Rename trnio.* to trrio.*

These routines write .trr files, and the old name was really confusing,
as there is also an efTRN, which means something different...
The routines will be renamed in a separate commit.

Removed unnecessary includes of trnio.h.

Change-Id: If02f561ad51c73eb2080195587795d0c8ae1b082

diff --git a/src/contrib/anaf.c b/src/contrib/anaf.c
index 044d987048438025bd5420b110705ca1396d8f03..df4d1f8681c6dc6f44f6ea02cb0c5b1afaf7cafb 100644 (file)
--- a/src/contrib/anaf.c
+++ b/src/contrib/anaf.c
@@ -51,7 +51,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "txtdump.h"
 #include "gromacs/math/vec.h"
 

diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c
index a60b847cdd9b881be02bcde7221ec663c71cf627..389a20386b4994a70acc4ea2701264e57f9cbc7b 100644 (file)
--- a/src/contrib/mkice.c
+++ b/src/contrib/mkice.c
@@ -50,7 +50,7 @@
 #include "gromacs/math/units.h"
 #include "names.h"
 #include "txtdump.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/confio.h"

diff --git a/src/contrib/test.c b/src/contrib/test.c
index 865f4b8b476812af1f80dfba784ccab4e7fcfcdc..888ae65950c9e26a8a7c97c44a6bbed5c561ea3b 100644 (file)
--- a/src/contrib/test.c
+++ b/src/contrib/test.c
@@ -51,7 +51,6 @@
 #include "gromacs/math/units.h"
 #include "names.h"
 #include "txtdump.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/confio.h"
 
 real pot(real x,real qq,real c6,real c12)

diff --git a/src/gromacs/fileio/CMakeLists.txt b/src/gromacs/fileio/CMakeLists.txt
index 0c638a78a8b7e026bb47f96b48ff3bca28d3bd9b..c3a4552954d9a0b4f4e0e1c6d425c4bbf9569cc3 100644 (file)
--- a/src/gromacs/fileio/CMakeLists.txt
+++ b/src/gromacs/fileio/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015, 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.
@@ -53,7 +53,7 @@ gmx_install_headers(
     pdbio.h
     tpxio.h
     trajectory_writing.h
-    trnio.h
+    trrio.h
     trx.h
     trxio.h
     xdr_datatype.h

diff --git a/src/gromacs/fileio/mdoutf.cpp b/src/gromacs/fileio/mdoutf.cpp
index db89c8ea6a45f38b1c99db5d8f85edbb07c9cf56..b6140640ff40c5af3932aee7ddf0ca415dd57454 100644 (file)
--- a/src/gromacs/fileio/mdoutf.cpp
+++ b/src/gromacs/fileio/mdoutf.cpp
@@ -40,7 +40,7 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/checkpoint.h"

diff --git a/src/gromacs/fileio/trnio.cpp b/src/gromacs/fileio/trrio.cpp
similarity index 99%
rename from src/gromacs/fileio/trnio.cpp
rename to src/gromacs/fileio/trrio.cpp
index b843db33176c6e9942a900468a688a16b40f2240..9951fba746458fc3e72e890bafcb0261ebebe4e5 100644 (file)
--- a/src/gromacs/fileio/trnio.cpp
+++ b/src/gromacs/fileio/trrio.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "trnio.h"
+#include "trrio.h"
 
 #include <cstring>
 

diff --git a/src/gromacs/fileio/trnio.h b/src/gromacs/fileio/trrio.h
similarity index 96%
rename from src/gromacs/fileio/trnio.h
rename to src/gromacs/fileio/trrio.h
index 3550790f912b067fc04bcb6963cf18b2334b8d92..cb45bb6c19289af502deebd60717fbb78a0101fe 100644 (file)
--- a/src/gromacs/fileio/trnio.h
+++ b/src/gromacs/fileio/trrio.h
@@ -34,9 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef GMX_FILEIO_TRNIO_H
-#define GMX_FILEIO_TRNIO_H
+#ifndef GMX_FILEIO_TRRIO_H
+#define GMX_FILEIO_TRRIO_H
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/basedefinitions.h"
@@ -50,9 +49,9 @@
  * The files are backward compatible, therefore the header holds
  * some unused variables.
  *
- * The routines in the corresponding c-file trnio.c
- * are based on the lower level routines in gmxfio.c
- * The integer file pointer returned from open_trn
+ * The routines in the corresponding c-file trrio.cpp
+ * are based on the lower level routines in gmxfio.cpp
+ * The file handle returned from open_trn
  * can also be used with the routines in gmxfio.h
  *
  **************************************************************/

diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp
index 116dc4c2a89a50633f9688ead9a19b15997d8d04..50bd6d5e3218d3adb3290a1f935fb6b510aa42a9 100644 (file)
--- a/src/gromacs/fileio/trxio.cpp
+++ b/src/gromacs/fileio/trxio.cpp
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/fileio/xtcio.h"

diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c
index 1561d5a4468974757b6cfe2788e78f076b931f32..1d421e51f538141a1072f231951413d4b74e9ffb 100644 (file)
--- a/src/gromacs/gmxana/eigio.c
+++ b/src/gromacs/gmxana/eigio.c
@@ -38,7 +38,8 @@
 
