a9 100644 (file)
--- a/src/gromacs/options/options.h
+++ b/src/gromacs/options/options.h
@@ -48,10 +48,9 @@
 
 #include <string>
 
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/optionsassigner.cpp b/src/gromacs/options/optionsassigner.cpp
index 6274213a55f4052b647e8324f0b661f9618c5c02..df3f1320d89da7ddb54996b610e7c5885d30a614 100644 (file)
--- a/src/gromacs/options/optionsassigner.cpp
+++ b/src/gromacs/options/optionsassigner.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/optionsassigner.h"
+#include "optionsassigner.h"
 
 #include <deque>
 

diff --git a/src/gromacs/options/optionsassigner.h b/src/gromacs/options/optionsassigner.h
index 5047b180dc7682899a2ac382e475893dae3cae28..d56529e7074dd456457914effea8b983ae98645a 100644 (file)
--- a/src/gromacs/options/optionsassigner.h
+++ b/src/gromacs/options/optionsassigner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,7 +47,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/optionstoragetemplate.h b/src/gromacs/options/optionstoragetemplate.h
index dae027c79ad8a08309ba1cd3b435b4b92eb4c08e..ad00611d04e2822af2235c2b67f8666f4c4cb44a 100644 (file)
--- a/src/gromacs/options/optionstoragetemplate.h
+++ b/src/gromacs/options/optionstoragetemplate.h
@@ -48,12 +48,11 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "../utility/common.h"
-#include "../utility/exceptions.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
-#include "abstractoptionstorage.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/optionsvisitor.cpp b/src/gromacs/options/optionsvisitor.cpp
index 9f74f946d69480692d47cf5d8232bb3db6484487..814ae734fdb2e19efa27e985ac0163ffb26b039c 100644 (file)
--- a/src/gromacs/options/optionsvisitor.cpp
+++ b/src/gromacs/options/optionsvisitor.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/optionsvisitor.h"
+#include "optionsvisitor.h"
 
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/options.h"

diff --git a/src/gromacs/options/optionsvisitor.h b/src/gromacs/options/optionsvisitor.h
index 862b28ee57c2eaa32c92beb27892e866eb0f831e..934efb97fb65a3c29f13f88ceb12129c7195b9c0 100644 (file)
--- a/src/gromacs/options/optionsvisitor.h
+++ b/src/gromacs/options/optionsvisitor.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,9 +47,8 @@
 
 #include <string>
 
-#include "../utility/common.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/tests/abstractoptionstorage.cpp b/src/gromacs/options/tests/abstractoptionstorage.cpp
index cdd5bbaf1b922bf7d1a4e0bec3f2bae50571c391..1682129575a0eec6f53c8cd1fd2ef746797d64d5 100644 (file)
--- a/src/gromacs/options/tests/abstractoptionstorage.cpp
+++ b/src/gromacs/options/tests/abstractoptionstorage.cpp
@@ -44,16 +44,16 @@
  */
 #include "gmxpre.h"
 
-#include <vector>
 #include <string>
+#include <vector>
 
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/options.h"
-#include "gromacs/options/optionstoragetemplate.h"
 #include "gromacs/options/optionsassigner.h"
+#include "gromacs/options/optionstoragetemplate.h"
 #include "gromacs/utility/exceptions.h"
 
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/options/tests/option.cpp b/src/gromacs/options/tests/option.cpp
index 2cc756bc94177f88d0496ef9056825e5a53e363c..70b513bdb79a3609c3ee92280d8d7a5d699184f9 100644 (file)
--- a/src/gromacs/options/tests/option.cpp
+++ b/src/gromacs/options/tests/option.cpp
@@ -44,8 +44,8 @@
  */
 #include "gmxpre.h"
 
-#include <vector>
 #include <string>
+#include <vector>
 
 #include <gtest/gtest.h>
 

diff --git a/src/gromacs/options/tests/optionsassigner.cpp b/src/gromacs/options/tests/optionsassigner.cpp
index 9b6e244c0a5a4976b7b5124704a0fd6aeea4331c..cf9648cc1cb269251fa421740ab36e7a0bfff30b 100644 (file)
--- a/src/gromacs/options/tests/optionsassigner.cpp
+++ b/src/gromacs/options/tests/optionsassigner.cpp
@@ -47,6 +47,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/options/optionsassigner.h"
+
 #include <limits>
 #include <vector>
 
@@ -54,7 +56,6 @@
 
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
-#include "gromacs/options/optionsassigner.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/options/tests/timeunitmanager.cpp b/src/gromacs/options/tests/timeunitmanager.cpp
index 11989bc002241da897d37c2e4c61ec4e44f890fd..9e5f57fd183107c56ec194894d50bb47811fdb29 100644 (file)
--- a/src/gromacs/options/tests/timeunitmanager.cpp
+++ b/src/gromacs/options/tests/timeunitmanager.cpp
@@ -43,12 +43,13 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/options/timeunitmanager.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsassigner.h"
-#include "gromacs/options/timeunitmanager.h"
 
 #include "testutils/testasserts.h"
 

diff --git a/src/gromacs/options/timeunitmanager.cpp b/src/gromacs/options/timeunitmanager.cpp
index d77e10700c4386d9bb562c6f56380b2695835924..b687c31bb7518ac606a33b23edfd94edd296683a 100644 (file)
--- a/src/gromacs/options/timeunitmanager.cpp
+++ b/src/gromacs/options/timeunitmanager.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/timeunitmanager.h"
+#include "timeunitmanager.h"
 
 #include <cstdlib>
 

diff --git a/src/gromacs/options/timeunitmanager.h b/src/gromacs/options/timeunitmanager.h
index 7ad7fe3243a56dcf88d11eee5d4699d0b0befd68..76e08312bebfe16603db5e5e015ba24f21d29c6f 100644 (file)
--- a/src/gromacs/options/timeunitmanager.h
+++ b/src/gromacs/options/timeunitmanager.h
@@ -43,7 +43,7 @@
 #ifndef GMX_OPTIONS_TIMEUNITMANAGER_H
 #define GMX_OPTIONS_TIMEUNITMANAGER_H
 
-#include "../utility/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/pbcutil/mshift.cpp b/src/gromacs/pbcutil/mshift.cpp
index fa47a80e1a19bf4ee2b77073af9216c325f32d91..346f029ead1de4ca142cc0102e3a0399418d4306 100644 (file)
--- a/src/gromacs/pbcutil/mshift.cpp
+++ b/src/gromacs/pbcutil/mshift.cpp
@@ -36,14 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/mshift.h"
+#include "mshift.h"
 
 #include <string.h>
 
 #include <algorithm>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/pbcutil/pbc.c b/src/gromacs/pbcutil/pbc.c
index cfdc3be419f2b3b7045f3c12f06c94f37250d43d..e6d4c49230387450964755547dd7aa24bfc51182 100644 (file)
--- a/src/gromacs/pbcutil/pbc.c
+++ b/src/gromacs/pbcutil/pbc.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/pbc.h"
+#include "pbc.h"
 
 #include <assert.h>
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/pbcutil/pbc.h b/src/gromacs/pbcutil/pbc.h
index 8fa140d8f0b29eda49bcd82966ec9a94541f843c..8fc7b68224ff6a0082ed7146ff07eb08c202b188 100644 (file)
--- a/src/gromacs/pbcutil/pbc.h
+++ b/src/gromacs/pbcutil/pbc.h
@@ -39,11 +39,11 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/types/inputrec.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/pbcutil/rmpbc.c b/src/gromacs/pbcutil/rmpbc.c
index 09f10c043c75ff044963601a5c5bbdc88e4ad7ae..4d91ac47830c3ed9280429680ea764e8746bd7e7 100644 (file)
--- a/src/gromacs/pbcutil/rmpbc.c
+++ b/src/gromacs/pbcutil/rmpbc.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/rmpbc.h"
+#include "rmpbc.h"
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
@@ -44,8 +44,8 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/idef.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {

diff --git a/src/gromacs/pbcutil/rmpbc.h b/src/gromacs/pbcutil/rmpbc.h
index 3f90bdb2655ea13dce24d8afcaa052359f6ad9a3..ff9107a7d2a27a8b4d5859530358eeccc674fa7c 100644 (file)
--- a/src/gromacs/pbcutil/rmpbc.h
+++ b/src/gromacs/pbcutil/rmpbc.h
@@ -37,7 +37,7 @@
 #ifndef GMX_PBCUTIL_RMPBC_H
 #define GMX_PBCUTIL_RMPBC_H
 
-#include "../math/vectypes.h"
+#include "gromacs/math/vectypes.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/pulling/pull.c b/src/gromacs/pulling/pull.c
index e84ad19714c9de45ac48b6138a26823ec83e0744..575e07ca87a405a6e0acf5720bdea51391f62a6d 100644 (file)
--- a/src/gromacs/pulling/pull.c
+++ b/src/gromacs/pulling/pull.c
@@ -36,28 +36,28 @@
  */
 #include "gmxpre.h"
 
+#include "pull.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "pull.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void pull_print_group_x(FILE *out, ivec dim, const t_pull_group *pgrp)

diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index d8362c53530e9c79cd32fc603f06ce5ee90be993..3a5f8d6b575553e4706f40acbd275d51e4cfc9e6 100644 (file)
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -50,8 +50,8 @@
 #ifndef GMX_PULLING_PULL_H
 #define GMX_PULLING_PULL_H
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/pulling/pull_rotation.c b/src/gromacs/pulling/pull_rotation.c
index 0aa84dbcce75152c75a6cd01e22e518a6d53563a..dd74b44df552cf7ba942084e83cb17eb2dc805f6 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.c
+++ b/src/gromacs/pulling/pull_rotation.c
@@ -36,37 +36,36 @@
  */
 #include "gmxpre.h"
 
+#include "pull_rotation.h"
+
 #include "config.h"
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/cyclecounter.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/qsort_threadsafe.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *RotStr = {"Enforced rotation:"};
 

diff --git a/src/gromacs/pulling/pull_rotation.h b/src/gromacs/pulling/pull_rotation.h
index 567b4e95c88dd092b9190bc31e80b51a7365bfab..28d380195b714029ad11e855aa49d709aef1c568 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.h
+++ b/src/gromacs/pulling/pull_rotation.h
@@ -48,9 +48,9 @@
 #ifndef GMX_PULLING_PULL_ROTATION_H
 #define GMX_PULLING_PULL_ROTATION_H
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/timing/wallcycle.h"
-#include "../fileio/filenm.h"
 
 
 #ifdef __cplusplus

diff --git a/src/gromacs/pulling/pullutil.c b/src/gromacs/pulling/pullutil.c
index 57bc3401c545909c558518b755d4600c6ff3caef..53072c1ef20393f2ae4c95eaf6ae6581d5bb5db8 100644 (file)
--- a/src/gromacs/pulling/pullutil.c
+++ b/src/gromacs/pulling/pullutil.c
@@ -38,19 +38,19 @@
 
 #include <stdlib.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "pull.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
                              rvec *x,

diff --git a/src/gromacs/random/random.c b/src/gromacs/random/random.c
index 9150e64f3eb12f7425d02e5f09c05e7cf6f58838..b8295a73d72b2c1a387c7baa6a51b4ea5a6d1474 100644 (file)
--- a/src/gromacs/random/random.c
+++ b/src/gromacs/random/random.c
@@ -38,13 +38,13 @@
 
 #include "random.h"
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
@@ -52,11 +52,11 @@
 #include <process.h>
 #endif
 
+#include "external/Random123-1.08/include/Random123/threefry.h"
+
 #include "gromacs/math/utilities.h"
 #include "gromacs/random/random_gausstable.h"
 
-#include "external/Random123-1.08/include/Random123/threefry.h"
-
 #define RNG_N 624
 #define RNG_M 397
 #define RNG_MATRIX_A 0x9908b0dfUL   /* constant vector a */

diff --git a/src/gromacs/selection.h b/src/gromacs/selection.h
index 0588ce36aaf531ca92d83e64735644c2708e961f..ef47702a211575f0ba0ce3314649fe117c22cef5 100644 (file)
--- a/src/gromacs/selection.h
+++ b/src/gromacs/selection.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -81,9 +81,9 @@
 #ifndef GMX_SELECTION_H
 #define GMX_SELECTION_H
 
