Renamed listed-forces to listed_forces

There should be consistency in naming. _ is used in almost
all cases (2744 to 122 in src/gromacs not counting files
changed here). Follow up changes will change the remaining
files.

Change-Id: Iea57accfd94d7ede180b9becd7d607425a8df7f6

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index 0f7e243b6bd3ed92a52b292cecf54be492b5ee00..09410e82d6eb878b43f299e366928296b872c9b6 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -7,7 +7,7 @@ domdec -> ewald
 domdec -> mdlib
 domdec -> pulling
 fileio -> gmxlib
-gmxlib -> listed-forces
+gmxlib -> listed_forces
 mdlib -> essentialdynamics
 mdlib -> imd
 mdlib -> ewald
@@ -15,4 +15,4 @@ mdlib -> pulling
 mdlib -> awh
 simd -> hardware
 gpu_utils -> hardware
-listed-forces -> mdlib
+listed_forces -> mdlib

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 71dceb857fda651590f897d23ff2a87747949925..4e242f1cc7c6508676135fd5cb1cbce13891a0e4 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -96,7 +96,7 @@ endfunction()
 add_subdirectory(gmxlib)
 add_subdirectory(mdlib)
 add_subdirectory(applied-forces)
-add_subdirectory(listed-forces)
+add_subdirectory(listed_forces)
 add_subdirectory(commandline)
 add_subdirectory(domdec)
 add_subdirectory(ewald)

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 48c3f849639be097b74b91e5912fb29fb982b026..6ed75fbeaaaddeff2019b6866e6d95f23be221c5 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, 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.
@@ -60,7 +60,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/hardware/hw_info.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/calc_verletbuf.h"

diff --git a/src/gromacs/gmxana/anadih.cpp b/src/gromacs/gmxana/anadih.cpp
index cf7869ced0ee85cec290c293dfa34323cc697dc8..7b94925c0e533e10db7644383d266285388b2fdc 100644 (file)
--- a/src/gromacs/gmxana/anadih.cpp
+++ b/src/gromacs/gmxana/anadih.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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 "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 095aa2da37d3f309a5a4f725d0e7f9754ec794e0..de453d4a292bd7d781d61413b18f8646cf2bd6a9 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -52,7 +52,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/linearalgebra/nrjac.h"
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index bb5438df7e741bef7856edb16001fde39da7bb75..389188933c833e3e34f185ea1e8b9888eaac1416 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -53,7 +53,7 @@
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
 #include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/listed-forces/disre.h"
+#include "gromacs/listed_forces/disre.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_eneconv.cpp b/src/gromacs/gmxana/gmx_eneconv.cpp
index 8ef0a0612963639a32a13d8b5dffd0a8005f9fcd..fd439e1003763b6d334ae70e9ec1311d1c48883a 100644 (file)
--- a/src/gromacs/gmxana/gmx_eneconv.cpp
+++ b/src/gromacs/gmxana/gmx_eneconv.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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 "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/listed-forces/disre.h"
+#include "gromacs/listed_forces/disre.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/gromacs/gmxana/hxprops.cpp b/src/gromacs/gmxana/hxprops.cpp
index 4e29b849bda8385aa1eab60bd58224d7540144ff..94a6671d87ae69f9cf092e11a394cb14e828639a 100644 (file)
--- a/src/gromacs/gmxana/hxprops.cpp
+++ b/src/gromacs/gmxana/hxprops.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -43,7 +43,7 @@
 
 #include <algorithm>
 
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/nrama.cpp b/src/gromacs/gmxana/nrama.cpp
index b721117b2abacea35562b004875f2dc66d512aee..689f6c17ee929fda6692e54c6c39336b6bda30b4 100644 (file)
--- a/src/gromacs/gmxana/nrama.cpp
+++ b/src/gromacs/gmxana/nrama.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -43,7 +43,7 @@
 
