Part of #1415 Get rid of legacyheaders.
Additional changes:
- provided doxygen-style documentation for functions in edsam.h
(partly copied over from edsam.c and removed there to avoid
duplication)
- uncrustified edsam.c and edsam.h
Change-Id: If4af498470c5200d50ac1d1b5537917c873380b5
add_subdirectory(timing)
add_subdirectory(utility)
add_subdirectory(fileio)
+add_subdirectory(essentialdynamics)
if (NOT GMX_BUILD_MDRUN_ONLY)
add_subdirectory(legacyheaders)
add_subdirectory(gmxana)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, 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.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# 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 ESSENTIALDYNAMICS_SOURCES *.cpp *.c)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ESSENTIALDYNAMICS_SOURCES} PARENT_SCOPE)
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif (BUILD_TESTING)
#include "physics.h"
#include "nrjac.h"
#include "mtop_util.h"
-#include "edsam.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/gmxfio.h"
#include "xvgr.h"
-#include "groupcoord.h"
+#include "gromacs/mdlib/groupcoord.h"
/* We use the same defines as in mvdata.c here */
* for any of the ED groups? */
static gmx_bool bNeedDoEdsam(t_edpar *edi)
{
- return edi->vecs.mon.neig
- || edi->vecs.linfix.neig
- || edi->vecs.linacc.neig
- || edi->vecs.radfix.neig
- || edi->vecs.radacc.neig
- || edi->vecs.radcon.neig;
+ return edi->vecs.mon.neig
+ || edi->vecs.linfix.neig
+ || edi->vecs.linacc.neig
+ || edi->vecs.radfix.neig
+ || edi->vecs.radacc.neig
+ || edi->vecs.radcon.neig;
}
/* Main flooding routine, called from do_force */
extern void do_flood(
- t_commrec *cr, /* Communication record */
- t_inputrec *ir, /* Input record */
- rvec x[], /* Positions on the local processor */
- rvec force[], /* forcefield forces, to these the flooding forces are added */
- gmx_edsam_t ed, /* ed data structure contains all ED and flooding groups */
- matrix box, /* the box */
- gmx_int64_t step, /* The relative time step since ir->init_step is already subtracted */
- gmx_bool bNS) /* Are we in a neighbor searching step? */
+ t_commrec *cr,
+ t_inputrec *ir,
+ rvec x[],
+ rvec force[],
+ gmx_edsam_t ed,
+ matrix box,
+ gmx_int64_t step,
+ gmx_bool bNS)
{
t_edpar *edi;
edi = ed->edpar;
for (nr_edi = 1; nr_edi <= nED; nr_edi++)
{
- if ( bNeedDoEdsam(edi) ) /* Only print ED legend if at least one ED option is on */
+ if (bNeedDoEdsam(edi)) /* Only print ED legend if at least one ED option is on */
{
nice_legend(&setname, &nsets, &LegendStr, "RMSD to ref", "nm", get_EDgroupChar(nr_edi, nED) );
}
-void init_edsam(gmx_mtop_t *mtop, /* global topology */
- t_inputrec *ir, /* input record */
- t_commrec *cr, /* communication record */
- gmx_edsam_t ed, /* contains all ED data */
- rvec x[], /* positions of the whole MD system */
- matrix box, /* the box */
+/* Init routine for ED and flooding. Calls init_edi in a loop for every .edi-cycle
+ * contained in the input file, creates a NULL terminated list of t_edpar structures */
+void init_edsam(gmx_mtop_t *mtop,
+ t_inputrec *ir,
+ t_commrec *cr,
+ gmx_edsam_t ed,
+ rvec x[],
+ matrix box,
edsamstate_t *EDstate)
{
t_edpar *edi = NULL; /* points to a single edi data set */
void do_edsam(t_inputrec *ir,
gmx_int64_t step,
t_commrec *cr,
- rvec xs[], /* The local current positions on this processor */
- rvec v[], /* The velocities */
+ rvec xs[],
+ rvec v[],
matrix box,
gmx_edsam_t ed)
{
while (edi != NULL)
{
edinr++;
- if ( bNeedDoEdsam(edi) )
+ if (bNeedDoEdsam(edi))
{
buf = edi->buf->do_edsam;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief
+ * Declares functions to calculate both essential dynamics constraints
+ * as well as flooding potentials and forces.
+ *
+ * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
+ * Carsten Kutzner <ckutzne@gwdg.de>
+ *
+ * \inlibraryapi
+ */
+#ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
+#define GMX_ESSENTIALDYNAMICS_EDSAM_H
+
+#include "typedefs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief Applies essential dynamics constrains as defined in the .edi input file.
+ *
+ * \param ir MD input parameter record.