-#include "selection/selection.h"
-#include "selection/selectioncollection.h"
-#include "selection/selectionoption.h"
-#include "selection/selectionoptionmanager.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/selection/selectionoptionmanager.h"
 
 #endif

diff --git a/src/gromacs/selection/centerofmass.cpp b/src/gromacs/selection/centerofmass.cpp
index a3fa6c369a2b85edf3a946e0b1fab3a127fb5752..474175ef89d0961fa9274a5606af9ea568917841 100644 (file)
--- a/src/gromacs/selection/centerofmass.cpp
+++ b/src/gromacs/selection/centerofmass.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/centerofmass.h"
+#include "centerofmass.h"
 
 #include <errno.h>
 

diff --git a/src/gromacs/selection/centerofmass.h b/src/gromacs/selection/centerofmass.h
index 494d39b26e0e703aeaed81156f5b5b72ebf03108..4aa7cf8288139ef599f024c977ed446427144a6c 100644 (file)
--- a/src/gromacs/selection/centerofmass.h
+++ b/src/gromacs/selection/centerofmass.h
@@ -74,8 +74,8 @@
 #ifndef GMX_SELECTION_CENTEROFMASS_H
 #define GMX_SELECTION_CENTEROFMASS_H
 
-#include "../legacyheaders/types/simple.h"
-#include "../math/vectypes.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
 
 struct t_block;
 struct t_blocka;

diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index 293073fd5019b57d2becd02901ae7e5c7c5818f6..4b696a29ae1095f31e6cd5ac41f0f3a0649e9639 100644 (file)
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -273,16 +273,14 @@
 
 #include "compiler.h"
 
-#include <algorithm>
-
 #include <math.h>
 #include <stdarg.h>
 
+#include <algorithm>
+
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
@@ -290,8 +288,10 @@
 #include "evaluate.h"
 #include "keywords.h"
 #include "mempool.h"
+#include "poscalc.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 using std::min;
 using gmx::SelectionTreeElement;

diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index 1a38971544b4a35176a85442ac3a332a22bfeb9a..dd3d3d1de59bccd2c6708afc0276ef6337408312 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -52,22 +52,23 @@
  */
 #include "gmxpre.h"
 
+#include "evaluate.h"
+
 #include <string.h>
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "evaluate.h"
 #include "mempool.h"
+#include "poscalc.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 using gmx::SelectionTreeElement;
 using gmx::SelectionTreeElementPointer;

diff --git a/src/gromacs/selection/indexutil.cpp b/src/gromacs/selection/indexutil.cpp
index 6fd4666a0131c4673d984cbd0bc7e490331ccb00..a38fe3620509088df357a6f44458da298d89c430 100644 (file)
--- a/src/gromacs/selection/indexutil.cpp
+++ b/src/gromacs/selection/indexutil.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/indexutil.h"
+#include "indexutil.h"
 
 #include <cstdlib>
 #include <cstring>

diff --git a/src/gromacs/selection/indexutil.h b/src/gromacs/selection/indexutil.h
index bdbaaf0076c176641e4569d71bd5978616c77932..dbfe7e77cf0ac6c43df66ea0e1477ed279a9e02b 100644 (file)
--- a/src/gromacs/selection/indexutil.h
+++ b/src/gromacs/selection/indexutil.h
@@ -65,8 +65,8 @@
 
 #include <string>
 
-#include "../legacyheaders/types/simple.h"
-#include "../topology/block.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/block.h"
 
 struct t_topology;
 

diff --git a/src/gromacs/selection/mempool.cpp b/src/gromacs/selection/mempool.cpp
index 99dd91dba61aa186a0c7b8ced58cad1644e23f9d..675932440febc6ce87158d6791ae37dd609570c9 100644 (file)
--- a/src/gromacs/selection/mempool.cpp
+++ b/src/gromacs/selection/mempool.cpp
@@ -41,6 +41,8 @@
  */
 #include "gmxpre.h"
 
+#include "mempool.h"
+
 #include <stdlib.h>
 
 #include <new>
@@ -50,8 +52,6 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "mempool.h"
-
 //! Alignment in bytes for all returned blocks.
 #define ALIGN_STEP 8
 

diff --git a/src/gromacs/selection/nbsearch.cpp b/src/gromacs/selection/nbsearch.cpp
index d626b66d4e98534da51c71cd21af6a6563a85741..7e32fa6536b1ad066a2d7cdb1bb9df420a9fc742 100644 (file)
--- a/src/gromacs/selection/nbsearch.cpp
+++ b/src/gromacs/selection/nbsearch.cpp
@@ -54,7 +54,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/nbsearch.h"
+#include "nbsearch.h"
 
 #include <cmath>
 #include <cstring>
@@ -65,7 +65,6 @@
 #include "thread_mpi/mutex.h"
 
 #include "gromacs/legacyheaders/names.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/selection/position.h"

diff --git a/src/gromacs/selection/nbsearch.h b/src/gromacs/selection/nbsearch.h
index be25e7a3fdfd90f0f3e4e08df14fcc6d0eeb4387..fd7b41b129b2ea892f6f6fdc5ae988b5989de1bb 100644 (file)
--- a/src/gromacs/selection/nbsearch.h
+++ b/src/gromacs/selection/nbsearch.h
@@ -51,11 +51,11 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../math/vectypes.h"
-#include "../utility/arrayref.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 struct t_blocka;
 struct t_pbc;

diff --git a/src/gromacs/selection/params.cpp b/src/gromacs/selection/params.cpp
index b8cac2501a78cd667f88384bde9e277e3fe41719..9c76fe7aea3d034e84c0512489df720e0eafa18e 100644 (file)
--- a/src/gromacs/selection/params.cpp
+++ b/src/gromacs/selection/params.cpp
@@ -46,8 +46,6 @@
 
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/selection/selparam.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
@@ -56,9 +54,10 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "parsetree.h"
-#include "position.h"
 #include "scanner.h"
 #include "selelem.h"
+#include "selmethod.h"
+#include "selparam.h"
 
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;

diff --git a/src/gromacs/selection/parser_internal.h b/src/gromacs/selection/parser_internal.h
index b74ce1a313c3e07be49b2d1298c1694003b9b515..b938adfa6c1207470bebc785764793572a8988d8 100644 (file)
--- a/src/gromacs/selection/parser_internal.h
+++ b/src/gromacs/selection/parser_internal.h
@@ -46,6 +46,8 @@
 #ifndef GMX_SELECTION_PARSER_INTERNAL_H
 #define GMX_SELECTION_PARSER_INTERNAL_H
 
+#include "config.h"
+
 #include <exception>
 
 #include <boost/scoped_ptr.hpp>
@@ -53,11 +55,8 @@
 #include "gromacs/utility/gmxassert.h"
 
 #include "parsetree.h"
-#include "selelem.h"
-
 #include "scanner.h"
-
-#include "config.h"
+#include "selelem.h"
 
 //! Error handler needed by Bison.
 static void

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index a978356c70192085354b81f917116dd9aa3cbd39..14d5d27dbdaddb8dc4d518fd3bbd6f7130c6ad4a 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -221,15 +221,15 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "parsetree.h"
+
 #include <stdarg.h>
+#include <stdio.h>
 
 #include <boost/exception_ptr.hpp>
 #include <boost/shared_ptr.hpp>
 
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
@@ -238,13 +238,13 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
-#include "parsetree.h"
+#include "poscalc.h"
+#include "scanner.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 #include "symrec.h"
 
-#include "scanner.h"
-
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;
 using gmx::SelectionParserValueListPointer;

diff --git a/src/gromacs/selection/poscalc.cpp b/src/gromacs/selection/poscalc.cpp
index 822791a6a0ffe0eead00e41ae7fa8e80200daf11..f193abd42c577b1445fc4d4707a106080528671e 100644 (file)
--- a/src/gromacs/selection/poscalc.cpp
+++ b/src/gromacs/selection/poscalc.cpp
@@ -61,20 +61,22 @@
  */
 #include "gmxpre.h"
 
+#include "poscalc.h"
+
 #include <string.h>
 
 #include <algorithm>
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/selection/centerofmass.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "centerofmass.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/selection/poscalc.h b/src/gromacs/selection/poscalc.h
index 47806069b1062921e6d0c47e20c742bd0161e6fb..83b95d6d3270296dbd50e49b2976ab037b66623d 100644 (file)
--- a/src/gromacs/selection/poscalc.h
+++ b/src/gromacs/selection/poscalc.h
@@ -54,7 +54,7 @@
 
 #include <cstdio>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 /*! \name Flags for position calculation.
  * \anchor poscalc_flags

diff --git a/src/gromacs/selection/position.cpp b/src/gromacs/selection/position.cpp
index e71a9aad98f477676427c5865ebc3ff0cdedbd1e..e5c6346f94e149531eb106c53f30752eacf96159 100644 (file)
--- a/src/gromacs/selection/position.cpp
+++ b/src/gromacs/selection/position.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/position.h"
+#include "position.h"
 
 #include <string.h>
 

diff --git a/src/gromacs/selection/position.h b/src/gromacs/selection/position.h
index cfe2e93189e7cfcbabf6c7739e1c57830cf06b8e..e8e662d1ec1d8e33c8bc37abbb537d5a6979a398 100644 (file)
--- a/src/gromacs/selection/position.h
+++ b/src/gromacs/selection/position.h
@@ -41,9 +41,8 @@
 #ifndef GMX_SELECTION_POSITION_H
 #define GMX_SELECTION_POSITION_H
 
-#include "../math/vectypes.h"
-
-#include "indexutil.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/selection/indexutil.h"
 
 /*! \brief
  * Stores a set of positions together with their origins.

diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp
index d7feb7d042ee8b56cd20db6af7d68119b9567926..f13031fd1a4e3abe373d96630217292775a97794 100644 (file)
--- a/src/gromacs/selection/scanner_internal.cpp
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -53,6 +53,8 @@
  */
 #include "gmxpre.h"
 
+#include "scanner_internal.h"
+
 #include <stdlib.h>
 #include <string.h>
 
@@ -65,16 +67,14 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "parser.h"
 #include "parsetree.h"
+#include "scanner.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 #include "symrec.h"
 
-#include "parser.h"
-#include "scanner.h"
-#include "scanner_internal.h"
-
 /*! \brief
  * Step in which the allocated memory for pretty-printed input is incremented.
  */

diff --git a/src/gromacs/selection/selection.cpp b/src/gromacs/selection/selection.cpp
index c114a4fa595ed5806d781c2060d0a63471c20b63..99bd2abd5ca4c5e5c6c1942bde16c7cb264f6cd4 100644 (file)
--- a/src/gromacs/selection/selection.cpp
+++ b/src/gromacs/selection/selection.cpp
@@ -43,10 +43,10 @@
 
 #include "selection.h"
 
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
 #include "gromacs/topology/topology.h"
 
-#include "nbsearch.h"
-#include "position.h"
 #include "selelem.h"
 #include "selvalue.h"
 

diff --git a/src/gromacs/selection/selection.h b/src/gromacs/selection/selection.h
index 30f060c5577ce72d813cd822faa0207d314d6885..55772ffbf50733b756cbed170a330ae7728146a2 100644 (file)
--- a/src/gromacs/selection/selection.h
+++ b/src/gromacs/selection/selection.h
@@ -46,12 +46,11 @@
 #include <string>
 #include <vector>
 