 #include <algorithm>
 
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
index 8ca8aa9ef65c606b9af335c3eeb2fb067cb8d663..cde937b75a55eb5da128c3451a826256caf15c4d 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
@@ -51,7 +51,7 @@
 #include "gromacs/gmxlib/nonbonded/nb_generic.h"
 #include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/enerdata.h"

diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp
index 568f88540ec4763f1fe647dc6ea64b44ee93b742..fdbe302c147adc926eea32f5d68b7473e98ecf46 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.cpp
+++ b/src/gromacs/gmxpreprocess/x2top.cpp
@@ -54,7 +54,7 @@
 #include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/gmxpreprocess/toputil.h"
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/listed-forces/CMakeLists.txt b/src/gromacs/listed_forces/CMakeLists.txt
similarity index 95%
rename from src/gromacs/listed-forces/CMakeLists.txt
rename to src/gromacs/listed_forces/CMakeLists.txt
index 4339a190fed9d9c538fcb15403b9c5551156da15..bd97c81fe1b3b53a84605087192297b6d9a0596e 100644 (file)
--- a/src/gromacs/listed-forces/CMakeLists.txt
+++ b/src/gromacs/listed_forces/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016,2018, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2018,2019, 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.
@@ -36,7 +36,7 @@ gmx_add_libgromacs_sources(
     bonded.cpp
     disre.cpp
     gpubonded-impl.cpp
-    listed-forces.cpp
+    listed_forces.cpp
     listed-internal.cpp
     manage-threading.cpp
     orires.cpp

diff --git a/src/gromacs/listed-forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp
similarity index 99%
rename from src/gromacs/listed-forces/bonded.cpp
rename to src/gromacs/listed_forces/bonded.cpp
index cbf89ad421e6c01c4497c982014fdae832eb2402..0ae06d19af587562abcf334359eb52d343a9908d 100644 (file)
--- a/src/gromacs/listed-forces/bonded.cpp
+++ b/src/gromacs/listed_forces/bonded.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -41,7 +41,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 
@@ -54,7 +54,7 @@
 
 #include <algorithm>
 
-#include "gromacs/listed-forces/pairs.h"
+#include "gromacs/listed_forces/pairs.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/listed-forces/bonded.h b/src/gromacs/listed_forces/bonded.h
similarity index 99%
rename from src/gromacs/listed-forces/bonded.h
rename to src/gromacs/listed_forces/bonded.h
index 814f4d080733ebe531812123714c87d41c68d9e2..9a139f035d153e867016036eca32090cd4c69208 100644 (file)
--- a/src/gromacs/listed-forces/bonded.h
+++ b/src/gromacs/listed_forces/bonded.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -41,7 +41,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #ifndef GMX_LISTED_FORCES_BONDED_H

diff --git a/src/gromacs/listed-forces/disre.cpp b/src/gromacs/listed_forces/disre.cpp
similarity index 99%
rename from src/gromacs/listed-forces/disre.cpp
rename to src/gromacs/listed_forces/disre.cpp
index 408601c06a9b9f27e3d90e5039b8cf14bf81a328..f827ada753d79784347a34b6f590b7bc45ddbc60 100644 (file)
--- a/src/gromacs/listed-forces/disre.cpp
+++ b/src/gromacs/listed_forces/disre.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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/listed-forces/disre.h b/src/gromacs/listed_forces/disre.h
similarity index 96%
rename from src/gromacs/listed-forces/disre.h
rename to src/gromacs/listed_forces/disre.h
index 211700d984939d0675ee85049c0087f88d5447d1..7cbce33908ba5cf0b493e6df90bdc95e4321c3c0 100644 (file)
--- a/src/gromacs/listed-forces/disre.h
+++ b/src/gromacs/listed_forces/disre.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  * Declares functions for handling distance restraints.
  *
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_DISRE_H
 #define GMX_LISTED_FORCES_DISRE_H

diff --git a/src/gromacs/listed-forces/gpubonded-impl.cpp b/src/gromacs/listed_forces/gpubonded-impl.cpp
similarity index 97%
rename from src/gromacs/listed-forces/gpubonded-impl.cpp
rename to src/gromacs/listed_forces/gpubonded-impl.cpp
index 998ad7a5c8e22a1257475e2d03045dc524de825b..77c3256510565b5bc93c743f34e32d834c49265d 100644 (file)
--- a/src/gromacs/listed-forces/gpubonded-impl.cpp
+++ b/src/gromacs/listed_forces/gpubonded-impl.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -38,7 +38,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #include "gmxpre.h"
@@ -47,7 +47,7 @@
 
 #include <string>
 
-#include "gromacs/listed-forces/gpubonded.h"
+#include "gromacs/listed_forces/gpubonded.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/stringutil.h"

diff --git a/src/gromacs/listed-forces/gpubonded-impl.cu b/src/gromacs/listed_forces/gpubonded-impl.cu
similarity index 98%
rename from src/gromacs/listed-forces/gpubonded-impl.cu
rename to src/gromacs/listed_forces/gpubonded-impl.cu
index 9df0a2d21536a90fbf0e106ee164e29d897eba19..8da1a9ffd052fbe3068f7e1603f025672515c9c4 100644 (file)
--- a/src/gromacs/listed-forces/gpubonded-impl.cu
+++ b/src/gromacs/listed_forces/gpubonded-impl.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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 +40,7 @@
  * \author Szilárd Páll <pall.szilard@gmail.com>
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #include "gmxpre.h"
@@ -52,7 +52,7 @@
 #include "gromacs/gpu_utils/gpu_vec.cuh"
 #include "gromacs/gpu_utils/gputraits.cuh"
 #include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/listed-forces/gpubonded.h"
+#include "gromacs/listed_forces/gpubonded.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/topology/forcefieldparameters.h"
 #include "gromacs/topology/idef.h"

diff --git a/src/gromacs/listed-forces/gpubonded-impl.h b/src/gromacs/listed_forces/gpubonded-impl.h
similarity index 98%
rename from src/gromacs/listed-forces/gpubonded-impl.h
rename to src/gromacs/listed_forces/gpubonded-impl.h
index 3720fe23fa7bf01f4c3a0f9ceb6350bc0c489557..79c0ad157e4bf3027624a93c197951187c6369e8 100644 (file)
--- a/src/gromacs/listed-forces/gpubonded-impl.h
+++ b/src/gromacs/listed_forces/gpubonded-impl.h
@@ -43,7 +43,7 @@
  * \author Szilárd Páll <pall.szilard@gmail.com>
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_GPUBONDED_IMPL_H
 #define GMX_LISTED_FORCES_GPUBONDED_IMPL_H
@@ -51,7 +51,7 @@
 #include "gromacs/gpu_utils/gpu_vec.cuh"
 #include "gromacs/gpu_utils/gputraits.cuh"
 #include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/listed-forces/gpubonded.h"
+#include "gromacs/listed_forces/gpubonded.h"
 #include "gromacs/topology/idef.h"
 
 struct gmx_ffparams_t;

diff --git a/src/gromacs/listed-forces/gpubonded.h b/src/gromacs/listed_forces/gpubonded.h
similarity index 97%
rename from src/gromacs/listed-forces/gpubonded.h
rename to src/gromacs/listed_forces/gpubonded.h
index e2c49f46606db063d5f1bf9df5bca0d0305f8360..442e42041febc5cd40f1585bcf1a6d96bbfa4b55 100644 (file)
--- a/src/gromacs/listed-forces/gpubonded.h
+++ b/src/gromacs/listed_forces/gpubonded.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -43,7 +43,7 @@
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_GPUBONDED_H
 #define GMX_LISTED_FORCES_GPUBONDED_H