+ * \param step Number of the time step.
+ * \param cr Data needed for MPI communication.
+ * \param xs The local positions on this processor.
+ * \param v The local velocities.
+ * \param box The simulation box.
+ * \param ed The essential dynamics data.
+ */
+void do_edsam(t_inputrec *ir, gmx_int64_t step,
+ t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed);
+
+
+/*! \brief Reads in the .edi file containing the essential dynamics and flooding data.
+ *
+ * This function opens the ED input and output files, reads in all datasets it finds
+ * in the input file, and cross-checks whether the .edi file information is consistent
+ * with the essential dynamics data found in the checkpoint file (if present).
+ * gmx make_edi can be used to create an .edi input file.
+ *
+ * \param natoms Number of atoms of the whole MD system.
+ * \param EDstate Essential dynamics and flooding data stored in the checkpoint file.
+ * \param nfile Number of entries (files) in the fnm structure.
+ * \param fnm The filenames struct; it contains also the names of the
+ * essential dynamics and flooding in + output files.
+ * \param Flags Flags passed over from main, used to determine
+ * whether we are appending.
+ * \param oenv Needed to open the output xvgr file.
+ * \param cr Data needed for MPI communication.
+ * \returns Pointer to the initialized essential dynamics / flooding data.
+ */
+gmx_edsam_t ed_open(int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[],
+ unsigned long Flags, const output_env_t oenv, t_commrec *cr);
+
+
+/*! \brief Initializes the essential dynamics and flooding module.
+ *
+ * \param mtop Molecular topology.
+ * \param ir MD input parameter record.
+ * \param cr Data needed for MPI communication.
+ * \param ed The essential dynamics data.
+ * \param x Positions of the whole MD system.
+ * \param box The simulation box.
+ * \param EDstate ED data stored in the checkpoint file.
+ */
+void init_edsam(gmx_mtop_t *mtop, t_inputrec *ir, t_commrec *cr,
+ gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *EDstate);
+
+
+/*! \brief Make a selection of the home atoms for the ED groups.
+ *
+ * Should be called at every domain decomposition.
+ *
+ * \param dd Domain decomposition data.
+ * \param ed Essential dynamics and flooding data.
+ */
+void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam_t ed);
+
+
+/*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
+ *
+ * \param cr Data needed for MPI communication.
+ * \param ir MD input parameter record.
+ * \param x Positions on the local processor.
+ * \param force Forcefield forces to which the flooding forces are added.
+ * \param ed The essential dynamics data.
+ * \param box The simulation box.
+ * \param step Number of the time step.
+ * \param bNS Are we in a neighbor searching step?
+ */
+void do_flood(t_commrec *cr, t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
+ matrix box, gmx_int64_t step, gmx_bool bNS);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, 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.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef _edsam_h
-#define _edsam_h
-
-#include "typedefs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-void do_edsam(t_inputrec *ir, gmx_int64_t step,
- t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed);
-/* Essential dynamics constraints, called from constrain() */
-
-gmx_edsam_t ed_open(int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[],
- unsigned long Flags, const output_env_t oenv, t_commrec *cr);
-/* Sets the ED input/output filenames, opens output file */
-
-void init_edsam(gmx_mtop_t *mtop, t_inputrec *ir, t_commrec *cr,
- gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *edsamstate);
-/* Init routine for ED and flooding. Calls init_edi in a loop for every .edi-cycle
- * contained in the input file, creates a NULL terminated list of t_edpar structures */
-
-void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam_t ed);
-/* Make a selection of the home atoms for the ED groups.
- * Should be called at every domain decomposition. */
-
-void do_flood(t_commrec *cr, t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
- matrix box, gmx_int64_t step, gmx_bool bNS);
-/* Flooding - called from do_force() */
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _edsam_h */
#include "tgroup.h"
#include "../fileio/filenm.h"
#include "mshift.h"
-#include "edsam.h"
#include "mdebin.h"
#include "vcm.h"
#include "vsite.h"
#include "gromacs/fileio/gmxfio.h"
#include "macros.h"
#include "gmx_omp_nthreads.h"
+#include "gromacs/essentialdynamics/edsam.h"
+
typedef struct gmx_constr {
int ncon_tot; /* The total number of constraints */
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "adress.h"
#include "qmmm.h"
#include "txtdump.h"
#include "mdrun.h"
#include "constr.h"
-#include "edsam.h"
#include "pull.h"
#include "disre.h"
#include "orires.h"
#include "macros.h"
#include "main.h"
#include "gromacs/fileio/futil.h"
-#include "edsam.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "index.h"
#include "physics.h"
#include "names.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/essentialdynamics/edsam.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff