From 54d52e0f05a92e7d7d889139d0c003bae388bb74 Mon Sep 17 00:00:00 2001 From: Paul Bauer Date: Tue, 8 Sep 2020 07:29:07 +0000 Subject: [PATCH] Move densityfitting to its own directory Preparing for adding more applied_forces modules Change-Id: Ieec20d1f0752a369d26352ec6b0997812decd21e --- docs/doxygen/cycle-suppressions.txt | 3 +++ src/gromacs/CMakeLists.txt | 1 - src/gromacs/applied_forces/CMakeLists.txt | 1 + .../{ => applied_forces}/awh/CMakeLists.txt | 18 +++++++++++++++--- src/gromacs/{ => applied_forces}/awh/awh.cpp | 0 src/gromacs/{ => applied_forces}/awh/awh.h | 2 +- src/gromacs/{ => applied_forces}/awh/bias.cpp | 0 src/gromacs/{ => applied_forces}/awh/bias.h | 0 .../{ => applied_forces}/awh/biasgrid.cpp | 0 .../{ => applied_forces}/awh/biasgrid.h | 0 .../{ => applied_forces}/awh/biasparams.cpp | 0 .../{ => applied_forces}/awh/biasparams.h | 0 .../{ => applied_forces}/awh/biassharing.cpp | 0 .../{ => applied_forces}/awh/biassharing.h | 2 +- .../{ => applied_forces}/awh/biasstate.cpp | 0 .../{ => applied_forces}/awh/biasstate.h | 0 .../{ => applied_forces}/awh/biaswriter.cpp | 2 +- .../{ => applied_forces}/awh/biaswriter.h | 2 +- .../{ => applied_forces}/awh/coordstate.cpp | 0 .../{ => applied_forces}/awh/coordstate.h | 0 .../awh/correlationgrid.cpp | 2 +- .../{ => applied_forces}/awh/correlationgrid.h | 0 .../awh/correlationhistory.cpp | 2 +- .../awh/correlationhistory.h | 2 +- .../awh/correlationtensor.cpp | 2 +- .../awh/correlationtensor.h | 2 +- .../{ => applied_forces}/awh/dimparams.h | 0 .../{ => applied_forces}/awh/histogramsize.cpp | 0 .../{ => applied_forces}/awh/histogramsize.h | 0 .../{ => applied_forces}/awh/pointstate.cpp | 0 .../{ => applied_forces}/awh/pointstate.h | 0 .../{ => applied_forces}/awh/read_params.cpp | 2 +- .../{ => applied_forces}/awh/read_params.h | 0 .../awh/tests/CMakeLists.txt | 0 .../{ => applied_forces}/awh/tests/bias.cpp | 6 +++--- .../awh/tests/bias_fep_lambda_state.cpp | 6 +++--- .../awh/tests/biasgrid.cpp | 2 +- .../awh/tests/biasstate.cpp | 6 +++--- .../awh/tests/pmf_target_format0.xvg | 0 .../awh/tests/pmf_target_format1.xvg | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_0.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_1.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_2.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_3.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_4.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_5.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_6.xml | 0 ..._BiasFepLambdaStateTest_ForcesBiasPmf_7.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_0.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_1.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_2.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_3.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_4.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_5.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_6.xml | 0 ...WithParameters_BiasTest_ForcesBiasPmf_7.xml | 0 .../densityfitting/tests/CMakeLists.txt | 3 ++- .../tests/densityfittingforceprovider.cpp | 4 ++-- .../applied_forces/tests/CMakeLists.txt | 1 - src/gromacs/gmxpreprocess/grompp.cpp | 2 +- src/gromacs/gmxpreprocess/readir.cpp | 2 +- src/gromacs/mdlib/energyoutput.cpp | 2 +- src/gromacs/mdlib/sim_util.cpp | 2 +- src/gromacs/mdrun/md.cpp | 2 +- src/gromacs/mdrun/mimic.cpp | 2 +- src/gromacs/mdrun/rerun.cpp | 2 +- 66 files changed, 50 insertions(+), 35 deletions(-) rename src/gromacs/{ => applied_forces}/awh/CMakeLists.txt (70%) rename src/gromacs/{ => applied_forces}/awh/awh.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/awh.h (99%) rename src/gromacs/{ => applied_forces}/awh/bias.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/bias.h (100%) rename src/gromacs/{ => applied_forces}/awh/biasgrid.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/biasgrid.h (100%) rename src/gromacs/{ => applied_forces}/awh/biasparams.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/biasparams.h (100%) rename src/gromacs/{ => applied_forces}/awh/biassharing.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/biassharing.h (97%) rename src/gromacs/{ => applied_forces}/awh/biasstate.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/biasstate.h (100%) rename src/gromacs/{ => applied_forces}/awh/biaswriter.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/biaswriter.h (98%) rename src/gromacs/{ => applied_forces}/awh/coordstate.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/coordstate.h (100%) rename src/gromacs/{ => applied_forces}/awh/correlationgrid.cpp (98%) rename src/gromacs/{ => applied_forces}/awh/correlationgrid.h (100%) rename src/gromacs/{ => applied_forces}/awh/correlationhistory.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/correlationhistory.h (97%) rename src/gromacs/{ => applied_forces}/awh/correlationtensor.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/correlationtensor.h (99%) rename src/gromacs/{ => applied_forces}/awh/dimparams.h (100%) rename src/gromacs/{ => applied_forces}/awh/histogramsize.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/histogramsize.h (100%) rename src/gromacs/{ => applied_forces}/awh/pointstate.cpp (100%) rename src/gromacs/{ => applied_forces}/awh/pointstate.h (100%) rename src/gromacs/{ => applied_forces}/awh/read_params.