-#include "../utility/arrayref.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "position.h"
-#include "selectionenums.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
 
 struct t_topology;
 

diff --git a/src/gromacs/selection/selectioncollection-impl.h b/src/gromacs/selection/selectioncollection-impl.h
index a478143880c90f6ac544da149aa57071ceba95a0..abc938683067dc98fc8485b784db340a83292066 100644 (file)
--- a/src/gromacs/selection/selectioncollection-impl.h
+++ b/src/gromacs/selection/selectioncollection-impl.h
@@ -50,12 +50,13 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/uniqueptr.h"
-#include "indexutil.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/uniqueptr.h"
+
 #include "poscalc.h"
-#include "selection.h" // For gmx::SelectionList
-#include "selectioncollection.h"
 #include "selelem.h"
 
 struct gmx_sel_mempool_t;

diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index 288bcea5e0d9ae5b36ade0f859c3a1d47b6c2445..f4bfd210a0663e69171982c1769970f3d5a9dc5f 100644 (file)
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -51,14 +51,14 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "gromacs/legacyheaders/oenv.h"
-
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/onlinehelp/helpmanager.h"
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/selection/selhelp.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
@@ -72,10 +72,8 @@
 #include "parser.h"
 #include "poscalc.h"
 #include "scanner.h"
-#include "selection.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
-#include "selhelp.h"
 #include "selmethod.h"
 #include "symrec.h"
 

diff --git a/src/gromacs/selection/selectioncollection.h b/src/gromacs/selection/selectioncollection.h
index 87f923c7bc99b8e98a714202fe09d8ad2a297afb..281b473abc3924c77bf909f390418bd33db43149 100644 (file)
--- a/src/gromacs/selection/selectioncollection.h
+++ b/src/gromacs/selection/selectioncollection.h
@@ -48,10 +48,9 @@
 #include <string>
 #include <vector>
 
-#include "../legacyheaders/types/oenv.h"
-
-#include "../utility/common.h"
-#include "selection.h" // For gmx::SelectionList
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
 
 struct gmx_ana_indexgrps_t;
 struct t_pbc;

diff --git a/src/gromacs/selection/selectionenums.h b/src/gromacs/selection/selectionenums.h
index d401ac56c175fc604040697d1b206e01d787ce6f..2523ea8876d6e0479984ef1251be6663d54eae38 100644 (file)
--- a/src/gromacs/selection/selectionenums.h
+++ b/src/gromacs/selection/selectionenums.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_SELECTION_SELECTIONENUMS_H
 #define GMX_SELECTION_SELECTIONENUMS_H
 
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
 
 /*! \brief
  * Defines the type of covered fraction.

diff --git a/src/gromacs/selection/selectionfileoption.h b/src/gromacs/selection/selectionfileoption.h
index 324d33fdc7f84ffefc4be373c6ecab1a3b021e2d..369d6256dbb50bf3c15f2a17fe1676467fc081a1 100644 (file)
--- a/src/gromacs/selection/selectionfileoption.h
+++ b/src/gromacs/selection/selectionfileoption.h
@@ -43,7 +43,7 @@
 #ifndef GMX_SELECTION_SELECTIONFILEOPTION_H
 #define GMX_SELECTION_SELECTIONFILEOPTION_H
 
-#include "../options/abstractoption.h"
+#include "gromacs/options/abstractoption.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selectionfileoptionstorage.h b/src/gromacs/selection/selectionfileoptionstorage.h
index ac628bf7ba26a7b47ab034a0614b2ed883d8dbb5..9d877945982e7116c878598a8f8e12467059afaf 100644 (file)
--- a/src/gromacs/selection/selectionfileoptionstorage.h
+++ b/src/gromacs/selection/selectionfileoptionstorage.h
@@ -42,8 +42,8 @@
 #ifndef GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
 #define GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
 
-#include "../options/abstractoptionstorage.h"
-#include "selectionfileoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/selection/selectionfileoption.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selectionoption.cpp b/src/gromacs/selection/selectionoption.cpp
index 923384d7e7fc2d1adaa9cd23510a4faa5d1e6543..f278723cc104fdc28ff49f818d4231a5cb29a201 100644 (file)
--- a/src/gromacs/selection/selectionoption.cpp
+++ b/src/gromacs/selection/selectionoption.cpp
@@ -42,19 +42,20 @@
 #include "gmxpre.h"
 
 #include "selectionoption.h"
-#include "selectionfileoption.h"
-#include "selectionoptionstorage.h"
-#include "selectionfileoptionstorage.h"
 
 #include <string>
 
 #include "gromacs/options/optionmanagercontainer.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionfileoption.h"
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
 
+#include "selectionfileoptionstorage.h"
+#include "selectionoptionstorage.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/selection/selectionoption.h b/src/gromacs/selection/selectionoption.h
index 4655585f37ce9b180e3b7a4807c6b1bedb90734a..0af37dddc73c36cb077d3446a9cbdc692321170a 100644 (file)
--- a/src/gromacs/selection/selectionoption.h
+++ b/src/gromacs/selection/selectionoption.h
@@ -43,10 +43,9 @@
 #ifndef GMX_SELECTION_SELECTIONOPTION_H
 #define GMX_SELECTION_SELECTIONOPTION_H
 
-#include "../options/abstractoption.h"
-
-#include "selection.h"
-#include "selectionenums.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selectionoptionmanager.cpp b/src/gromacs/selection/selectionoptionmanager.cpp
index a545c6736398def96b2e867aa86bc6e26e471cd9..ee1e486d0ca9a386830d49d836c820095b220e6b 100644 (file)
--- a/src/gromacs/selection/selectionoptionmanager.cpp
+++ b/src/gromacs/selection/selectionoptionmanager.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
-#include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/selection/selectionoption.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/selection/selectionoptionmanager.h b/src/gromacs/selection/selectionoptionmanager.h
index ec26193b58876a7a4e5ffae6a44622fa0a61dfa6..66a075dcafe8901138f90ac77fa3d56102a71984 100644 (file)
--- a/src/gromacs/selection/selectionoptionmanager.h
+++ b/src/gromacs/selection/selectionoptionmanager.h
@@ -45,8 +45,8 @@
 
 #include <string>
 
-#include "../options/options.h"
-#include "../utility/common.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selectionoptionstorage.h b/src/gromacs/selection/selectionoptionstorage.h
index fb9300d2b10eda04dba0e7fb1bb3ad5271c44c95..41ef1488dbf40c4b692b401fd18bab23f0e0b306 100644 (file)
--- a/src/gromacs/selection/selectionoptionstorage.h
+++ b/src/gromacs/selection/selectionoptionstorage.h
@@ -44,10 +44,10 @@
 
 #include <string>
 
-#include "../options/optionstoragetemplate.h"
-#include "selection.h"
-#include "selectionenums.h"
-#include "selectionoption.h"
+#include "gromacs/options/optionstoragetemplate.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/selection/selectionoption.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selelem.cpp b/src/gromacs/selection/selelem.cpp
index 367737e3389a57a7834b3cb6ff62126ff8276a59..76f65be97163fdfe2d6db303ef3eda0297ed12fc 100644 (file)
--- a/src/gromacs/selection/selelem.cpp
+++ b/src/gromacs/selection/selelem.cpp
@@ -41,12 +41,12 @@
  */
 #include "gmxpre.h"
 
+#include "selelem.h"
+
 #include <cstring>
 
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
@@ -54,7 +54,7 @@
 
 #include "keywords.h"
 #include "mempool.h"
-#include "selelem.h"
+#include "poscalc.h"
 #include "selmethod.h"
 
 /*!

diff --git a/src/gromacs/selection/selelem.h b/src/gromacs/selection/selelem.h
index 1a1e86bf611d7644c65de9dcf8748dfb27d0f97e..ddc429850f7f3e8d7d2a89a33a72afad46d54e37 100644 (file)
--- a/src/gromacs/selection/selelem.h
+++ b/src/gromacs/selection/selelem.h
@@ -53,10 +53,10 @@
 
 #include <boost/shared_ptr.hpp>
 
+#include "gromacs/selection/indexutil.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/real.h"
 
-#include "indexutil.h"
 #include "selvalue.h"
 
 struct gmx_ana_poscalc_t;

diff --git a/src/gromacs/selection/selhelp.cpp b/src/gromacs/selection/selhelp.cpp
index 0b707c8b2793b01c750a9126e2e78ef295b39362..4a52815f378e9bc15b1bf8cc47196309d4dc19ff 100644 (file)
--- a/src/gromacs/selection/selhelp.cpp
+++ b/src/gromacs/selection/selhelp.cpp
@@ -41,9 +41,11 @@
  */
 #include "gmxpre.h"
 
+#include "selhelp.h"
+
 #include <string>
-#include <vector>
 #include <utility>
+#include <vector>
 
 #include <boost/scoped_ptr.hpp>
 
@@ -53,7 +55,6 @@
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "selhelp.h"
 #include "selmethod.h"
 #include "symrec.h"
 

diff --git a/src/gromacs/selection/selhelp.h b/src/gromacs/selection/selhelp.h
index 225434b3f961c30f678ec68d6070977f6361777f..b29251d31aaf2f2cd1438117570388b8110dfc22 100644 (file)
--- a/src/gromacs/selection/selhelp.h
+++ b/src/gromacs/selection/selhelp.h
@@ -43,7 +43,7 @@
 #ifndef GMX_SELECTION_SELHELP_H
 #define GMX_SELECTION_SELHELP_H
 
-#include "../onlinehelp/helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/selmethod.cpp b/src/gromacs/selection/selmethod.cpp
index b8a8645a9b6a03925b94690505aeff34a70a0f53..6524f2fec92f83ed86e2b1fb37d06e5cd7a79f86 100644 (file)
--- a/src/gromacs/selection/selmethod.cpp
+++ b/src/gromacs/selection/selmethod.cpp
@@ -41,12 +41,12 @@
  */
 #include "gmxpre.h"
 
+#include "selmethod.h"
+
 #include <ctype.h>
 #include <stdarg.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 

diff --git a/src/gromacs/selection/selparam.h b/src/gromacs/selection/selparam.h
index 9f471ccf5ea4c3ec9e018df9dca833b006a42dd2..bedfaadff149383a59ebaa2244d09845a953d1ce 100644 (file)
--- a/src/gromacs/selection/selparam.h
+++ b/src/gromacs/selection/selparam.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,7 +48,8 @@
 #ifndef GMX_SELECTION_SELPARAM_H
 #define GMX_SELECTION_SELPARAM_H
 
-#include "indexutil.h"
+#include "gromacs/selection/indexutil.h"
+
 #include "selvalue.h"
 
 /*! \name Parameter flags

diff --git a/src/gromacs/selection/selvalue.cpp b/src/gromacs/selection/selvalue.cpp
index c41ba668a9a4b1888a0275aa2734aaa932e9a5c5..86edfba070fa72c3cc207e17c3c6094c53aed62c 100644 (file)
--- a/src/gromacs/selection/selvalue.cpp
+++ b/src/gromacs/selection/selvalue.cpp
@@ -41,9 +41,10 @@
  */
 #include "gmxpre.h"
 
+#include "selvalue.h"
+
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selvalue.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/selection/selvalue.h b/src/gromacs/selection/selvalue.h
index 759fdfc046cae5556495896e95aa6a69ce798433..63f260b2b417c296027b52723eb8e5f5ba448c42 100644 (file)
--- a/src/gromacs/selection/selvalue.h
+++ b/src/gromacs/selection/selvalue.h
@@ -45,7 +45,7 @@
 #ifndef GMX_SELECTION_SELVALUE_H
 #define GMX_SELECTION_SELVALUE_H
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 /** Defines the value type of a different selection objects. */
 typedef enum

diff --git a/src/gromacs/selection/sm_compare.cpp b/src/gromacs/selection/sm_compare.cpp
index 5ff24d7423257fcf202f56e770a027e0b81c7590..51aa8a6d47d49c7efb9d2f57aef3784c23f3d1dd 100644 (file)
--- a/src/gromacs/selection/sm_compare.cpp
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -44,13 +44,13 @@
 #include <cmath>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/utilities.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "selmethod.h"
+
 /** Defines the comparison operator for comparison expressions. */
 typedef enum
 {

diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp
index a7725533f3d045bb5e5fa832877fc5e54ff4d8ca..636d28c1124a042945426a1dcbb3be9267c6ec9a 100644 (file)
--- a/src/gromacs/selection/sm_distance.cpp
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -45,13 +45,13 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/nbsearch.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 
+#include "selmethod.h"
+
 /*! \internal
  * \brief
  * Data structure for distance-based selection method.

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 1c37cb4b32000056de23cc6222ad19a29d0fdb70..9c163e097f2db673c3f30e10791c1e66af9a0ae1 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -114,12 +114,11 @@
  */
 #include "gmxpre.h"
 
-#include <algorithm>
-
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
+#include <algorithm>
 
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -127,11 +126,11 @@
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "selelem.h"
+#include "selmethod.h"
 
 using std::min;
 using std::max;

diff --git a/src/gromacs/selection/sm_keywords.cpp b/src/gromacs/selection/sm_keywords.cpp
index 13d126ca455a76bca473b182ca1e045fa2aafc9a..32d478ed00bfd63ae5f1de79aba80027d0721198 100644 (file)
--- a/src/gromacs/selection/sm_keywords.cpp
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -50,19 +50,18 @@
 #include <boost/shared_ptr.hpp>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxregex.h"
 #include "gromacs/utility/messagestringcollector.h"
-#include "gromacs/utility/stringutil.h"
 #include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
 #include "parsetree.h"
 #include "scanner.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \brief
  * Allocates data for integer keyword evaluation.

diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index 828bea37d4bbbae324fd2ed743b1421d249ab56e..9c8d2e3041d188cb7d6936a48bf825b7f1b52446 100644 (file)
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -42,14 +42,14 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "selmethod.h"
+
 /*! \internal \brief
  * Data structure for the merging selection modifiers.
  */

diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp
index ebd7c72b5adcb3f49828e4574dffa37baa6e2ea6..a4f52fe150e3e97b472a5e59996b4446153778f5 100644 (file)
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -42,14 +42,14 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "selmethod.h"
+
 /*! \internal \brief
  * Data structure for the \p permute selection modifier.
  */

diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp
index b0108818469d6d71ad80ac89c69f5c039ff293a9..3a92f82d69edb8972e5f757fc4a59920de4de58b 100644 (file)
--- a/src/gromacs/selection/sm_position.cpp
+++ b/src/gromacs/selection/sm_position.cpp
@@ -42,16 +42,15 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
+#include "poscalc.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \internal \brief
  * Data structure for position keyword evaluation.

diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index 5009ede9576c96d86e528ebaf5998cd7b34e7a87..cb8126171bb215283086f6f3dc560c3458187d5d 100644 (file)
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -44,14 +44,13 @@
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
 #include "parsetree.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \internal
  * \brief

diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index 709aa247b74494641e13c65b4540828d621cf506..de1a6fc650d4a5e3890397d3f13296da2f5d41b8 100644 (file)
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -44,12 +44,12 @@
 #include <cctype>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/topology/topology.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/topology/topology.h"
 #include "gromacs/utility/exceptions.h"
 
+#include "selmethod.h"
+
 /** Evaluates the \p all selection keyword. */
 static void
 evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,

diff --git a/src/gromacs/selection/symrec.cpp b/src/gromacs/selection/symrec.cpp
index 3df67883dbfcd9469f305ae734dba1f8c86393ff..cd648f60efc0261e932ed93050c6a9b20a44774d 100644 (file)
--- a/src/gromacs/selection/symrec.cpp
+++ b/src/gromacs/selection/symrec.cpp
@@ -41,12 +41,13 @@
  */
 #include "gmxpre.h"
 
+#include "symrec.h"
+
 #include <map>
 #include <string>
 #include <utility>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
@@ -54,7 +55,6 @@
 
 #include "poscalc.h"
 #include "selelem.h"
-#include "symrec.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/tests/indexutil.cpp b/src/gromacs/selection/tests/indexutil.cpp
index caf5d0462ded16fe05aa5b9c877a66d54aba4e71..5efd13423eae867ad77bb32c1708d92d2010c96a 100644 (file)
--- a/src/gromacs/selection/tests/indexutil.cpp
+++ b/src/gromacs/selection/tests/indexutil.cpp
@@ -44,9 +44,10 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/indexutil.h"
+
 #include <gtest/gtest.h>
 
-#include "gromacs/selection/indexutil.h"
 #include "gromacs/topology/block.h"
 
 #include "testutils/refdata.h"

diff --git a/src/gromacs/selection/tests/nbsearch.cpp b/src/gromacs/selection/tests/nbsearch.cpp
index ac7cba62a518b9b0cb901c33844d53faec7299d8..c3bc49f92bcedf882bc0f06a7e9a9739b05a7561 100644 (file)
--- a/src/gromacs/selection/tests/nbsearch.cpp
+++ b/src/gromacs/selection/tests/nbsearch.cpp
@@ -48,8 +48,6 @@
 
 #include "gromacs/selection/nbsearch.h"
 
-#include <gtest/gtest.h>
-
 #include <cmath>
 
 #include <algorithm>
@@ -57,6 +55,8 @@
 #include <numeric>
 #include <vector>
 
+#include <gtest/gtest.h>
+
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"

diff --git a/src/gromacs/selection/tests/poscalc.cpp b/src/gromacs/selection/tests/poscalc.cpp
index 4ca53be929923da0a1609e23d636cfffb0ea1df4..1608a5b11b599847c823f1db12454413dfca30ca 100644 (file)
--- a/src/gromacs/selection/tests/poscalc.cpp
+++ b/src/gromacs/selection/tests/poscalc.cpp
@@ -41,14 +41,15 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
+#include "gromacs/selection/poscalc.h"
 
 #include <vector>
 
+#include <gtest/gtest.h>
+
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/selection/tests/selectioncollection.cpp b/src/gromacs/selection/tests/selectioncollection.cpp
index 4e252346f9894e0c37ff6b3e458fa18792f93762..9e6fd86281b473c7d77929ad4c57422547526ea8 100644 (file)
--- a/src/gromacs/selection/tests/selectioncollection.cpp
+++ b/src/gromacs/selection/tests/selectioncollection.cpp
@@ -41,13 +41,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/selectioncollection.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arrayref.h"

diff --git a/src/gromacs/selection/tests/selectionoption.cpp b/src/gromacs/selection/tests/selectionoption.cpp
index 072170fccf37ee7268ffd9c82ea9e848569b33ba..8f3397cf430bc0a8c24c4747eda61281009b75fc 100644 (file)
--- a/src/gromacs/selection/tests/selectionoption.cpp
+++ b/src/gromacs/selection/tests/selectionoption.cpp
@@ -41,6 +41,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/selectionoption.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/options/options.h"
@@ -48,7 +50,6 @@
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selectionfileoption.h"
-#include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/utility/exceptions.h"
 

diff --git a/src/gromacs/selection/tests/toputils.cpp b/src/gromacs/selection/tests/toputils.cpp
index b27c636f09a005de1409942fba3c93e9713e2185..eff1e0c3560af5c52fd69eac7fbb3c92742a0655 100644 (file)
--- a/src/gromacs/selection/tests/toputils.cpp
+++ b/src/gromacs/selection/tests/toputils.cpp
@@ -45,10 +45,10 @@
 
 #include <cstring>
 
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h b/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
index 8508941b56efa8fca266f18bc402325094d7c8f5..67418f98d06262d4c323be355a6456c1d31b61f1 100644 (file)
--- a/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
+++ b/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_INTEL_MIC_H
 #define GMX_SIMD_IMPL_INTEL_MIC_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* Intel Xeon Phi, or
  * the-artist-formerly-known-as-Knight's-corner, or

diff --git a/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h b/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
index 195fdbc2953715e4ff60e28373f6c1663a749d15..e19320add3d7f9a00ac0618a3b1ea6cac4bdced7 100644 (file)
--- a/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
+++ b/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX2_256_H
 #define GMX_SIMD_IMPL_X86_AVX2_256_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* x86 256-bit AVX2 SIMD instruction wrappers
  *

diff --git a/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h b/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
index 7c946d10d257af1a549ebe4238dfd36e725168a0..c13e847ffa6659c6bf5dc1ea511206c6c4993062 100644 (file)
--- a/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
+++ b/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
@@ -36,12 +36,13 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX_128_FMA_H
 #define GMX_SIMD_IMPL_X86_AVX_128_FMA_H
 
+#include "config.h"
+
 #include <math.h>
+
 #include <immintrin.h>
 #include <x86intrin.h>
 
-#include "config.h"
-
 /* x86 128-bit AVX with FMA SIMD instruction wrappers
  *
  * Please see documentation in gromacs/simd/simd.h for details

diff --git a/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h b/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
index e688d14c94d7beb4678777131968fea812f595de..999b417d6899ce2fdf1da590f279546262a1b193 100644 (file)
--- a/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
+++ b/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX_256_H
 #define GMX_SIMD_IMPL_X86_AVX_256_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* It is cleaner to start the AVX implementation from scratch rather than
  * first inheriting from SSE4.1, which in turn inherits from SSE2. However,

diff --git a/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h b/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
index c16d3d4d576793cf9f01115e4657026d210b18b0..2d3f908f56e626e6479bd6d16f7f44a1cf1992c3 100644 (file)
--- a/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
+++ b/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_SSE2_H
 #define GMX_SIMD_IMPL_X86_SSE2_H
 
+#include "config.h"
+
 #include <math.h>
-#include <emmintrin.h>
 
-#include "config.h"
+#include <emmintrin.h>
 
 /* Set capabilities that can be inherited */
 #define GMX_SIMD_X86_SSE2_OR_HIGHER

diff --git a/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h b/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
index 91bef05ac67b02b077287895fd12a5590fa83df3..8b8384a835a7e42cedcfeda76abea73d1bb9ba90 100644 (file)
--- a/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
+++ b/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_SSE4_1_H
 #define GMX_SIMD_IMPL_X86_SSE4_1_H
 
+#include "config.h"
+
 #include <math.h>
-#include <smmintrin.h>
 
-#include "config.h"
+#include <smmintrin.h>
 
 /* x86 SSE4.1 SIMD instruction wrappers
  *

diff --git a/src/gromacs/simd/math_x86_avx_128_fma_double.h b/src/gromacs/simd/math_x86_avx_128_fma_double.h
index fed6d546946bda6576d1216ff83f5a521c51627b..9ee80edbd7acbfabeb82067134cd6a67a125b622 100644 (file)
--- a/src/gromacs/simd/math_x86_avx_128_fma_double.h
+++ b/src/gromacs/simd/math_x86_avx_128_fma_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
 #define GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_avx_128_fma_single.h b/src/gromacs/simd/math_x86_avx_128_fma_single.h
index fc7113dd3a426f645a9f18890b2cb6d254ad10fc..014508d9773fea2cc8e195dc5c7bcb29254c33e2 100644 (file)
--- a/src/gromacs/simd/math_x86_avx_128_fma_single.h
+++ b/src/gromacs/simd/math_x86_avx_128_fma_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
 #define GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_avx_256_double.h b/src/gromacs/simd/math_x86_avx_256_double.h
index 8eb7941765156707b4f48af3517ed8254609c8ba..6a1963cbaf31ecd64d68956b4bcade8ca7fd42e5 100644 (file)
--- a/src/gromacs/simd/math_x86_avx_256_double.h
+++ b/src/gromacs/simd/math_x86_avx_256_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_256_DOUBLE_H
 #define GMX_SIMD_MATH_AVX_256_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_avx_256_single.h b/src/gromacs/simd/math_x86_avx_256_single.h
index b23712a2595d9eff9a19c4e6da4a851ced18b939..ad72a1057955088188bbaead4c124a0994923cae 100644 (file)
--- a/src/gromacs/simd/math_x86_avx_256_single.h
+++ b/src/gromacs/simd/math_x86_avx_256_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_256_SINGLE_H
 #define GMX_SIMD_MATH_AVX_256_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_sse2_double.h b/src/gromacs/simd/math_x86_sse2_double.h
index 9332dc3d3666a752f3b9a7363082b3e4c77c4532..857f4ee2ef58d6c18ade96bd500df00249542a29 100644 (file)
--- a/src/gromacs/simd/math_x86_sse2_double.h
+++ b/src/gromacs/simd/math_x86_sse2_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE2_DOUBLE_H
 #define GMX_SIMD_MATH_SSE2_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_sse2_single.h b/src/gromacs/simd/math_x86_sse2_single.h
index 054fd2c1bc8261c1ba27258171635259183706a1..67ebf7f7cd2104fbd5e966655d69ee61b12a6f3c 100644 (file)
--- a/src/gromacs/simd/math_x86_sse2_single.h
+++ b/src/gromacs/simd/math_x86_sse2_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE2_SINGLE_H
 #define GMX_SIMD_MATH_SSE2_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_sse4_1_double.h b/src/gromacs/simd/math_x86_sse4_1_double.h
index 4d8955a51c1ca87d1603e8b84a7110eed5eedddb..e7f7a06249b02e64a35ef65988cc836a536cc9fd 100644 (file)
--- a/src/gromacs/simd/math_x86_sse4_1_double.h
+++ b/src/gromacs/simd/math_x86_sse4_1_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE4_1_DOUBLE_H
 #define GMX_SIMD_MATH_SSE4_1_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/math_x86_sse4_1_single.h b/src/gromacs/simd/math_x86_sse4_1_single.h
index 2fbdf23b3aa76f1f4b274c2e92d80cec3abee377..7c78dd57b9510d11b361b63f82d64b3a548558b0 100644 (file)
--- a/src/gromacs/simd/math_x86_sse4_1_single.h
+++ b/src/gromacs/simd/math_x86_sse4_1_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE4_1_SINGLE_H
 #define GMX_SIMD_MATH_SSE4_1_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need

