Move densityfitting to its own directory

Preparing for adding more applied_forces modules

Change-Id: Ieec20d1f0752a369d26352ec6b0997812decd21e

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index b325f579673548e8688369b8224d0955cb9e0210..840e2797f7814d9b570182574f4c4ff235359729 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -25,3 +25,6 @@ modularsimulator -> mdrun
 # Cycle counters in timing use comrec for the set up, which is in the mdtypes. This introduces
 # cyclic dependencies if the cycle counting is used anywhere in mdtypes.
 timing -> mdtypes
+
+# awh has dependencies in mdlib and pulling that need resolving.
+mdlib -> applied_forces

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 1a35de1591e7bd0be6ce368c88dd11a1c03fbd1c..48636cdc863fe2a165551dd650088a0ef63afbd3 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -103,7 +103,6 @@ add_subdirectory(trajectory)
 add_subdirectory(swap)
 add_subdirectory(essentialdynamics)
 add_subdirectory(pulling)
-add_subdirectory(awh)
 add_subdirectory(simd)
 add_subdirectory(imd)
 add_subdirectory(compat)

diff --git a/src/gromacs/applied_forces/CMakeLists.txt b/src/gromacs/applied_forces/CMakeLists.txt
index bdca6f54ec64d47bbd7d9874403994e219d85d8a..498d44a220d3a56134a412990a8954b135cb83aa 100644 (file)
--- a/src/gromacs/applied_forces/CMakeLists.txt
+++ b/src/gromacs/applied_forces/CMakeLists.txt
@@ -36,6 +36,7 @@ gmx_add_libgromacs_sources(
     electricfield.cpp
     )
 
+add_subdirectory(awh)
 add_subdirectory(densityfitting)
 
 if (BUILD_TESTING)

diff --git a/src/gromacs/awh/CMakeLists.txt b/src/gromacs/applied_forces/awh/CMakeLists.txt
similarity index 70%
rename from src/gromacs/awh/CMakeLists.txt
rename to src/gromacs/applied_forces/awh/CMakeLists.txt
index 8fc400a9e7892fd1d57b798842243292c9eadc5a..0917be1d833bb8fcefc178ecba9a4f93c62c9c22 100644 (file)
--- a/src/gromacs/awh/CMakeLists.txt
+++ b/src/gromacs/applied_forces/awh/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017,2020, 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.
@@ -32,8 +32,20 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
-file(GLOB AWH_SOURCES *.cpp)
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${AWH_SOURCES} PARENT_SCOPE)
+gmx_add_libgromacs_sources(awh.cpp
+                           bias.cpp
+                           biasgrid.cpp
+                           biasparams.cpp
+                           biassharing.cpp
+                           biasstate.cpp
+                           biaswriter.cpp
+                           coordstate.cpp
+                           correlationgrid.cpp
+                           correlationhistory.cpp
+                           correlationtensor.cpp
+                           histogramsize.cpp
+                           pointstate.cpp
+                           read_params.cpp)
 
 if (BUILD_TESTING)
     add_subdirectory(tests)

diff --git a/src/gromacs/awh/awh.cpp b/src/gromacs/applied_forces/awh/awh.cpp
similarity index 100%
rename from src/gromacs/awh/awh.cpp
rename to src/gromacs/applied_forces/awh/awh.cpp

diff --git a/src/gromacs/awh/awh.h b/src/gromacs/applied_forces/awh/awh.h
similarity index 99%
rename from src/gromacs/awh/awh.h
rename to src/gromacs/applied_forces/awh/awh.h
index efd7c80a43c38ced4a439d3cdbf8644013412a30..30b0a25b1a3506b9ecf778f7f6d603a8900df57e 100644 (file)
--- a/src/gromacs/awh/awh.h
+++ b/src/gromacs/applied_forces/awh/awh.h
@@ -35,7 +35,7 @@
 
 /*! \libinternal
  * \defgroup module_awh Accelerated weight histogram (AWH) method
- * \ingroup group_mdrun
+ * \ingroup module_applied_forces
  * \brief
  * Implements the "accelerated weight histogram" sampling method.
  *

diff --git a/src/gromacs/awh/bias.cpp b/src/gromacs/applied_forces/awh/bias.cpp
similarity index 100%
rename from src/gromacs/awh/bias.cpp
rename to src/gromacs/applied_forces/awh/bias.cpp

diff --git a/src/gromacs/awh/bias.h b/src/gromacs/applied_forces/awh/bias.h
similarity index 100%
rename from src/gromacs/awh/bias.h
rename to src/gromacs/applied_forces/awh/bias.h

