Another part of #1415 Get rid of legacy headers.
Other changes:
- updated pulling-related include guards to new format
- updated documentation for doxygen
- updated .h includes
- uncrustified pull.h and pull_rotation.h
- updated copyright year for all files touched by this commit
Change-Id: Ief1ed3543b84f651d1bff01f1952b342850f5c22
add_subdirectory(utility)
add_subdirectory(fileio)
add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
if (NOT GMX_BUILD_MDRUN_ONLY)
add_subdirectory(legacyheaders)
add_subdirectory(gmxana)
*
* 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
+ * Copyright (c) 2013,2014 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.
#include <string.h>
#include "mdatoms.h"
#include "pbc.h"
-#include "pull.h"
+#include "gromacs/pulling/pull.h"
static char pulldim[STRLEN];
*
* 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
+ * Copyright (c) 2013,2014, 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.
#include "mdebin.h"
#include "vcm.h"
#include "vsite.h"
-#include "pull.h"
#include "update.h"
#include "types/membedt.h"
#include "types/globsig.h"
+++ /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 _pull_h
-#define _pull_h
-
-#include "vec.h"
-#include "typedefs.h"
-#include "../fileio/filenm.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-/* This file contains datatypes and function declarations necessary
- for mdrun to interface with the pull code */
-
-/* Get the distance to the reference and deviation for pull coord coord_ind */
-void get_pull_coord_distance(const t_pull *pull,
- int coord_ind,
- const t_pbc *pbc, double t,
- dvec dr, double *dev);
-
-/* Set the all the pull forces to zero */
-void clear_pull_forces(t_pull *pull);
-
-/* Determine the COM pull forces and add them to f, return the potential */
-real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
- t_commrec *cr, double t, real lambda,
- rvec *x, rvec *f, tensor vir, real *dvdlambda);
-
-/* Constrain the coordinates xp in the directions in x
- * and also constrain v when v!=NULL.
- */
-void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
- t_commrec *cr, double dt, double t,
- rvec *x, rvec *xp, rvec *v, tensor vir);
-
-/* Make a selection of the home atoms for all pull groups.
- * Should be called at every domain decomposition.
- */
-void dd_make_local_pull_groups(gmx_domdec_t *dd,
- t_pull *pull, t_mdatoms *md);
-
-/* get memory and initialize the fields of pull that still need it, and
- do runtype specific initialization */
-void init_pull(FILE *fplog,
- t_inputrec *ir, /* the inputrec */
- int nfile,
- const t_filenm fnm[], /* standard filename struct */
- gmx_mtop_t *mtop, /* the topology of the whole system */
- t_commrec * cr, /* struct for communication info */
- const output_env_t oenv, /* output options */
- real lambda, /* FEP lambda */
- gmx_bool bOutFile, /* open output files */
- unsigned long Flags);
-
-/* Close the pull output files */
-void finish_pull(t_pull *pull);
-
-/* Print the pull output (x and/or f) */
-void pull_print_output(t_pull *pull, gmx_int64_t step, double time);
-
-/* In pullutil.c */
-
-/* Calculates centers of mass all pull groups */
-void pull_calc_coms(t_commrec *cr,
- t_pull *pull, /* the pull group */
- t_mdatoms *md, /* all atoms */
- t_pbc *pbc,
- double t, /* only used for cylinder ref. */
- rvec x[], /* local coordinates */
- rvec *xp /* updated x, can be NULL */
- );
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
#include "mshift.h"
#include "tgroup.h"
#include "network.h"
-#include "pull.h"
#include "gmx_random.h"
+#include "vec.h"
+
#ifdef __cplusplus
extern "C" {
*
* 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
+ * Copyright (c) 2013,2014, 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.