 #include "eigio.h"
 
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 88304ed029ab441202a6c11e67934f7e0000ba37..67208e0f89ea49040728f1fe0edbdc7eee01fc41 100644 (file)
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -41,7 +41,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/correlationfunctions/autocorr.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"

diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index 3a746b6eb330681bc4e570e07acf6a2c72b12530..011fe580e29347bb9092f6b99c17b051ca5e0bcb 100644 (file)
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -43,7 +43,6 @@
 #include "gromacs/commandline/pargs.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/gmxana/cmat.h"

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index bad3518ababad410abcb8c924d8ff9d719c8dfcd..779326f0b5a91ab8473a45f602a691da66ba2b33 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -42,7 +42,6 @@
 #include "gromacs/commandline/pargs.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/gmxana/eigio.h"

diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
index f426fe4e5135a2e6d29f6320744ba205b2900907..3866506b280c0e65b57091e7a9bada03eb1c743d 100644 (file)
--- a/src/gromacs/gmxana/gmx_sigeps.c
+++ b/src/gromacs/gmxana/gmx_sigeps.c
@@ -40,9 +40,6 @@
 #include <stdio.h>
 
 #include "gromacs/commandline/pargs.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/legacyheaders/names.h"

diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index 6f8463f63e58755937499a4b84245e3cdb939473..d6c2335650c06fa4d2aeee205abe5af5fc829234 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -46,7 +46,6 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index 9db84bee50493dd295a364001c5e80fbb7aaec1e..f0e64ed790cb3b9b17dc3017be559f46cdf5d3b4 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 304e68c20b450385650962f701dcd93262957fd9..8a6e43c666382223b157bbf261700cd739252faa 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -52,7 +52,6 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"

diff --git a/src/gromacs/gmxpreprocess/readrot.cpp b/src/gromacs/gmxpreprocess/readrot.cpp
index 6968670a27e557690725cb15c82ea7a3c20837f7..4615d2faf3ff5853082f15ca94b7e7f4c9ec1b80 100644 (file)
--- a/src/gromacs/gmxpreprocess/readrot.cpp
+++ b/src/gromacs/gmxpreprocess/readrot.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"

diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index f1a1bce5e8f7ddb1938771ae27f55a58514473ed..402662de4c31989a0eb6c13f3a657c3fe60cd7cd 100644 (file)
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
@@ -40,7 +40,6 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/confio.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"

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index 08ae193dff8597e59a38d4a67692e55326eb7d27..fc906209eb9d83335513753baa4f3768621c1346 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -40,7 +40,6 @@
 #include <string.h>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/constr.h"

diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp
index 187fef017fe8490b57f09ff2f290630e7fff1b8c..a44e84a47775c7458ea11f481ce12081fdce3b13 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.cpp
+++ b/src/gromacs/pulling/pull_rotation.cpp
@@ -48,7 +48,6 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"

diff --git a/src/gromacs/tools/check.cpp b/src/gromacs/tools/check.cpp
index cc19905b072b0d06a8d053070335c61e36d3908d..0c34c66cb142f9d418ecef8106a38e07a2d86ab7 100644 (file)
--- a/src/gromacs/tools/check.cpp
+++ b/src/gromacs/tools/check.cpp
@@ -45,7 +45,6 @@
 #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/fileio/xtcio.h"
 #include "gromacs/legacyheaders/macros.h"

diff --git a/src/gromacs/tools/convert_tpr.cpp b/src/gromacs/tools/convert_tpr.cpp
index 696f61c20289b3a56dcf575a392e33062d06cbbd..a222ef578f579f1c6181e2097359a11cf635476a 100644 (file)
--- a/src/gromacs/tools/convert_tpr.cpp
+++ b/src/gromacs/tools/convert_tpr.cpp
@@ -41,7 +41,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/macros.h"

diff --git a/src/gromacs/tools/dump.cpp b/src/gromacs/tools/dump.cpp
index d9b20863d961305c046d3dc13fb2d1adca760c2c..65a028ced8a7e67ad6d7555040818778f2394e88 100644 (file)
--- a/src/gromacs/tools/dump.cpp
+++ b/src/gromacs/tools/dump.cpp
@@ -50,7 +50,7 @@
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trrio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"
 #include "gromacs/legacyheaders/checkpoint.h"