diff --git a/src/gromacs/listed-forces/gpubondedkernels.cu b/src/gromacs/listed_forces/gpubondedkernels.cu
similarity index 99%
rename from src/gromacs/listed-forces/gpubondedkernels.cu
rename to src/gromacs/listed_forces/gpubondedkernels.cu
index ea494f01448fd78c7c4d56b8df4cf9c7d3959dcf..2f7848634057b8bed9112b5802d8e319ff2403bb 100644 (file)
--- a/src/gromacs/listed-forces/gpubondedkernels.cu
+++ b/src/gromacs/listed_forces/gpubondedkernels.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -43,7 +43,7 @@
  * \author Alan Gray <alang@nvidia.com>
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #include "gmxpre.h"
@@ -54,8 +54,8 @@
 #include "gromacs/gpu_utils/devicebuffer.h"
 #include "gromacs/gpu_utils/gpu_vec.cuh"
 #include "gromacs/gpu_utils/gputraits.cuh"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/listed_forces.h"
 #include "gromacs/math/units.h"
 #include "gromacs/mdlib/force_flags.h"
 #include "gromacs/mdtypes/enerdata.h"

diff --git a/src/gromacs/listed-forces/listed-internal.cpp b/src/gromacs/listed_forces/listed-internal.cpp
similarity index 94%
rename from src/gromacs/listed-forces/listed-internal.cpp
rename to src/gromacs/listed_forces/listed-internal.cpp
index a753f76cc7325823e53d6298748254b3ca28e455..2161bff3c5567090fb6703c8aef9e7a12561dd70 100644 (file)
--- a/src/gromacs/listed-forces/listed-internal.cpp
+++ b/src/gromacs/listed_forces/listed-internal.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2017,2018,2019, 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.
@@ -37,7 +37,7 @@
  * \brief This file defines functions needed internally by the module.
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 

diff --git a/src/gromacs/listed-forces/listed-internal.h b/src/gromacs/listed_forces/listed-internal.h
similarity index 99%
rename from src/gromacs/listed-forces/listed-internal.h
rename to src/gromacs/listed_forces/listed-internal.h
index 01b11aa255b53c35c5c20d3fc5450544a55682b0..ad4f3f680f2ca1f06c247598c2a0a0fb082201ab 100644 (file)
--- a/src/gromacs/listed-forces/listed-internal.h
+++ b/src/gromacs/listed_forces/listed-internal.h
@@ -38,7 +38,7 @@
  * internally by the module.
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_LISTED_INTERNAL_H
 #define GMX_LISTED_FORCES_LISTED_INTERNAL_H

diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed_forces/listed_forces.cpp
similarity index 98%
rename from src/gromacs/listed-forces/listed-forces.cpp
rename to src/gromacs/listed_forces/listed_forces.cpp
index fd5f9b76c53c09765fcbc52f098cc36693b2288d..97255fe9a954599a780bceb4d27fc63573d204e6 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.cpp
+++ b/src/gromacs/listed_forces/listed_forces.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -39,11 +39,11 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 
-#include "listed-forces.h"
+#include "listed_forces.h"
 
 #include <cassert>
 
@@ -52,11 +52,11 @@
 
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/listed-forces/bonded.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/orires.h"
-#include "gromacs/listed-forces/pairs.h"
-#include "gromacs/listed-forces/position-restraints.h"
+#include "gromacs/listed_forces/bonded.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/orires.h"
+#include "gromacs/listed_forces/pairs.h"
+#include "gromacs/listed_forces/position-restraints.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/force_flags.h"

diff --git a/src/gromacs/listed-forces/listed-forces.h b/src/gromacs/listed_forces/listed_forces.h
similarity index 97%
rename from src/gromacs/listed-forces/listed-forces.h
rename to src/gromacs/listed_forces/listed_forces.h
index 9c1d4526162d69ac75d24e04efd8371124f7006a..165ebffc7df08a9bc23bf5c47aaf892fd2c63479 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.h
+++ b/src/gromacs/listed_forces/listed_forces.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -32,7 +32,7 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-/*! \defgroup module_listed-forces Interactions between lists of particles
+/*! \defgroup module_listed_forces Interactions between lists of particles
  * \ingroup group_mdrun
  *
  * \brief Handles computing energies and forces for listed
@@ -61,7 +61,7 @@
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_LISTED_FORCES_H
 #define GMX_LISTED_FORCES_LISTED_FORCES_H

diff --git a/src/gromacs/listed-forces/manage-threading.cpp b/src/gromacs/listed_forces/manage-threading.cpp
similarity index 99%
rename from src/gromacs/listed-forces/manage-threading.cpp
rename to src/gromacs/listed_forces/manage-threading.cpp
index c1fc232fc8f2f4ef6e377a5a9bca3c0ca585b782..5aa96feb880b5762321d0af5de86abf11c079f38 100644 (file)
--- a/src/gromacs/listed-forces/manage-threading.cpp
+++ b/src/gromacs/listed_forces/manage-threading.cpp
@@ -39,7 +39,7 @@
  * interactions.
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 
@@ -55,7 +55,7 @@
 #include <algorithm>
 #include <string>
 
