From: Mark Abraham Date: Tue, 20 Jan 2015 18:26:20 +0000 (+0100) Subject: Update mdrun Doxygen X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=bff590b053da7efdaa89902110fcfff26a72e382;p=alexxy%2Fgromacs.git Update mdrun Doxygen Define module_mdrun. Added suppression for the observation by make check-source that this is not consistent with other module naming - we haven't made a final decision yet. Move integration test Doxygen to module_mdrun_integration_tests. Change-Id: I817488a67d37d5edeaf34b7c29067c6b36436aa8 --- diff --git a/docs/doxygen/suppressions.txt b/docs/doxygen/suppressions.txt index 71d9f29d23..ca354bb4c2 100644 --- a/docs/doxygen/suppressions.txt +++ b/docs/doxygen/suppressions.txt @@ -13,6 +13,10 @@ src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" fir src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h" src/gromacs/utility/baseversion-gen.c: warning: does not include "gmxpre.h" first +# There's no decision yet on how to name and organize modules of functionality +# specific to mdrun +: error: no matching directory for module: module_mdrun + # This module name doesn't really fall into any currently used pattern; needs some thought : error: no matching directory for module: module_mdrun_integration_tests diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp index 989c8b4ddc..f1e045a2ea 100644 --- a/src/programs/mdrun/mdrun.cpp +++ b/src/programs/mdrun/mdrun.cpp @@ -34,6 +34,22 @@ * 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_mdrun Implementation of mdrun + * \ingroup group_mdrun + * + * \brief This module contains code that implements mdrun. + */ +/*! \internal \file + * + * \brief This file implements mdrun + * + * \author Berk Hess + * \author David van der Spoel + * \author Erik Lindahl + * \author Mark Abraham + * + * \ingroup module_mdrun + */ #include "gmxpre.h" #include "config.h" @@ -56,6 +72,8 @@ #include "mdrun_main.h" +/*! \brief Return whether either of the command-line parameters that + * will trigger a multi-simulation is set */ static bool is_multisim_option_set(int argc, const char *const argv[]) { for (int i = 0; i < argc; ++i) @@ -68,6 +86,7 @@ static bool is_multisim_option_set(int argc, const char *const argv[]) return false; } +//! Implements C-style main function for mdrun int gmx_mdrun(int argc, char *argv[]) { const char *desc[] = { @@ -242,7 +261,7 @@ int gmx_mdrun(int argc, char *argv[]) { efXVG, "-if", "imdforces", ffOPTWR }, { efXVG, "-swap", "swapions", ffOPTWR } }; -#define NFILE asize(fnm) + const int NFILE = asize(fnm); /* Command line options ! */ gmx_bool bDDBondCheck = TRUE; diff --git a/src/programs/mdrun/tests/compressed_x_output.cpp b/src/programs/mdrun/tests/compressed_x_output.cpp index 4cc1b106f2..6617da987c 100644 --- a/src/programs/mdrun/tests/compressed_x_output.cpp +++ b/src/programs/mdrun/tests/compressed_x_output.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -38,7 +38,7 @@ * Tests for the mdrun -x functionality * * \author Mark Abraham - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/interactiveMD.cpp b/src/programs/mdrun/tests/interactiveMD.cpp index a4b7b3dfe6..417d8f1140 100644 --- a/src/programs/mdrun/tests/interactiveMD.cpp +++ b/src/programs/mdrun/tests/interactiveMD.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -38,7 +38,7 @@ * Tests utilities for interactive molecular dynamics (IMD) setups. * * \author Carsten Kutzner - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/moduletest.cpp b/src/programs/mdrun/tests/moduletest.cpp index 1e8a6373c5..718e4c647b 100644 --- a/src/programs/mdrun/tests/moduletest.cpp +++ b/src/programs/mdrun/tests/moduletest.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -37,7 +37,7 @@ * Implements classes in moduletest.h. * * \author Mark Abraham - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/replicaexchange.cpp b/src/programs/mdrun/tests/replicaexchange.cpp index 5b581f4d8a..061c9a186d 100644 --- a/src/programs/mdrun/tests/replicaexchange.cpp +++ b/src/programs/mdrun/tests/replicaexchange.cpp @@ -38,7 +38,7 @@ * Tests for the mdrun replica-exchange functionality * * \author Mark Abraham - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/rerun.cpp b/src/programs/mdrun/tests/rerun.cpp index a73f2623be..1e11fd5ef4 100644 --- a/src/programs/mdrun/tests/rerun.cpp +++ b/src/programs/mdrun/tests/rerun.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -38,7 +38,7 @@ * Tests for the mdrun -rerun functionality * * \author Mark Abraham - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/swapcoords.cpp b/src/programs/mdrun/tests/swapcoords.cpp index ac43152206..beeef88e22 100644 --- a/src/programs/mdrun/tests/swapcoords.cpp +++ b/src/programs/mdrun/tests/swapcoords.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -38,7 +38,7 @@ * Tests utilities for "Computational Electrophysiology" setups. * * \author Carsten Kutzner - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h" diff --git a/src/programs/mdrun/tests/trajectory_writing.cpp b/src/programs/mdrun/tests/trajectory_writing.cpp index fafb1c3f92..e61ad87636 100644 --- a/src/programs/mdrun/tests/trajectory_writing.cpp +++ b/src/programs/mdrun/tests/trajectory_writing.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -38,7 +38,7 @@ * Tests for the .mdp nst*out functionality * * \author Mark Abraham - * \ingroup module_mdrun + * \ingroup module_mdrun_integration_tests */ #include "gmxpre.h"