diff --git a/src/gromacs/awh/biasgrid.cpp b/src/gromacs/applied_forces/awh/biasgrid.cpp
similarity index 100%
rename from src/gromacs/awh/biasgrid.cpp
rename to src/gromacs/applied_forces/awh/biasgrid.cpp

diff --git a/src/gromacs/awh/biasgrid.h b/src/gromacs/applied_forces/awh/biasgrid.h
similarity index 100%
rename from src/gromacs/awh/biasgrid.h
rename to src/gromacs/applied_forces/awh/biasgrid.h

diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/applied_forces/awh/biasparams.cpp
similarity index 100%
rename from src/gromacs/awh/biasparams.cpp
rename to src/gromacs/applied_forces/awh/biasparams.cpp

diff --git a/src/gromacs/awh/biasparams.h b/src/gromacs/applied_forces/awh/biasparams.h
similarity index 100%
rename from src/gromacs/awh/biasparams.h
rename to src/gromacs/applied_forces/awh/biasparams.h

diff --git a/src/gromacs/awh/biassharing.cpp b/src/gromacs/applied_forces/awh/biassharing.cpp
similarity index 100%
rename from src/gromacs/awh/biassharing.cpp
rename to src/gromacs/applied_forces/awh/biassharing.cpp

diff --git a/src/gromacs/awh/biassharing.h b/src/gromacs/applied_forces/awh/biassharing.h
similarity index 97%
rename from src/gromacs/awh/biassharing.h
rename to src/gromacs/applied_forces/awh/biassharing.h
index b98a4344a8bbf39a9d9e2a2fdd9dbbea31ded369..751fe2f9a5f9b7c8bbce89d6684013023dcdc437 100644 (file)
--- a/src/gromacs/awh/biassharing.h
+++ b/src/gromacs/applied_forces/awh/biassharing.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020, 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.

diff --git a/src/gromacs/awh/biasstate.cpp b/src/gromacs/applied_forces/awh/biasstate.cpp
similarity index 100%
rename from src/gromacs/awh/biasstate.cpp
rename to src/gromacs/applied_forces/awh/biasstate.cpp

diff --git a/src/gromacs/awh/biasstate.h b/src/gromacs/applied_forces/awh/biasstate.h
similarity index 100%
rename from src/gromacs/awh/biasstate.h
rename to src/gromacs/applied_forces/awh/biasstate.h

diff --git a/src/gromacs/awh/biaswriter.cpp b/src/gromacs/applied_forces/awh/biaswriter.cpp
similarity index 99%
rename from src/gromacs/awh/biaswriter.cpp
rename to src/gromacs/applied_forces/awh/biaswriter.cpp
index 3d25af4edbb9d5b822574d966ba60b8ace288232..8fd09eedbca37be6fa5be9238867923a958b1b37 100644 (file)
--- a/src/gromacs/awh/biaswriter.cpp
+++ b/src/gromacs/applied_forces/awh/biaswriter.cpp
@@ -40,7 +40,7 @@
 #include <cassert>
 #include <cmath>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/trajectory/energyframe.h"

diff --git a/src/gromacs/awh/biaswriter.h b/src/gromacs/applied_forces/awh/biaswriter.h
similarity index 98%
rename from src/gromacs/awh/biaswriter.h
rename to src/gromacs/applied_forces/awh/biaswriter.h
index 14625b54dc542145a735b4ef2eac88d3fb810ccf..420a26ff630de93f7d2bef46b9cecebb423e0549 100644 (file)
--- a/src/gromacs/awh/biaswriter.h
+++ b/src/gromacs/applied_forces/awh/biaswriter.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.

diff --git a/src/gromacs/awh/coordstate.cpp b/src/gromacs/applied_forces/awh/coordstate.cpp
similarity index 100%
rename from src/gromacs/awh/coordstate.cpp
rename to src/gromacs/applied_forces/awh/coordstate.cpp

diff --git a/src/gromacs/awh/coordstate.h b/src/gromacs/applied_forces/awh/coordstate.h
similarity index 100%
rename from src/gromacs/awh/coordstate.h
rename to src/gromacs/applied_forces/awh/coordstate.h

diff --git a/src/gromacs/awh/correlationgrid.cpp b/src/gromacs/applied_forces/awh/correlationgrid.cpp
similarity index 98%
rename from src/gromacs/awh/correlationgrid.cpp
rename to src/gromacs/applied_forces/awh/correlationgrid.cpp
index ac1b48edb47de453a66500edfe6520ec8fc35769..1181dd1999c14718fe9180ccf466921eae66601e 100644 (file)
--- a/src/gromacs/awh/correlationgrid.cpp
+++ b/src/gromacs/applied_forces/awh/correlationgrid.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020, 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.

diff --git a/src/gromacs/awh/correlationgrid.h b/src/gromacs/applied_forces/awh/correlationgrid.h
similarity index 100%
rename from src/gromacs/awh/correlationgrid.h
rename to src/gromacs/applied_forces/awh/correlationgrid.h

diff --git a/src/gromacs/awh/correlationhistory.cpp b/src/gromacs/applied_forces/awh/correlationhistory.cpp
similarity index 99%
rename from src/gromacs/awh/correlationhistory.cpp
rename to src/gromacs/applied_forces/awh/correlationhistory.cpp
index 3dac473fe0f3f41a0ee1591d45ec59dca71fb6a6..f77ba399387046ca91da0ce91c72505193043181 100644 (file)
--- a/src/gromacs/awh/correlationhistory.cpp
+++ b/src/gromacs/applied_forces/awh/correlationhistory.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.

diff --git a/src/gromacs/awh/correlationhistory.h b/src/gromacs/applied_forces/awh/correlationhistory.h
similarity index 97%
rename from src/gromacs/awh/correlationhistory.h
rename to src/gromacs/applied_forces/awh/correlationhistory.h
index 61e70d95070b9b0ecc7a65a621984e4422de7735..05ac52845f7da0db3c0461be460097e92b4c22b1 100644 (file)
--- a/src/gromacs/awh/correlationhistory.h
+++ b/src/gromacs/applied_forces/awh/correlationhistory.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020, 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.

diff --git a/src/gromacs/awh/correlationtensor.cpp b/src/gromacs/applied_forces/awh/correlationtensor.cpp
similarity index 99%
rename from src/gromacs/awh/correlationtensor.cpp
rename to src/gromacs/applied_forces/awh/correlationtensor.cpp
index ebcd1aa5900a09cf1d047d0b58d88c38b7508954..b2a42d905c7216b4778904bf0ee77f95f8a66af1 100644 (file)
--- a/src/gromacs/awh/correlationtensor.cpp
+++ b/src/gromacs/applied_forces/awh/correlationtensor.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.

diff --git a/src/gromacs/awh/correlationtensor.h b/src/gromacs/applied_forces/awh/correlationtensor.h
similarity index 99%
rename from src/gromacs/awh/correlationtensor.h
rename to src/gromacs/applied_forces/awh/correlationtensor.h
index e9fe9537dadd1bba13f92c10984d7213e1a0fd85..9da3928dc9ef0fcfaa985c6e445393017cadf1c9 100644 (file)
--- a/src/gromacs/awh/correlationtensor.h
+++ b/src/gromacs/applied_forces/awh/correlationtensor.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.

diff --git a/src/gromacs/awh/dimparams.h b/src/gromacs/applied_forces/awh/dimparams.h
similarity index 100%
rename from src/gromacs/awh/dimparams.h
rename to src/gromacs/applied_forces/awh/dimparams.h

diff --git a/src/gromacs/awh/histogramsize.cpp b/src/gromacs/applied_forces/awh/histogramsize.cpp
similarity index 100%
rename from src/gromacs/awh/histogramsize.cpp
rename to src/gromacs/applied_forces/awh/histogramsize.cpp

diff --git a/src/gromacs/awh/histogramsize.h b/src/gromacs/applied_forces/awh/histogramsize.h
similarity index 100%
rename from src/gromacs/awh/histogramsize.h
rename to src/gromacs/applied_forces/awh/histogramsize.h

diff --git a/src/gromacs/awh/pointstate.cpp b/src/gromacs/applied_forces/awh/pointstate.cpp
similarity index 100%
rename from src/gromacs/awh/pointstate.cpp
rename to src/gromacs/applied_forces/awh/pointstate.cpp

diff --git a/src/gromacs/awh/pointstate.h b/src/gromacs/applied_forces/awh/pointstate.h
similarity index 100%
rename from src/gromacs/awh/pointstate.h
rename to src/gromacs/applied_forces/awh/pointstate.h

diff --git a/src/gromacs/awh/read_params.cpp b/src/gromacs/applied_forces/awh/read_params.cpp
similarity index 99%
rename from src/gromacs/awh/read_params.cpp
rename to src/gromacs/applied_forces/awh/read_params.cpp
index 0eb30ee0f8fbe0564a0d35a77ff9ef9eb0e6db58..d301bd83d9240375263af5bed02b49b3c8978407 100644 (file)
--- a/src/gromacs/awh/read_params.cpp
+++ b/src/gromacs/applied_forces/awh/read_params.cpp
@@ -39,7 +39,7 @@
 
 #include "read_params.h"
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/warninp.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/awh/read_params.h b/src/gromacs/applied_forces/awh/read_params.h
similarity index 100%
rename from src/gromacs/awh/read_params.h
rename to src/gromacs/applied_forces/awh/read_params.h

diff --git a/src/gromacs/awh/tests/CMakeLists.txt b/src/gromacs/applied_forces/awh/tests/CMakeLists.txt
similarity index 100%
rename from src/gromacs/awh/tests/CMakeLists.txt
rename to src/gromacs/applied_forces/awh/tests/CMakeLists.txt

diff --git a/src/gromacs/awh/tests/bias.cpp b/src/gromacs/applied_forces/awh/tests/bias.cpp
similarity index 98%
rename from src/gromacs/awh/tests/bias.cpp
rename to src/gromacs/applied_forces/awh/tests/bias.cpp
index c59fb1327f92fbc44d08a4c13fc2898872fbaab0..7d49ffdc80c6612a63947680d5660e6d73c492aa 100644 (file)
--- a/src/gromacs/awh/tests/bias.cpp
+++ b/src/gromacs/applied_forces/awh/tests/bias.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/awh/bias.h"
+#include "gromacs/applied_forces/awh/bias.h"
 
 #include <cmath>
 
@@ -45,8 +45,8 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/awh/correlationgrid.h"
-#include "gromacs/awh/pointstate.h"
+#include "gromacs/applied_forces/awh/correlationgrid.h"
+#include "gromacs/applied_forces/awh/pointstate.h"
 #include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/awh/tests/bias_fep_lambda_state.cpp b/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
similarity index 99%
rename from src/gromacs/awh/tests/bias_fep_lambda_state.cpp
rename to src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
index 1e4b452a81198ecf0975205b95b3c790d6dfd305..78b84e95e88f21e50dcd8a1923368694bcdb4150 100644 (file)
--- a/src/gromacs/awh/tests/bias_fep_lambda_state.cpp
+++ b/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
@@ -44,9 +44,9 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/awh/bias.h"
-#include "gromacs/awh/correlationgrid.h"
-#include "gromacs/awh/pointstate.h"
+#include "gromacs/applied_forces/awh/bias.h"
+#include "gromacs/applied_forces/awh/correlationgrid.h"
+#include "gromacs/applied_forces/awh/pointstate.h"
 #include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/awh/tests/biasgrid.cpp b/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
similarity index 99%
rename from src/gromacs/awh/tests/biasgrid.cpp
rename to src/gromacs/applied_forces/awh/tests/biasgrid.cpp
index ebc2791074f31d4496ccff54529e45df24a7b260..9203f6cfc60826f17f861bd9262c85e19631c6c9 100644 (file)
--- a/src/gromacs/awh/tests/biasgrid.cpp
+++ b/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/awh/biasgrid.h"
+#include "gromacs/applied_forces/awh/biasgrid.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/applied_forces/awh/tests/biasstate.cpp
similarity index 97%
rename from src/gromacs/awh/tests/biasstate.cpp
rename to src/gromacs/applied_forces/awh/tests/biasstate.cpp
index 60fe0d44d0ad537a2137a94e3e0fcd2d33794403..db11a9a5ca8a553d93266b8f094e4c1a5b255efa 100644 (file)
--- a/src/gromacs/awh/tests/biasstate.cpp
+++ b/src/gromacs/applied_forces/awh/tests/biasstate.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/awh/biasstate.h"
+#include "gromacs/applied_forces/awh/biasstate.h"
 
 #include <cmath>
 
@@ -44,8 +44,8 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/awh/biasgrid.h"
-#include "gromacs/awh/pointstate.h"
+#include "gromacs/applied_forces/awh/biasgrid.h"
+#include "gromacs/applied_forces/awh/pointstate.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/arrayref.h"

diff --git a/src/gromacs/awh/tests/pmf_target_format0.xvg b/src/gromacs/applied_forces/awh/tests/pmf_target_format0.xvg
similarity index 100%
rename from src/gromacs/awh/tests/pmf_target_format0.xvg
rename to src/gromacs/applied_forces/awh/tests/pmf_target_format0.xvg

diff --git a/src/gromacs/awh/tests/pmf_target_format1.xvg b/src/gromacs/applied_forces/awh/tests/pmf_target_format1.xvg
similarity index 100%
rename from src/gromacs/awh/tests/pmf_target_format1.xvg
rename to src/gromacs/applied_forces/awh/tests/pmf_target_format1.xvg

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml

diff --git a/src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml b/src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml
similarity index 100%
rename from src/gromacs/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml
rename to src/gromacs/applied_forces/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml

diff --git a/src/gromacs/applied_forces/densityfitting/tests/CMakeLists.txt b/src/gromacs/applied_forces/densityfitting/tests/CMakeLists.txt
index 5d6e61d8c1e628ac676d5c5d28af49537e7d8fc5..fd53edda9b3dcf880a21b1f27c4a75bee1aa0c94 100644 (file)
--- a/src/gromacs/applied_forces/densityfitting/tests/CMakeLists.txt
+++ b/src/gromacs/applied_forces/densityfitting/tests/CMakeLists.txt
@@ -35,6 +35,7 @@
 gmx_add_unit_test(DensityFittingAppliedForcesUnitTest density_fitting_applied_forces-test
     CPP_SOURCE_FILES
         densityfitting.cpp
-        densityfittingoptions.cpp
         densityfittingamplitudelookup.cpp
+        densityfittingforceprovider.cpp
+        densityfittingoptions.cpp
         )

diff --git a/src/gromacs/applied_forces/tests/densityfittingforceprovider.cpp b/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
similarity index 100%
rename from src/gromacs/applied_forces/tests/densityfittingforceprovider.cpp
rename to src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
index c5274315a8111e37cd10b10cf97e060d1540fdc8..45722d21a34acee4cda7420a39e4222db871d6b0 100644 (file)
--- a/src/gromacs/applied_forces/tests/densityfittingforceprovider.cpp
+++ b/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/applied_forces/densityfitting/densityfittingforceprovider.h"
 
+#include <gtest/gtest.h>
+
 namespace gmx
 {
 

diff --git a/src/gromacs/applied_forces/tests/CMakeLists.txt b/src/gromacs/applied_forces/tests/CMakeLists.txt
index f3e37c3e84a5983a89c231affa91520a3ad0422a..48ff8a85ad5dda7a3d28a1a7b6e390fd7f3d6d7f 100644 (file)
--- a/src/gromacs/applied_forces/tests/CMakeLists.txt
+++ b/src/gromacs/applied_forces/tests/CMakeLists.txt
@@ -34,6 +34,5 @@
 
 gmx_add_unit_test(AppliedForcesUnitTest applied_forces-test
     CPP_SOURCE_FILES
-        densityfittingforceprovider.cpp
         electricfield.cpp
         )

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 61fadce8db84768b7f5c4ffd8c9a10a2a5cfdb47..ae10d65d75064e5915e3d520a3413513fe00da7b 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -50,7 +50,7 @@
 
 #include <sys/types.h>
 
-#include "gromacs/awh/read_params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 66f7522eac0797c204a2cd4b9c24cb0d78d4cce6..db9cba464eaed759a9b128825d70a27c5cab93c5 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -47,7 +47,7 @@
 #include <algorithm>
 #include <string>
 
-#include "gromacs/awh/read_params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
 #include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxlib/network.h"

diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp
index f658ea377f5cfe768f30c019ea30b484b2d34274..b4bcbf975adbc67e57408b16e38798c38da82e7e 100644 (file)
--- a/src/gromacs/mdlib/energyoutput.cpp
+++ b/src/gromacs/mdlib/energyoutput.cpp
@@ -55,7 +55,7 @@
 #include <array>
 #include <string>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 53cff6eefd29b52f57a2eba69e17f11e6e1965e5..72160eda1a8b24c95a2eaac38376fed92b22765a 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -45,7 +45,7 @@
 
 #include <array>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/domdec/dlbtiming.h"
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index a97e0eeb75703f174c08ff5c2f848494ff2ad7a5..03f95e679732b88307517e9dfa42529c4cda34f1 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -52,7 +52,7 @@
 #include <memory>
 #include <numeric>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/domdec/collect.h"
 #include "gromacs/domdec/dlbtiming.h"

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index edd2814e5897fa0d2e91a01ee0be2eb2408c6eea..eab7080e7571d9c5ac3e9ce169d98acaef3de778 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -50,7 +50,7 @@
 #include <algorithm>
 #include <memory>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/domdec/collect.h"
 #include "gromacs/domdec/dlbtiming.h"

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index 8230157ded92d002fd10ea995d2f99484102e7b0..9b7dcf22265bc528ff045063b09a04e74c9d463a 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -49,7 +49,7 @@
 #include <algorithm>
 #include <memory>
 
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/domdec/collect.h"
 #include "gromacs/domdec/dlbtiming.h"