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/read_params.h (100%) rename src/gromacs/{ => applied_forces}/awh/tests/CMakeLists.txt (100%) rename src/gromacs/{ => applied_forces}/awh/tests/bias.cpp (98%) rename src/gromacs/{ => applied_forces}/awh/tests/bias_fep_lambda_state.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/tests/biasgrid.cpp (99%) rename src/gromacs/{ => applied_forces}/awh/tests/biasstate.cpp (97%) rename src/gromacs/{ => applied_forces}/awh/tests/pmf_target_format0.xvg (100%) rename src/gromacs/{ => applied_forces}/awh/tests/pmf_target_format1.xvg (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_0.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_1.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_2.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_3.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_4.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_5.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_6.xml (100%) rename src/gromacs/{ => applied_forces}/awh/tests/refdata/WithParameters_BiasTest_ForcesBiasPmf_7.xml (100%) rename src/gromacs/applied_forces/{ => densityfitting}/tests/densityfittingforceprovider.cpp (100%) diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt index b325f57967..840e2797f7 100644 --- 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 1a35de1591..48636cdc86 100644 --- 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 bdca6f54ec..498d44a220 100644 --- 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 8fc400a9e7..0917be1d83 100644 --- 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 efd7c80a43..30b0a25b1a 100644 --- 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 b98a4344a8..751fe2f9a5 100644 --- 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 3d25af4edb..8fd09eedbc 100644 --- a/src/gromacs/awh/biaswriter.cpp +++ b/src/gromacs/applied_forces/awh/biaswriter.cpp @@ -40,7 +40,7 @@ #include #include -#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 14625b54dc..420a26ff63 100644 --- 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 ac1b48edb4..1181dd1999 100644 --- 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 3dac473fe0..f77ba39938 100644 --- 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 61e70d9507..05ac52845f 100644 --- 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 ebcd1aa590..b2a42d905c 100644 --- 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 e9fe9537da..9da3928dc9 100644 --- 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 0eb30ee0f8..d301bd83d9 100644 --- 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 c59fb1327f..7d49ffdc80 100644 --- 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 @@ -45,8 +45,8 @@ #include #include -#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 1e4b452a81..78b84e95e8 100644 --- 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 #include -#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 ebc2791074..9203f6cfc6 100644 --- 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 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 60fe0d44d0..db11a9a5ca 100644 --- 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 @@ -44,8 +44,8 @@ #include #include -#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 5d6e61d8c1..fd53edda9b 100644 --- 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 c5274315a8..45722d21a3 100644 --- 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 - #include "gromacs/applied_forces/densityfitting/densityfittingforceprovider.h" +#include + namespace gmx { diff --git a/src/gromacs/applied_forces/tests/CMakeLists.txt b/src/gromacs/applied_forces/tests/CMakeLists.txt index f3e37c3e84..48ff8a85ad 100644 --- 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 61fadce8db..ae10d65d75 100644 --- a/src/gromacs/gmxpreprocess/grompp.cpp +++ b/src/gromacs/gmxpreprocess/grompp.cpp @@ -50,7 +50,7 @@ #include -#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 66f7522eac..db9cba464e 100644 --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@ -47,7 +47,7 @@ #include #include -#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 f658ea377f..b4bcbf975a 100644 --- a/src/gromacs/mdlib/energyoutput.cpp +++ b/src/gromacs/mdlib/energyoutput.cpp @@ -55,7 +55,7 @@ #include #include -#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 53cff6eefd..72160eda1a 100644 --- a/src/gromacs/mdlib/sim_util.cpp +++ b/src/gromacs/mdlib/sim_util.cpp @@ -45,7 +45,7 @@ #include -#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 a97e0eeb75..03f95e6797 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -52,7 +52,7 @@ #include #include -#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 edd2814e58..eab7080e75 100644 --- a/src/gromacs/mdrun/mimic.cpp +++ b/src/gromacs/mdrun/mimic.cpp @@ -50,7 +50,7 @@ #include #include -#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 8230157ded..9b7dcf2226 100644 --- a/src/gromacs/mdrun/rerun.cpp +++ b/src/gromacs/mdrun/rerun.cpp @@ -49,7 +49,7 @@ #include #include -#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" -- 2.22.0