diff --git a/src/gromacs/simd/simd.h b/src/gromacs/simd/simd.h
index a979fd3e45ad930a0f14bcc11af13eae5dccd09b..988ae650443687edb7081b09c90a14cbaa6e6bb3 100644 (file)
--- a/src/gromacs/simd/simd.h
+++ b/src/gromacs/simd/simd.h
@@ -112,32 +112,32 @@ static gmx_inline double * gmx_simd4_align_d(double *p);
  * file with different SIMD definitions for different files.
  */
 #if defined __MIC__
-#    include "gromacs/simd/impl_intel_mic/impl_intel_mic.h"
+#    include "impl_intel_mic/impl_intel_mic.h"
 #elif defined GMX_SIMD_X86_AVX2_256
-#    include "gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h"
+#    include "impl_x86_avx2_256/impl_x86_avx2_256.h"
 #elif defined GMX_SIMD_X86_AVX_256
-#    include "gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h"
+#    include "impl_x86_avx_256/impl_x86_avx_256.h"
 #elif defined GMX_SIMD_X86_AVX_128_FMA
-#    include "gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
+#    include "impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
 #elif defined GMX_SIMD_X86_SSE4_1
-#    include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h"
+#    include "impl_x86_sse4_1/impl_x86_sse4_1.h"
 #elif defined GMX_SIMD_X86_SSE2
-#    include "gromacs/simd/impl_x86_sse2/impl_x86_sse2.h"
+#    include "impl_x86_sse2/impl_x86_sse2.h"
 #elif defined GMX_SIMD_ARM_NEON
-#    include "gromacs/simd/impl_arm_neon/impl_arm_neon.h"
+#    include "impl_arm_neon/impl_arm_neon.h"
 #elif defined GMX_SIMD_ARM_NEON_ASIMD
-#    include "gromacs/simd/impl_arm_neon_asimd/impl_arm_neon_asimd.h"
+#    include "impl_arm_neon_asimd/impl_arm_neon_asimd.h"
 #elif defined GMX_SIMD_IBM_QPX
-#    include "gromacs/simd/impl_ibm_qpx/impl_ibm_qpx.h"
+#    include "impl_ibm_qpx/impl_ibm_qpx.h"
 #elif defined GMX_SIMD_SPARC64_HPC_ACE
-#    include "gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
+#    include "impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
 #elif (defined GMX_SIMD_REFERENCE) || (defined DOXYGEN)
 /* Plain C SIMD reference implementation, also serves as documentation.
  * For now this code path will also be taken for Sparc64_HPC_ACE since we have
  * not yet added the verlet kernel extensions there. The group kernels do not
  * depend on this file, so they will still be accelerated with SIMD.
  */
-#    include "gromacs/simd/impl_reference/impl_reference.h"
+#    include "impl_reference/impl_reference.h"
 #else
 /* Turn off the GMX_SIMD flag if we do not even have reference support */
 #    undef GMX_SIMD

diff --git a/src/gromacs/simd/simd_math.h b/src/gromacs/simd/simd_math.h
index 177aed4b07650c0e6ae2a6f922e46e327ea7a443..85d545c3d0e25c842eab857e6dfb18118221926c 100644 (file)
--- a/src/gromacs/simd/simd_math.h
+++ b/src/gromacs/simd/simd_math.h
@@ -55,13 +55,13 @@
  * \ingroup module_simd
  */
 
+#include "config.h"
+
 #include <math.h>
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/simd/simd.h"
 
-#include "config.h"
-
 /*! \cond libapi */
 /*! \addtogroup module_simd */
 /*! \{ */

diff --git a/src/gromacs/simd/tests/base.cpp b/src/gromacs/simd/tests/base.cpp
index fed78480451ca1e032ad9fdff1ca83e4e0c1043a..115707363a3cdad89c9379bd84eef2fef2dd2cf9 100644 (file)
--- a/src/gromacs/simd/tests/base.cpp
+++ b/src/gromacs/simd/tests/base.cpp
@@ -34,13 +34,14 @@
  */
 #include "gmxpre.h"
 
+#include "base.h"
+
 #include <math.h>
 
-#include "testutils/testoptions.h"
-#include "gromacs/options/options.h"
 #include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
 
-#include "base.h"
+#include "testutils/testoptions.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/simd/tests/simd.h b/src/gromacs/simd/tests/simd.h
index 551546fbf69dc3e4ce778ce752a04a96a6ea19dd..26cdf9e74bc695dc0b05db3898ee3403dc75b215 100644 (file)
--- a/src/gromacs/simd/tests/simd.h
+++ b/src/gromacs/simd/tests/simd.h
@@ -75,7 +75,9 @@
  * \ingroup module_simd
  */
 #include <vector>
+
 #include <gtest/gtest.h>
+
 #include "gromacs/simd/simd.h"
 
 #include "base.h"

diff --git a/src/gromacs/simd/tests/simd4.h b/src/gromacs/simd/tests/simd4.h
index 3f3df63154698ded482748208a90e904df7d3efd..83cb794a741f4b1ec7ecfe5a5233ea29c28a80c6 100644 (file)
--- a/src/gromacs/simd/tests/simd4.h
+++ b/src/gromacs/simd/tests/simd4.h
@@ -48,9 +48,12 @@
  */
 
 #include <vector>
+
 #include <gtest/gtest.h>
+
 #include "gromacs/simd/simd.h"
-#include "gromacs/simd/tests/base.h"
+
+#include "base.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/simd/tests/simd4_floatingpoint.cpp b/src/gromacs/simd/tests/simd4_floatingpoint.cpp
index c51c71532fcf960aa4aef037f5637899a1b2f5d6..68a448e3db70155b124f39bd4a5295d6a2a1857a 100644 (file)
--- a/src/gromacs/simd/tests/simd4_floatingpoint.cpp
+++ b/src/gromacs/simd/tests/simd4_floatingpoint.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/math/utilities.h"
 
 #include "simd4.h"

diff --git a/src/gromacs/simd/tests/simd4_math.cpp b/src/gromacs/simd/tests/simd4_math.cpp
index 3e6555c967c3c695108eac8a11930c0c1f091132..2345c037e41c106e06c46762da3189e0faa5d060 100644 (file)
--- a/src/gromacs/simd/tests/simd4_math.cpp
+++ b/src/gromacs/simd/tests/simd4_math.cpp
@@ -37,10 +37,11 @@
 #include "config.h"
 
 #include <vector>
+
 #include "gromacs/math/utilities.h"
+#include "gromacs/options/basicoptions.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
-#include "gromacs/options/basicoptions.h"
 
 #include "simd4.h"
 

diff --git a/src/gromacs/simd/tests/simd4_vector_operations.cpp b/src/gromacs/simd/tests/simd4_vector_operations.cpp
index 17a070b25e587662d10f3cc2fa865e341d89eee0..02a29afd3d06562d343f6b22237d4c11d12835ce 100644 (file)
--- a/src/gromacs/simd/tests/simd4_vector_operations.cpp
+++ b/src/gromacs/simd/tests/simd4_vector_operations.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/vector_operations.h"
 

diff --git a/src/gromacs/simd/tests/simd_floatingpoint.cpp b/src/gromacs/simd/tests/simd_floatingpoint.cpp
index f0d07034a3e656746d24c48e150e9a3970bcd034..fb0a3414829ebce88cdef235857e25908f1810b3 100644 (file)
--- a/src/gromacs/simd/tests/simd_floatingpoint.cpp
+++ b/src/gromacs/simd/tests/simd_floatingpoint.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/math/utilities.h"
 
 #include "simd.h"

diff --git a/src/gromacs/simd/tests/simd_math.cpp b/src/gromacs/simd/tests/simd_math.cpp
index 6899a9ee00a8ced742097268d5c95222bcfaab6e..17c61ce05e3b58c717182dd7cd10d070d25ce340 100644 (file)
--- a/src/gromacs/simd/tests/simd_math.cpp
+++ b/src/gromacs/simd/tests/simd_math.cpp
@@ -34,13 +34,15 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/simd/simd_math.h"
+
 #include "config.h"
 
 #include <vector>
+
 #include "gromacs/math/utilities.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/simd/simd_math.h"
 #include "gromacs/options/basicoptions.h"
+#include "gromacs/simd/simd.h"
 
 #include "simd.h"
 

diff --git a/src/gromacs/simd/tests/simd_vector_operations.cpp b/src/gromacs/simd/tests/simd_vector_operations.cpp
index 58c1e6f2af07bb05e602e40cef4e9bb1e9b886f3..9393c24c985e794d7db1850b1fcf5553cb14e583 100644 (file)
--- a/src/gromacs/simd/tests/simd_vector_operations.cpp
+++ b/src/gromacs/simd/tests/simd_vector_operations.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/vector_operations.h"
 

diff --git a/src/gromacs/simd/vector_operations.h b/src/gromacs/simd/vector_operations.h
index d24c25f4db80a4695609baf2b102a9dc891bac6d..30713524c7be42425d943e3808560c79de98b47e 100644 (file)
--- a/src/gromacs/simd/vector_operations.h
+++ b/src/gromacs/simd/vector_operations.h
@@ -46,10 +46,10 @@
 #ifndef GMX_SIMD_VECTOR_OPERATIONS_H
 #define GMX_SIMD_VECTOR_OPERATIONS_H
 
-#include "gromacs/simd/simd.h"
-
 #include "config.h"
 
+#include "gromacs/simd/simd.h"
+
 /*! \cond libapi */
 /*! \addtogroup module_simd */
 /*! \{ */

diff --git a/src/gromacs/statistics/statistics_test.c b/src/gromacs/statistics/statistics_test.c
index 7baff7bfaca5a48c364878649f7eb668cfbd83d8..4b3dbf8a6658ad5778971620707ecc09b0ee70d0 100644 (file)
--- a/src/gromacs/statistics/statistics_test.c
+++ b/src/gromacs/statistics/statistics_test.c
@@ -36,12 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include "statistics.h"
-
 #include <stdio.h>
 
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/swap/swapcoords.c b/src/gromacs/swap/swapcoords.c
index 734b13b5e73a7dcb9da596c706d5949b0ddcbf31..c81f4bba1e60d02a4894595dbe17c458c9e341f6 100644 (file)
--- a/src/gromacs/swap/swapcoords.c
+++ b/src/gromacs/swap/swapcoords.c
@@ -41,28 +41,28 @@
  */
 #include "gmxpre.h"
 