-#include "gromacs/listed-forces/gpubonded.h"
+#include "gromacs/listed_forces/gpubonded.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/topology/ifunc.h"

diff --git a/src/gromacs/listed-forces/manage-threading.h b/src/gromacs/listed_forces/manage-threading.h
similarity index 96%
rename from src/gromacs/listed-forces/manage-threading.h
rename to src/gromacs/listed_forces/manage-threading.h
index a395956d152235e7fa6eb735f6d816e918ad6b6a..f50e98e4d0a0164d5a7ecb4a51f97a5256567637 100644 (file)
--- a/src/gromacs/listed-forces/manage-threading.h
+++ b/src/gromacs/listed_forces/manage-threading.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, 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.
@@ -39,7 +39,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_MANAGE_THREADING_H
 #define GMX_LISTED_FORCES_MANAGE_THREADING_H

diff --git a/src/gromacs/listed-forces/orires.cpp b/src/gromacs/listed_forces/orires.cpp
similarity index 100%
rename from src/gromacs/listed-forces/orires.cpp
rename to src/gromacs/listed_forces/orires.cpp

diff --git a/src/gromacs/listed-forces/orires.h b/src/gromacs/listed_forces/orires.h
similarity index 97%
rename from src/gromacs/listed-forces/orires.h
rename to src/gromacs/listed_forces/orires.h
index d7066e1380c47c30641f36ff17a79e07d12a3916..83e8b13e25ecbfb4559486f908f1250300fd5896 100644 (file)
--- a/src/gromacs/listed-forces/orires.h
+++ b/src/gromacs/listed_forces/orires.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  * Declares functions for handling orientation restraints.
  *
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_ORIRES_H
 #define GMX_LISTED_FORCES_ORIRES_H

diff --git a/src/gromacs/listed-forces/pairs.cpp b/src/gromacs/listed_forces/pairs.cpp
similarity index 99%
rename from src/gromacs/listed-forces/pairs.cpp
rename to src/gromacs/listed_forces/pairs.cpp
index 8de6b30d4a91ecf2f639ac78db9114a68db37409..e910e592275cb495faadd988ba2de3c7b8e45a48 100644 (file)
--- a/src/gromacs/listed-forces/pairs.cpp
+++ b/src/gromacs/listed_forces/pairs.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 

diff --git a/src/gromacs/listed-forces/pairs.h b/src/gromacs/listed_forces/pairs.h
similarity index 95%
rename from src/gromacs/listed-forces/pairs.h
rename to src/gromacs/listed_forces/pairs.h
index 88af8347c4ca50460884b7febe5569095fd6b1fc..31f8b61d6478cc4a1514cde4fdc7490ba533662a 100644 (file)
--- a/src/gromacs/listed-forces/pairs.h
+++ b/src/gromacs/listed_forces/pairs.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_PAIRS_H
 #define GMX_LISTED_FORCES_PAIRS_H

diff --git a/src/gromacs/listed-forces/position-restraints.cpp b/src/gromacs/listed_forces/position-restraints.cpp
similarity index 99%
rename from src/gromacs/listed-forces/position-restraints.cpp
rename to src/gromacs/listed_forces/position-restraints.cpp
index 0fa2a2fed8cfd4e00faef9a406fd90b415c97a78..f6c865b30ba91a6d12acfe01096891198b0218bd 100644 (file)
--- a/src/gromacs/listed-forces/position-restraints.cpp
+++ b/src/gromacs/listed_forces/position-restraints.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #include "gmxpre.h"

diff --git a/src/gromacs/listed-forces/position-restraints.h b/src/gromacs/listed_forces/position-restraints.h
similarity index 96%
rename from src/gromacs/listed-forces/position-restraints.h
rename to src/gromacs/listed_forces/position-restraints.h
index a02cae052491edb45490c265a8ec0357e517156d..79387ecb419e39f12e82edc9a233272bff9a0322 100644 (file)
--- a/src/gromacs/listed-forces/position-restraints.h
+++ b/src/gromacs/listed_forces/position-restraints.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019, 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 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  * \inlibraryapi
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #ifndef GMX_LISTED_FORCES_POSITION_RESTRAINTS_H

diff --git a/src/gromacs/listed-forces/restcbt.cpp b/src/gromacs/listed_forces/restcbt.cpp
similarity index 99%
rename from src/gromacs/listed-forces/restcbt.cpp
rename to src/gromacs/listed_forces/restcbt.cpp
index f264029e43622540483b83781b1a89dbcc529eb2..6e88355ff27285d6f285be24e8d1560b5d293522 100644 (file)
--- a/src/gromacs/listed-forces/restcbt.cpp
+++ b/src/gromacs/listed_forces/restcbt.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019, 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.
@@ -41,7 +41,7 @@
  *
  * \author Nicolae Goga
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 

diff --git a/src/gromacs/listed-forces/restcbt.h b/src/gromacs/listed_forces/restcbt.h
similarity index 99%
rename from src/gromacs/listed-forces/restcbt.h
rename to src/gromacs/listed_forces/restcbt.h
index 7b6cabd8162c4b2769aa145933ae2d706f759ee2..56dca730fe5d6059bb3a7b5e025a10a099fa057e 100644 (file)
--- a/src/gromacs/listed-forces/restcbt.h
+++ b/src/gromacs/listed_forces/restcbt.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019, 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.
@@ -43,7 +43,7 @@
  *
  * \author Nicolae Goga
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 
 #ifndef GMX_LISTED_FORCES_RESTCBT_H

diff --git a/src/gromacs/listed-forces/tests/CMakeLists.txt b/src/gromacs/listed_forces/tests/CMakeLists.txt
similarity index 93%
rename from src/gromacs/listed-forces/tests/CMakeLists.txt
rename to src/gromacs/listed_forces/tests/CMakeLists.txt
index 254fc1b936d8d6afdae6052799fb30c3e6529217..e987e69a4b8281460b2f3092b0d62efef939c00f 100644 (file)
--- a/src/gromacs/listed-forces/tests/CMakeLists.txt
+++ b/src/gromacs/listed_forces/tests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2016, by the GROMACS development team, led by
+# Copyright (c) 2016,2019, 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.
@@ -32,6 +32,6 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
-gmx_add_unit_test(ListedForcesTest listed-forces-test
+gmx_add_unit_test(ListedForcesTest listed_forces-test
   bonded.cpp)
 

diff --git a/src/gromacs/listed-forces/tests/bonded.cpp b/src/gromacs/listed_forces/tests/bonded.cpp
similarity index 98%
rename from src/gromacs/listed-forces/tests/bonded.cpp
rename to src/gromacs/listed_forces/tests/bonded.cpp
index 21130615a20bb6e169b45e5e73ea2b37423457f6..11541a522bf05206f7eac9225edb752a03f1a31d 100644 (file)
--- a/src/gromacs/listed-forces/tests/bonded.cpp
+++ b/src/gromacs/listed_forces/tests/bonded.cpp
@@ -37,11 +37,11 @@
  * Implements test of bonded force routines
  *
  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #include "gmxpre.h"
 
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
 
 #include <cmath>
 
@@ -49,7 +49,7 @@
 
 #include <gtest/gtest.h>
 
-#include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/listed_forces/listed_forces.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_7.xml
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diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_0.xml
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diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_1.xml
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diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml

diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml
similarity index 100%
rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml
rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml

diff --git a/src/gromacs/listed-forces/utilities.h b/src/gromacs/listed_forces/utilities.h
similarity index 95%
rename from src/gromacs/listed-forces/utilities.h
rename to src/gromacs/listed_forces/utilities.h
index 96ab324b416e4b19adefbecf059f7f6b63f5a97c..c652fa5ae336b3f79e8bcb20a9a20884ced6693d 100644 (file)
--- a/src/gromacs/listed-forces/utilities.h
+++ b/src/gromacs/listed_forces/utilities.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
@@ -39,7 +39,7 @@
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
  *
- * \ingroup module_listed-forces
+ * \ingroup module_listed_forces
  */
 #ifndef GMX_LISTED_FORCES_UTILITIES_H
 #define GMX_LISTED_FORCES_UTILITIES_H

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 7e70646bd57822a56a2a221fe981f20f087b4368..5e0c61b0fdcc4c74725b1d7d19084ec3f1e325e3 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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.
@@ -48,8 +48,8 @@
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/orires.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index e86d4eee6170e1c9e23111a89454ba4fcfab1e04..7847aaa8cc8595e067505c3dc16a1a308cbec6e4 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -52,7 +52,7 @@
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
-#include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/listed_forces/listed_forces.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vecdump.h"
 #include "gromacs/mdlib/force_flags.h"

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index f43b13e7a274c15392230a841155e79cf44691db..c231eace7bc4279261b094b2ee9fd6eaab0f988c 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -58,9 +58,9 @@
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/hardware/hw_info.h"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/listed-forces/pairs.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/pairs.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp
index 3ff4978346434052a89ea11589679d2eedc1daf2..6477842305c8ec816a895e582bb1dc6914638e88 100644 (file)
--- a/src/gromacs/mdlib/mdebin.cpp
+++ b/src/gromacs/mdlib/mdebin.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -49,8 +49,8 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/orires.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/mdsetup.cpp b/src/gromacs/mdlib/mdsetup.cpp
index 62558c8552c112e101a3a318939c062a2d00212d..5a5bb53164779213b7163f194dde1401c69e4ac3 100644 (file)
--- a/src/gromacs/mdlib/mdsetup.cpp
+++ b/src/gromacs/mdlib/mdsetup.cpp
@@ -39,7 +39,7 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/shellfc.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 8e7af55869e7b0531c45ebb992f1da137f955376..c6c02e77a0179fb27a5f1fa47ab2d462b80e2b1b 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -61,11 +61,11 @@
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed-forces/bonded.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/listed-forces/orires.h"
+#include "gromacs/listed_forces/bonded.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/arrayrefwithpadding.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index e6f39df9bc17b0f77db5e4b1dc377f60747cd98c..311d1622980ed37caa564465701074fbd5302cc5 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -48,8 +48,8 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/orires.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/invertmatrix.h"
 #include "gromacs/math/paddedvector.h"

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 82923ab02b7266454fc5f23a6f4ab9914bb44bbb..86c7bea16a62524f644139bfc59a260e0cea9f3f 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -67,7 +67,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index dc315a49e3149c27c26ce4646728816c1c0c54b5..aaec3bbf1f7b51c78397f1596686168109db31f8 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -66,7 +66,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
index 7a11fdbbb6054fb59e4e92cf504a30d8109e8e49..d7f720018e2dc98a837c79cdfda38446b66d9ae5 100644 (file)
--- a/src/gromacs/mdrun/minimize.cpp
+++ b/src/gromacs/mdrun/minimize.cpp
@@ -65,7 +65,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index a8ae9395ff72f37e43575602d6f71bf3d0b04f63..6ca622a2a12ec64fda6e5308874e54976f5ecf06 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -67,7 +67,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage-threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index f553e9f7bb125564accf86404b1ead4fed1800a9..7dfeb1293a94aa1b305ac987a715a8154af0673c 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -74,9 +74,9 @@
 #include "gromacs/hardware/cpuinfo.h"
 #include "gromacs/hardware/detecthardware.h"
 #include "gromacs/hardware/printhardware.h"
-#include "gromacs/listed-forces/disre.h"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/orires.h"
+#include "gromacs/listed_forces/disre.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"