+#include "swapcoords.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/timing/wallcycle.h"
-#include "swapcoords.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *SwS      = {"SWAP:"};                                           /**< For output that comes from the swap module */
 static char *SwSEmpty = {"     "};                                           /**< Placeholder for multi-line output */

diff --git a/src/gromacs/timing/cyclecounter.c b/src/gromacs/timing/cyclecounter.c
index a48bf35aa1c42d69ca54fa6154cf1ac83bc7b036..780587e11477cca335e5de29aa0139d04aa0088a 100644 (file)
--- a/src/gromacs/timing/cyclecounter.c
+++ b/src/gromacs/timing/cyclecounter.c
@@ -37,10 +37,10 @@
 
 #include "cyclecounter.h"
 
-#include <time.h>
-
 #include "config.h"
 
+#include <time.h>
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif

diff --git a/src/gromacs/timing/cyclecounter.h b/src/gromacs/timing/cyclecounter.h
index fcacc5e2042bfc42d1fccfaf2d19b7f99ad3b3cc..4b3bede73610ad1a63a82d059f4bd4fa1f7956cd 100644 (file)
--- a/src/gromacs/timing/cyclecounter.h
+++ b/src/gromacs/timing/cyclecounter.h
@@ -148,8 +148,8 @@ typedef hrtime_t
 
 #elif defined(__xlC__) && defined (_AIX)
 /* AIX compilers */
-#include <sys/time.h>
 #include <sys/systemcfg.h>
+#include <sys/time.h>
 typedef unsigned long long
     gmx_cycles_t;
 

diff --git a/src/gromacs/timing/wallcycle.c b/src/gromacs/timing/wallcycle.c
index cedfaa6c83ca009c3207e13ce36def1e82d51c69..c6f468e3ed4bc0f89b584cd4b4769335b9c4b216 100644 (file)
--- a/src/gromacs/timing/wallcycle.c
+++ b/src/gromacs/timing/wallcycle.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/timing/wallcycle.h"
+#include "wallcycle.h"
 
 #include "config.h"
 
@@ -45,13 +45,12 @@
 
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/timing/cyclecounter.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "cyclecounter.h"
-
 /* DEBUG_WCYCLE adds consistency checking for the counters.
  * It checks if you stop a counter different from the last
  * one that was opened and if you do nest too deep.

diff --git a/src/gromacs/timing/wallcycle.h b/src/gromacs/timing/wallcycle.h
index 70b0341081876fd49ac1ef5ca8c3e0434601e096..a03a0ade68cbfb70c1b231e710e1a71328e00889 100644 (file)
--- a/src/gromacs/timing/wallcycle.h
+++ b/src/gromacs/timing/wallcycle.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/timing/walltime_accounting.c b/src/gromacs/timing/walltime_accounting.c
index d7c711127f606dddf1751301799992fe50c16d34..25c723d4d6a20a1aa902f3891bc3a6be99ec3c71 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.c
+++ b/src/gromacs/timing/walltime_accounting.c
@@ -37,10 +37,10 @@
 
 #include "walltime_accounting.h"
 
-#include <time.h>
-
 #include "config.h"
 
+#include <time.h>
+
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/timing/walltime_accounting.h b/src/gromacs/timing/walltime_accounting.h
index b80d138d8f724cc45de4ad059a20ab899a2e02ad..f131f26dd27e2acc5bed8ca7f01f3695b4d0641a 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.h
+++ b/src/gromacs/timing/walltime_accounting.h
@@ -38,7 +38,7 @@
 #ifndef GMX_TIMING_WALLTIME_ACCOUNTING_H
 #define GMX_TIMING_WALLTIME_ACCOUNTING_H
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 63fd7cffb1febdc80b25167c62ccd43ce9f83400..ddb578dc0693d8511d116dfa4bfbda00359ec5c9 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -40,31 +40,29 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/xtcio.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/tools/compare.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "compare.h"
-
 typedef struct {
     int bStep;
     int bTime;

diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c
index 7dfe7a93d6e0150efe78e4c841f92d8a06c5514b..e2ee20b87144d242f13f26c2f07daa73f2b58b33 100644 (file)
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.c
@@ -40,17 +40,18 @@
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/names.h"
+
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)
 {

diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 814f7ee1e441624840a549f3e142058a2a607b84..deaa798fced75621e8e528e696f73384ae3332b5 100644 (file)
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -38,25 +38,24 @@
 
 #include <math.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/gmxpreprocess/readir.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/utility/futil.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index 9c57a293d435a1c97bc95b4e9dd3b814e311bb25..302ce2652552c062758599bb1a9211f48ea39695 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -36,13 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/topology/atomprop.cpp b/src/gromacs/topology/atomprop.cpp
index 864c2855905520813381efc2e0a9fd478065583d..a2fdfece3e5efe715f5aab3f0c3d32139ee59be9 100644 (file)
--- a/src/gromacs/topology/atomprop.cpp
+++ b/src/gromacs/topology/atomprop.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/atomprop.h"
+#include "atomprop.h"
 
 #include <ctype.h>
 #include <string.h>

diff --git a/src/gromacs/topology/atomprop.h b/src/gromacs/topology/atomprop.h
index 33b0c60da845e6c479f9a476daf7029f1d6324ed..5723123ac7b15718670ebb5d5b4d81641e59c1b9 100644 (file)
--- a/src/gromacs/topology/atomprop.h
+++ b/src/gromacs/topology/atomprop.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_ATOMPROP_H
 #define GMX_TOPOLOGY_ATOMPROP_H
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/atoms.cpp b/src/gromacs/topology/atoms.cpp
index 0f4fada2355ea11375785f05e4c4c34f120a4c79..9d084240c26c8dede5e200df1f68552d4b521073 100644 (file)
--- a/src/gromacs/topology/atoms.cpp
+++ b/src/gromacs/topology/atoms.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/atoms.h"
+#include "atoms.h"
 
 #include <cstring>
 

diff --git a/src/gromacs/topology/atoms.h b/src/gromacs/topology/atoms.h
index 4a619b0eb7d68c7a3bbb95cf8af695eeb86e762d..ed8d96c2aedd73de512a27d1c6ffbed588855f2a 100644 (file)
--- a/src/gromacs/topology/atoms.h
+++ b/src/gromacs/topology/atoms.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_ATOMS_H
 #define GMX_TOPOLOGY_ATOMS_H
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/block.cpp b/src/gromacs/topology/block.cpp
index 9acf7ebe29680afe1e89ff8ba2887ea99228ab38..c4b2e51c27d4c9484129b0b1a8a642190d2a2100 100644 (file)
--- a/src/gromacs/topology/block.cpp
+++ b/src/gromacs/topology/block.cpp
@@ -36,8 +36,9 @@
  */
 #include "gmxpre.h"
 
+#include "block.h"
+
 #include <algorithm>
-#include "gromacs/topology/block.h"
 
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/topology/block.h b/src/gromacs/topology/block.h
index 599a4bd901157e2f5825c914a3ce274219c7f539..a3680e1a62a9d5e3ae4c04a7f824aa67266e3f5d 100644 (file)
--- a/src/gromacs/topology/block.h
+++ b/src/gromacs/topology/block.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_BLOCK_H
 #define GMX_TOPOLOGY_BLOCK_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/idef.h b/src/gromacs/topology/idef.h
index 00ce01cd6dcda9fb43ba54902b0b3798b97d3a34..aaac95175fa4ef19e84fe86f36abde60f042fc58 100644 (file)
--- a/src/gromacs/topology/idef.h
+++ b/src/gromacs/topology/idef.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_IDEF_H
 #define GMX_TOPOLOGY_IDEF_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/index.cpp b/src/gromacs/topology/index.cpp
index 615c38a1bf6c9c1b973c740794ca1b7f2ec273d3..153554d9009fab4e086fdfa0b3157bcd9366675a 100644 (file)
--- a/src/gromacs/topology/index.cpp
+++ b/src/gromacs/topology/index.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/index.h"
+#include "index.h"
 
 #include <assert.h>
 #include <ctype.h>
@@ -45,11 +45,10 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"

diff --git a/src/gromacs/topology/index.h b/src/gromacs/topology/index.h
index 4bba1f80217541ebd406653a493be3fa0698d0c2..e361be73d5e3f819e5ea5d42962c07bb6478c448 100644 (file)
--- a/src/gromacs/topology/index.h
+++ b/src/gromacs/topology/index.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/invblock.c b/src/gromacs/topology/invblock.c
index c41dd0c0f81398a236f33e4670f1255cb498cf29..48107b2c5f82b2b7116f38add9b08e9d4a18f10c 100644 (file)
--- a/src/gromacs/topology/invblock.c
+++ b/src/gromacs/topology/invblock.c
@@ -37,10 +37,9 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/topology/invblock.h"
+#include "invblock.h"
 
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/topology/invblock.h b/src/gromacs/topology/invblock.h
index a3c79c7edd32e3b6d873ee16eda9e521fc5f1ca3..f30e98a95798c3229de2bd245d4b3f5b466171ab 100644 (file)
--- a/src/gromacs/topology/invblock.h
+++ b/src/gromacs/topology/invblock.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_INVBLOCK_H
 #define GMX_TOPOLOGY_INVBLOCK_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/mtop_util.c b/src/gromacs/topology/mtop_util.c
index 622d4e46fe12aedc33370adc5b215e96eb4bbc20..b069c64419ed63d48d8fbfa2b16773b61cc654d9 100644 (file)
--- a/src/gromacs/topology/mtop_util.c
+++ b/src/gromacs/topology/mtop_util.c
@@ -34,14 +34,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/mtop_util.h"
+#include "mtop_util.h"
 
 #include <stdlib.h>
 #include <string.h>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/topology/mtop_util.h b/src/gromacs/topology/mtop_util.h
index a0cfef1aff277f1ea6e09ea8a5dc174a636ced67..308476ea764b87d249d83d201d3b0f2d56982bb8 100644 (file)
--- a/src/gromacs/topology/mtop_util.h
+++ b/src/gromacs/topology/mtop_util.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
 #define GMX_TOPOLOGY_MTOP_UTIL_H
 
-#include "../legacyheaders/types/inputrec.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/residuetypes.cpp b/src/gromacs/topology/residuetypes.cpp
index 5bf67099a38ebe260e675ee2d7314c2d51896093..6745c96d378d69f9799c85fb6b94a2a6d0320414 100644 (file)
--- a/src/gromacs/topology/residuetypes.cpp
+++ b/src/gromacs/topology/residuetypes.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/residuetypes.h"
+#include "residuetypes.h"
 
 #include <cassert>
 #include <cstdio>

diff --git a/src/gromacs/topology/symtab.cpp b/src/gromacs/topology/symtab.cpp
index 35134a5134a9350b26c3256bd9efd8303ee30e1c..678088f47842a79d9eacfc45b67dfead0d784115 100644 (file)
--- a/src/gromacs/topology/symtab.cpp
+++ b/src/gromacs/topology/symtab.cpp
@@ -44,7 +44,6 @@
 #include <algorithm>
 
 #include "gromacs/legacyheaders/txtdump.h"
-
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/topology/topology.cpp b/src/gromacs/topology/topology.cpp
index e554a942401246c8c79f7218720a6b97e788f5e9..e5ff05371d40f97d7c97d4871b02bc97f7470727 100644 (file)
--- a/src/gromacs/topology/topology.cpp
+++ b/src/gromacs/topology/topology.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/topology.h"
+#include "topology.h"
 
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/topology/topology.h b/src/gromacs/topology/topology.h
index b961fd932f8b762e51cc39bdc7b493ee0bce7b95..6f4e4792d47133634de53c4fa2f3545a13bbc24c 100644 (file)
--- a/src/gromacs/topology/topology.h
+++ b/src/gromacs/topology/topology.h
@@ -37,11 +37,11 @@
 #ifndef GMX_TOPOLOGY_TOPOLOGY_H
 #define GMX_TOPOLOGY_TOPOLOGY_H
 
-#include "../math/vectypes.h"
-#include "atoms.h"
-#include "block.h"
-#include "idef.h"
-#include "symtab.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/symtab.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/topology/topsort.c b/src/gromacs/topology/topsort.c
index 8f1a00783183fc85102a083e5b2f0b9d4495efc7..1f8749916616d201eb55eb5b309eda5f7fe0ee80 100644 (file)
--- a/src/gromacs/topology/topsort.c
+++ b/src/gromacs/topology/topsort.c
@@ -36,12 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/topsort.h"
+#include "topsort.h"
 
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
-
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/trajectoryanalysis.h b/src/gromacs/trajectoryanalysis.h
index 3a33b0d2cbf5bb6d0c98ee7d89f7d29607b28067..a79edd567ace198f30587eb3c25f9ec664c536ba 100644 (file)
--- a/src/gromacs/trajectoryanalysis.h
+++ b/src/gromacs/trajectoryanalysis.h
@@ -276,17 +276,16 @@
 #ifndef GMX_TRAJECTORYANALYSIS_H
 #define GMX_TRAJECTORYANALYSIS_H
 
-#include "analysisdata.h"
-#include "options.h"
-#include "selection.h"
-
-#include "fileio/trx.h"
-#include "selection/nbsearch.h"
-#include "topology/topology.h"
-#include "trajectoryanalysis/analysismodule.h"
-#include "trajectoryanalysis/analysissettings.h"
-#include "trajectoryanalysis/cmdlinerunner.h"
-#include "utility/arrayref.h"
-#include "utility/exceptions.h"
+#include "gromacs/analysisdata.h"
+#include "gromacs/options.h"
+#include "gromacs/selection.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
 
 #endif

diff --git a/src/gromacs/trajectoryanalysis/analysismodule.cpp b/src/gromacs/trajectoryanalysis/analysismodule.cpp
index 01d73254f6c6204bbe15e7e54b9cf5689bbb279c..a64a95fec7ec0f53d213d9beefd50f054e69c060 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysismodule.cpp
+++ b/src/gromacs/trajectoryanalysis/analysismodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "analysismodule.h"
 
 #include <utility>
 

diff --git a/src/gromacs/trajectoryanalysis/analysismodule.h b/src/gromacs/trajectoryanalysis/analysismodule.h
index af1cfbbf18bfeb1b86b5996f626ab93514fab5ce..a3846214b7ea14b2282c5857d3e6bd6c0a12c02d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysismodule.h
+++ b/src/gromacs/trajectoryanalysis/analysismodule.h
@@ -49,8 +49,8 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
 
 struct t_pbc;
 struct t_trxframe;

diff --git a/src/gromacs/trajectoryanalysis/analysissettings-impl.h b/src/gromacs/trajectoryanalysis/analysissettings-impl.h
index a19c73b0ab81e1f3e1117499eb9a33b9480ee319..b42defaaa610f6e899c34e627f51a58e96a3fa9a 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings-impl.h
+++ b/src/gromacs/trajectoryanalysis/analysissettings-impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,10 +42,9 @@
 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
 #define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
 
-#include "analysissettings.h"
-
-#include "../analysisdata/modules/plot.h"
-#include "../options/timeunitmanager.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/analysissettings.h b/src/gromacs/trajectoryanalysis/analysissettings.h
index 7687fdf1784cf87ee887284669119eaae664cd89..5d40d2ac836da5712afd3304a804606aad83b814 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings.h
+++ b/src/gromacs/trajectoryanalysis/analysissettings.h
@@ -43,9 +43,9 @@
 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
 #define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
 
-#include "../options/timeunitmanager.h"
-#include "../math/vectypes.h"
-#include "../utility/common.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
 
 struct t_topology;
 

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index d826b870a8db22340e25068acf4f639bad65de39..60684c401919c1f7be6f5a8bd7820265acdba565 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -57,11 +57,12 @@
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/trajectoryanalysis/analysismodule.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
-#include "gromacs/trajectoryanalysis/runnercommon.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/gmxassert.h"
 
+#include "runnercommon.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.h b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
index 0b87455e851a6960341e3426276e3178f3d41392..242a6299598ac69d784c4b832bb5f5245377ce11 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.h
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,8 +43,8 @@
 #ifndef GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
 #define GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
 
-#include "analysismodule.h"
-#include "../utility/common.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules.cpp b/src/gromacs/trajectoryanalysis/modules.cpp
index 423d585e8261923e87f9adf2020886d27fd553dc..07a3a8c378bf63d7c7534d1f3d5f3f6b911f79fb 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules.cpp
+++ b/src/gromacs/trajectoryanalysis/modules.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/trajectoryanalysis/modules.h"
+#include "modules.h"
 
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/angle.h b/src/gromacs/trajectoryanalysis/modules/angle.h
index 80976ebca4b6d243920368b9216233a1a1b80f74..24b81c73560306575729a2a3428cd36e5d6c9d68 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/angle.h
+++ b/src/gromacs/trajectoryanalysis/modules/angle.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/distance.h b/src/gromacs/trajectoryanalysis/modules/distance.h
index 7d354e38942a9fe92bab7bcc2d136187370b1172..519176d57724559d5540486fba6c0117fa4ffc58 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/distance.h
+++ b/src/gromacs/trajectoryanalysis/modules/distance.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/freevolume.cpp b/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
index 31785088a38156405f215a9eec52377293c39386..127a834b1baca86426d04114f7755471c68f6026 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
@@ -45,12 +45,11 @@
 
 #include <string>
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/average.h"
 #include "gromacs/analysisdata/modules/plot.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/freevolume.h b/src/gromacs/trajectoryanalysis/modules/freevolume.h
index cc96d6a8e693ad7a6fac34766c34b80a1278716f..ba24de0951712d44bdd852e389a3fba05828caef 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/freevolume.h
+++ b/src/gromacs/trajectoryanalysis/modules/freevolume.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.cpp b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
index 015e1e043d7d0cd31ed3f66a338064f946980042..6fec3377ab50d3c6af96232aa1c61ce0c1e13917 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@ -49,14 +49,13 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/average.h"
 #include "gromacs/analysisdata/modules/plot.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.h b/src/gromacs/trajectoryanalysis/modules/sasa.h
index dcf73297024b07c15033f8df33e21f25e9237389..4e2ca5eb1efe4dd82e03f72b4245a56d05786611 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/sasa.h
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.h
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/select.h b/src/gromacs/trajectoryanalysis/modules/select.h
index 90c4898fa3fcc16e3c6af02ab9d13f40cce81722..62b26a34af0aed34046a5f6bcdfcb2b16b3913f3 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/select.h
+++ b/src/gromacs/trajectoryanalysis/modules/select.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index bf610b382722e270004a6b8c0875f9032ee7d583..4d9513ed28d6268e8245c7eebea9125b1f535e7f 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -45,12 +45,11 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/oenv.h"
-
 #include "gromacs/fileio/timecontrol.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"

diff --git a/src/gromacs/trajectoryanalysis/tests/angle.cpp b/src/gromacs/trajectoryanalysis/tests/angle.cpp
index 70a6aec5a360d535e90cc0313f502962e5cc5c9e..94701813fb08dd994ced5de2174cef7c121a2787 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/angle.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/angle.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/angle.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"

diff --git a/src/gromacs/trajectoryanalysis/tests/distance.cpp b/src/gromacs/trajectoryanalysis/tests/distance.cpp
index 2719c1a1b4525efcdf4ea2f07f162ae46428c457..5a63636346d0f6b1af0f47651165f3c62b894658 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/distance.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/distance.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/distance.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"

diff --git a/src/gromacs/trajectoryanalysis/tests/freevolume.cpp b/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
index 4b85fd956f614b412e746c4384587f90c5b67a5f..f199976cc5dfa1547aa94d2628de95d0fdd6379d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/freevolume.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"

diff --git a/src/gromacs/trajectoryanalysis/tests/sasa.cpp b/src/gromacs/trajectoryanalysis/tests/sasa.cpp
index 6a9c975900177cbb6349f3b8c4aeef87678b6b69..75a60d69df988d07239464b25129885138fec9f5 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/sasa.cpp
@@ -54,10 +54,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/sasa.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 #include "testutils/testasserts.h"
 

diff --git a/src/gromacs/trajectoryanalysis/tests/select.cpp b/src/gromacs/trajectoryanalysis/tests/select.cpp
index 5232cc9e6056eee58b05ca42ce52743faddad4d6..05a24a4707aed057f5583427175a7a749f72b97d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/select.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/select.cpp
@@ -49,10 +49,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/select.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"

diff --git a/src/gromacs/utility.h b/src/gromacs/utility.h
index 9abfa1cbb69b7ef5ad3219c0d1c6d7fb18eda994..a25f70cb10d6db246b409ffa13615e27c5d9b000 100644 (file)
--- a/src/gromacs/utility.h
+++ b/src/gromacs/utility.h
@@ -160,10 +160,10 @@
 #ifndef GMX_UTILITY_H
 #define GMX_UTILITY_H
 
-#include "utility/errorcodes.h"
-#include "utility/exceptions.h"
-#include "utility/gmxassert.h"
-#include "utility/init.h"
-#include "utility/programcontext.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/init.h"
+#include "gromacs/utility/programcontext.h"
 
 #endif

diff --git a/src/gromacs/utility/arrayref.h b/src/gromacs/utility/arrayref.h
index 982c712b7d4128cdd72027290082d6d6e29fc467..fb4778d24a7573b6cc6d3cad83538c712c4bf7d1 100644 (file)
--- a/src/gromacs/utility/arrayref.h
+++ b/src/gromacs/utility/arrayref.h
@@ -50,7 +50,7 @@
 #include <utility>
 #include <vector>
 
-#include "gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/baseversion.cpp b/src/gromacs/utility/baseversion.cpp
index dff527782c657eed6bf0ea186a8e77e37398f072..876dbeb5b10175a2d618c0a452d2234e695ff83e 100644 (file)
--- a/src/gromacs/utility/baseversion.cpp
+++ b/src/gromacs/utility/baseversion.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include "baseversion.h"
+
 #include "baseversion-gen.h"
 
 const char *gmx_version()

diff --git a/src/gromacs/utility/cstringutil.c b/src/gromacs/utility/cstringutil.c
index 85cbd41c0af55b776340fcaa385f24f2992ce70a..14f010c077cc26bf34b63c065e43ff22c560ecc1 100644 (file)
--- a/src/gromacs/utility/cstringutil.c
+++ b/src/gromacs/utility/cstringutil.c
@@ -39,6 +39,8 @@
 
 #include "cstringutil.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <stdio.h>
@@ -48,8 +50,6 @@
 
 #include <sys/types.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif

diff --git a/src/gromacs/utility/cstringutil.h b/src/gromacs/utility/cstringutil.h
index a8b7460e4a7f5a39d08e19bdaced6b33c2a84f73..9bd8e3b85e8d0ededf394c8cffbdb95793db4b59 100644 (file)
--- a/src/gromacs/utility/cstringutil.h
+++ b/src/gromacs/utility/cstringutil.h
@@ -43,12 +43,12 @@
 #ifndef GMX_UTILITY_CSTRINGUTIL_H
 #define GMX_UTILITY_CSTRINGUTIL_H
 
+#include "gromacs/utility/gmx_header_config.h"
+
 #include <stdio.h>
 #include <time.h>
 
-#include "basedefinitions.h"
-
-#include "gmx_header_config.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/utility/errorcodes.cpp b/src/gromacs/utility/errorcodes.cpp
index 4d513a1365d1676d8e1127057c9e8622726e07f8..00c57aa67c4ac86d3f71fba0b1c96aaedf72d883 100644 (file)
--- a/src/gromacs/utility/errorcodes.cpp
+++ b/src/gromacs/utility/errorcodes.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/errorcodes.h"
+#include "errorcodes.h"
 
 #include <cstdlib>
 

diff --git a/src/gromacs/utility/errorformat.cpp b/src/gromacs/utility/errorformat.cpp
index a5ba90bf01fd448dbf3432d40648da741860a0ac..a8f7159c296e910c5ee7c90380928a15ba1fda06 100644 (file)
--- a/src/gromacs/utility/errorformat.cpp
+++ b/src/gromacs/utility/errorformat.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include "errorformat.h"
 
+#include "config.h"
+
 #include <cctype>
 #include <cstdio>
 #include <cstring>

diff --git a/src/gromacs/utility/exceptions.cpp b/src/gromacs/utility/exceptions.cpp
index 5ccd830707c82f9f20407f7fcebd205287131f2f..952383ffad3c4b86f003be6a2063ed8c422ddb06 100644 (file)
--- a/src/gromacs/utility/exceptions.cpp
+++ b/src/gromacs/utility/exceptions.cpp
@@ -51,8 +51,8 @@
 #include <stdexcept>
 #include <typeinfo>
 
-#include <boost/exception/get_error_info.hpp>
 #include <boost/shared_ptr.hpp>
+#include <boost/exception/get_error_info.hpp>
 
 #include "thread_mpi/system_error.h"
 

diff --git a/src/gromacs/utility/exceptions.h b/src/gromacs/utility/exceptions.h
index ace7b66224c830146d2d9bc503b8f3e840234987..e6a8929320c640cccbf30276af1f8867414fff5c 100644 (file)
--- a/src/gromacs/utility/exceptions.h
+++ b/src/gromacs/utility/exceptions.h
@@ -51,11 +51,11 @@
 #include <vector>
 
 #include <boost/exception_ptr.hpp>
+#include <boost/throw_exception.hpp>
 #include <boost/exception/errinfo_api_function.hpp>
 #include <boost/exception/errinfo_errno.hpp>
 #include <boost/exception/exception.hpp>
 #include <boost/exception/info.hpp>
-#include <boost/throw_exception.hpp>
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/fatalerror.h b/src/gromacs/utility/fatalerror.h
index 7d380bc419122c43a0e50157b3b4180db52a76e3..1dd4cff339c1fe4cc1333c72c4f72a590e16f720 100644 (file)
--- a/src/gromacs/utility/fatalerror.h
+++ b/src/gromacs/utility/fatalerror.h
@@ -47,7 +47,7 @@
 #include <stdarg.h>
 #include <stdio.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/utility/file.cpp b/src/gromacs/utility/file.cpp
index 31055f28b8637ee408f8dbb038a15b512f5c46fc..174fa00803bc8898cf4796b516944c64c8fd5516 100644 (file)
--- a/src/gromacs/utility/file.cpp
+++ b/src/gromacs/utility/file.cpp
@@ -43,6 +43,8 @@
 
 #include "file.h"
 
+#include "config.h"
+
 #include <cerrno>
 #include <cstdio>
 #include <cstring>
@@ -53,8 +55,6 @@
 
 #include <sys/stat.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/utility/file.h b/src/gromacs/utility/file.h
index 15b48d16a559533fcb7507d625e3e008df17a6d2..ef837b4a842b5357bc6f38c68c0a56aff5a984e8 100644 (file)
--- a/src/gromacs/utility/file.h
+++ b/src/gromacs/utility/file.h
@@ -47,7 +47,7 @@
 
 #include <string>
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/futil.cpp b/src/gromacs/utility/futil.cpp
index af28843ef532da32ed1df43370144d54af280627..546b875808bc1d69105bab65ac8a1fefb263a057 100644 (file)
--- a/src/gromacs/utility/futil.cpp
+++ b/src/gromacs/utility/futil.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/futil.h"
+#include "futil.h"
 
 #include "config.h"
 
@@ -44,9 +44,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include <sys/types.h>
-#include <sys/stat.h>
 #include <fcntl.h>
+#include <sys/stat.h>
+#include <sys/types.h>
 
 #ifdef HAVE_DIRENT_H
 /* POSIX */
@@ -58,9 +58,9 @@
 #endif
 
 #ifdef GMX_NATIVE_WINDOWS
-#include <windows.h>
 #include <direct.h>
 #include <io.h>
+#include <windows.h>
 #endif
 
 /* Windows file stuff, only necessary for visual studio */

diff --git a/src/gromacs/utility/futil.h b/src/gromacs/utility/futil.h
index 9f9477301623d37ba03183548e33fc08cb1a5535..8e669e09d301516d7f99fee65f0732651dd84371 100644 (file)
--- a/src/gromacs/utility/futil.h
+++ b/src/gromacs/utility/futil.h
@@ -48,7 +48,7 @@
 #include <limits.h>
 #include <stdio.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -57,7 +57,7 @@ extern "C" {
 }
 #endif
 
-#include "gmx_header_config.h"
+#include "gromacs/utility/gmx_header_config.h"
 /*! \def DIR_SEPARATOR
  * \brief
  * Directory separator on this OS.

diff --git a/src/gromacs/utility/gmxassert.h b/src/gromacs/utility/gmxassert.h
index b47d9d093331d0ecfb28aa667e67d578d1e50171..a919080d3259d00b214cf8c37ebb1057f83ae636 100644 (file)
--- a/src/gromacs/utility/gmxassert.h
+++ b/src/gromacs/utility/gmxassert.h
@@ -45,7 +45,7 @@
 
 #include <boost/current_function.hpp>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 //! \addtogroup module_utility
 //! \{

diff --git a/src/gromacs/utility/gmxmpi.h b/src/gromacs/utility/gmxmpi.h
index bb6570cdfa4917d78fbf1f85254711031fad878f..cacc0a0cbeb8153f5d862ab6e61f779c20397d35 100644 (file)
--- a/src/gromacs/utility/gmxmpi.h
+++ b/src/gromacs/utility/gmxmpi.h
@@ -73,8 +73,8 @@
 #endif /*MPI_INT64_T*/
 #else
 #ifdef GMX_THREAD_MPI
-#include "thread_mpi/tmpi.h"
 #include "thread_mpi/mpi_bindings.h"
+#include "thread_mpi/tmpi.h"
 #else
 typedef void* MPI_Comm;
 typedef void* MPI_Request;

diff --git a/src/gromacs/utility/gmxomp.cpp b/src/gromacs/utility/gmxomp.cpp
index 04abd12a8e89bfddb6690fb1272066670dcbccc5..15989a16fe89251d373a631449092cf8d3cf9ea6 100644 (file)
--- a/src/gromacs/utility/gmxomp.cpp
+++ b/src/gromacs/utility/gmxomp.cpp
@@ -40,7 +40,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/gmxomp.h"
+#include "gmxomp.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/utility/gmxomp.h b/src/gromacs/utility/gmxomp.h
index f0e67a593f4af86bfbcfe62cf2d5f5c821aa0a52..553eadc09294483bc5555c83eecbb11e7f4bed7c 100644 (file)
--- a/src/gromacs/utility/gmxomp.h
+++ b/src/gromacs/utility/gmxomp.h
@@ -67,7 +67,7 @@
 #include <windows.h>
 #endif
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/utility/gmxregex.h b/src/gromacs/utility/gmxregex.h
index a80f523beeb616cf151b7bb74db229f1661f3b13..9385163082cc0dbfe5c457bfe477827576e55d25 100644 (file)
--- a/src/gromacs/utility/gmxregex.h
+++ b/src/gromacs/utility/gmxregex.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/init.cpp b/src/gromacs/utility/init.cpp
index 3fbc8c554cf3bbe66e6d071a3c5e1bdb0a91244b..f2110535746b66991231117ba7577eeed875a686 100644 (file)
--- a/src/gromacs/utility/init.cpp
+++ b/src/gromacs/utility/init.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/init.h"
+#include "init.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/utility/messagestringcollector.cpp b/src/gromacs/utility/messagestringcollector.cpp
index 9d631acbce6c43af4a68e9701b7008fddfdaa57d..937bb541cb99510b665d0426b72a066b5ff73321 100644 (file)
--- a/src/gromacs/utility/messagestringcollector.cpp
+++ b/src/gromacs/utility/messagestringcollector.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/messagestringcollector.h"
+#include "messagestringcollector.h"
 
 #include <vector>
 

diff --git a/src/gromacs/utility/messagestringcollector.h b/src/gromacs/utility/messagestringcollector.h
index aca59a33b19ceaa93905a4b710a2eb3a5755c017..b78af98447bb56236e563560cbda4d3852f0705c 100644 (file)
--- a/src/gromacs/utility/messagestringcollector.h
+++ b/src/gromacs/utility/messagestringcollector.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/path.cpp b/src/gromacs/utility/path.cpp
index 0a0e54bc7618069440356f37bd90fe3b29efbf9d..1302d30f978b57d323732f0d6e32c2eb6f5452f5 100644 (file)
--- a/src/gromacs/utility/path.cpp
+++ b/src/gromacs/utility/path.cpp
@@ -43,6 +43,8 @@
 
 #include "path.h"
 
+#include "config.h"
+
 #include <cctype>
 #include <cerrno>
 #include <cstdlib>
@@ -52,8 +54,6 @@
 
 #include <sys/stat.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <direct.h>
 #else

diff --git a/src/gromacs/utility/programcontext.cpp b/src/gromacs/utility/programcontext.cpp
index 5b73060158cb3ca5578b452c03418b77ba64ad60..ac9bc13dd771acaf5fa671ca05fad0216f51b7e5 100644 (file)
--- a/src/gromacs/utility/programcontext.cpp
+++ b/src/gromacs/utility/programcontext.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/programcontext.h"
+#include "programcontext.h"
 
 #include <cstddef>
 

diff --git a/src/gromacs/utility/scoped_ptr_sfree.h b/src/gromacs/utility/scoped_ptr_sfree.h
index 3c1077ccaea4f97b63fcf114a972ed4ad3f0fe7b..7078a80aebfd6b9958df7838bac473d002d5baa2 100644 (file)
--- a/src/gromacs/utility/scoped_ptr_sfree.h
+++ b/src/gromacs/utility/scoped_ptr_sfree.h
@@ -43,7 +43,7 @@
 #ifndef GMX_UTILITY_SCOPED_PTR_SFREE_H
 #define GMX_UTILITY_SCOPED_PTR_SFREE_H
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 #include "gromacs/utility/smalloc.h"
 
 namespace gmx

diff --git a/src/gromacs/utility/smalloc.c b/src/gromacs/utility/smalloc.c
index e542c5532767e855591fca75a2f0f900a76453dc..16d70514b98267a527a371af3c59872c99e52017 100644 (file)
--- a/src/gromacs/utility/smalloc.c
+++ b/src/gromacs/utility/smalloc.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
+#include "smalloc.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/utility/smalloc.h b/src/gromacs/utility/smalloc.h
index 91e2ebe89eb9d4d8e4dc1e514f95bfdeb2b36b88..74d71a558642b28d2863554eec754883e0e0d723 100644 (file)
--- a/src/gromacs/utility/smalloc.h
+++ b/src/gromacs/utility/smalloc.h
@@ -73,7 +73,7 @@
 
 #include <stddef.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/utility/stringutil.cpp b/src/gromacs/utility/stringutil.cpp
index 3f33caeb1dafd37053b8c9f888ef5db2e24eb8ba..5b2c725017a6e585b14e9d6d3832f76a58571d8a 100644 (file)
--- a/src/gromacs/utility/stringutil.cpp
+++ b/src/gromacs/utility/stringutil.cpp
@@ -44,8 +44,8 @@
 #include "stringutil.h"
 
 #include <cctype>
-#include <cstdio>
 #include <cstdarg>
+#include <cstdio>
 #include <cstring>
 
 #include <algorithm>

diff --git a/src/gromacs/utility/tests/stringutil.cpp b/src/gromacs/utility/tests/stringutil.cpp
index c63a9c4559680ca7f02ec9b188a531a97c5a4b4f..dcdc5cba0c7553cf641afc1faf01f724e97c482f 100644 (file)
--- a/src/gromacs/utility/tests/stringutil.cpp
+++ b/src/gromacs/utility/tests/stringutil.cpp
@@ -45,14 +45,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/utility/stringutil.h"
+
 #include <string>
 #include <vector>
 
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/utility/stringutil.h"
-
 #include "testutils/refdata.h"
 #include "testutils/stringtest.h"