#include "macros.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pulling/pull.h"
typedef struct gmx_constr {
#include "names.h"
#include "force.h"
#include "pme.h"
-#include "pull.h"
-#include "pull_rotation.h"
#include "mdrun.h"
#include "nsgrid.h"
#include "shellfc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/qsort_threadsafe.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
#define DDRANK(dd, rank) (rank)
#define DDMASTERRANK(dd) (dd->masterrank)
*
* 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
+ * Copyright (c) 2013,2014, 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.
#include "constr.h"
#include "xvgr.h"
#include "copyrite.h"
-#include "pull_rotation.h"
#include "gmx_random.h"
#include "domdec.h"
#include "partdec.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
#include "adress.h"
#include "qmmm.h"
*
* 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
+ * Copyright (c) 2013,2014, 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.
#include "txtdump.h"
#include "mdrun.h"
#include "constr.h"
-#include "pull.h"
#include "disre.h"
#include "orires.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/fileio/futil.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/pulling/pull.h"
/*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
/*#define STARTFROMDT2*/
--- /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 PULLING_SOURCES *.cpp *.c)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${PULLING_SOURCES} PARENT_SCOPE)
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif (BUILD_TESTING)
*
* 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
+ * Copyright (c) 2013,2014, 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.
#include "gmx_ga2la.h"
#include "copyrite.h"
#include "macros.h"
+#include "vec.h"
static void pull_print_group_x(FILE *out, ivec dim, const t_pull_group *pgrp)
{
--- /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) 2013,2014, 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.
+ */
+
+/*! \libinternal \file
+ *
+ *
+ * \brief
+ * This file contains datatypes and function declarations necessary
+ for mdrun to interface with the pull code.
+ *
+ * \author Berk Hess
+ *
+ * \inlibraryapi
+ */
+
+#ifndef GMX_PULLING_PULL_H
+#define GMX_PULLING_PULL_H
+
+#include "typedefs.h"
+#include "../fileio/filenm.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/*! \brief Get the distance to the reference and deviation for pull coord coord_ind.
+ *
+ * \param[in] pull The pull group.
+ * \param[in] coord_ind Number of the pull coordinate.
+ * \param[in] pbc Information structure about periodicity.
+ * \param[in] t Time.
+ * \param[out] dr The pull coordinate difference vector.
+ * \param[out] dev The deviation from the reference distance.
+ */
+void get_pull_coord_distance(const t_pull *pull,
+ int coord_ind,
+ const t_pbc *pbc, double t,
+ dvec dr, double *dev);
+
+
+/*! \brief Set the all the pull forces to zero.
+ *
+ * \param pull The pull group.
+ */
+void clear_pull_forces(t_pull *pull);
+
+
+/*! \brief Determine the COM pull forces and add them to f, return the potential
+ *
+ * \param[in] ePull Enum defining the type of pulling: umbrella, const force, ...
+ * \param[in] pull The pull group.
+ * \param[in] md All atoms.
+ * \param[in] pbc Information struct about periodicity.
+ * \param[in] cr Struct for communication info.
+ * \param[in] t Time.
+ * \param[in] lambda The value of lambda in FEP calculations.
+ * \param[in] x Positions.
+ * \param[in] f Forces.
+ * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
+ * \param[out] dvdlambda Pull contribution to dV/d(lambda).
+ *
+ * \returns The pull potential energy.
+ */
+real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+ t_commrec *cr, double t, real lambda,
+ rvec *x, rvec *f, tensor vir, real *dvdlambda);
+
+
+/*! \brief Constrain the coordinates xp in the directions in x
+ * and also constrain v when v != NULL.
+ *
+ * \param[in] pull The pull group.
+ * \param[in] md All atoms.
+ * \param[in] pbc Information struct about periodicity.
+ * \param[in] cr Struct for communication info.
+ * \param[in] dt The time step length.
+ * \param[in] t The time.
+ * \param[in] x Positions.
+ * \param[in,out] xp Updated x, can be NULL.
+ * \param[in,out] v Velocities, which may get a pull correction.
+ * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
+ */
+void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+ t_commrec *cr, double dt, double t,
+ rvec *x, rvec *xp, rvec *v, tensor vir);
+
+
+/*! \brief Make a selection of the home atoms for all pull groups.
+ * Should be called at every domain decomposition.
+ *
+ * \param dd Structure containing domain decomposition data.
+ * \param pull The pull group.
+ * \param md All atoms.
+ */
+void dd_make_local_pull_groups(gmx_domdec_t *dd,
+ t_pull *pull, t_mdatoms *md);
+
+
+/*! \brief Get memory and initialize the fields of pull that still need it, and
+ * do runtype specific initialization.
+ *
+ * \param fplog General output file, normally md.log.
+ * \param ir The inputrec.
+ * \param nfile Number of files.
+ * \param fnm Standard filename struct.
+ * \param mtop The topology of the whole system.
+ * \param cr Struct for communication info.
+ * \param oenv Output options.
+ * \param lambda FEP lambda.
+ * \param bOutFile Open output files?
+ * \param Flags Flags passed over from main, used to determine
+ * whether or not we are appending.
+ */
+void init_pull(FILE *fplog,
+ t_inputrec *ir,
+ int nfile,
+ const t_filenm fnm[],
+ gmx_mtop_t *mtop,
+ t_commrec * cr,
+ const output_env_t oenv,
+ real lambda,
+ gmx_bool bOutFile,
+ unsigned long Flags);
+
+
+/*! \brief Close the pull output files.
+ *
+ * \param pull The pull group.
+ */
+void finish_pull(t_pull *pull);
+
+
+/*! \brief Print the pull output (x and/or f)
+ *
+ * \param pull The pull group.
+ * \param step Time step number.
+ * \param time Time.
+ */
+void pull_print_output(t_pull *pull, gmx_int64_t step, double time);
+
+
+/*! \brief Calculates centers of mass all pull groups.
+ *
+ * \param[in] cr Struct for communication info.
+ * \param[in] pull The pull group.
+ * \param[in] md All atoms.
+ * \param[in] pbc Information struct about periodicity.
+ * \param[in] t Time, only used for cylinder ref.
+ * \param[in] x The local positions.
+ * \param[in,out] xp Updated x, can be NULL.
+ *
+ */
+void pull_calc_coms(t_commrec *cr,
+ t_pull *pull,
+ t_mdatoms *md,
+ t_pbc *pbc,
+ double t,
+ rvec x[],
+ rvec *xp);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
#include "vec.h"
#include "gmx_ga2la.h"
#include "xvgr.h"
-#include "groupcoord.h"
-#include "pull_rotation.h"
#include "copyrite.h"
#include "macros.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/qsort_threadsafe.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/mdlib/groupcoord.h"
static char *RotStr = {"Enforced rotation:"};
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file pull_rotation.h
+/*! \libinternal \file
*
- * @brief Enforced rotation of protein parts or other groups of particles.
+ * \brief
+ * Declares functions to enforce rotational motion upon a group of particles.
*
- * This file contains routines that are used to enforce rotational motion
- * upon a subgroup of particles.
+ * \author Carsten Kutzner <ckutzne@gwdg.de>
*
+ * \inlibraryapi
*/
-#ifndef _pull_rotation_h
-#define _pull_rotation_h
+#ifndef GMX_PULLING_PULL_ROTATION_H
+#define GMX_PULLING_PULL_ROTATION_H
-#include "vec.h"
#include "typedefs.h"
+#include "../fileio/filenm.h"
#ifdef __cplusplus
#endif
-/*! \brief Initialize the enforced rotation groups.
+/*! \brief Initializes the enforced rotation groups.
*
* This routine does the memory allocation for various helper arrays, opens
* the output files etc.
*
- * \param fplog General output file, normally md.log.
- * \param ir Struct containing MD input parameters, among those
- * also the enforced rotation parameters.
- * \param nfile Number of entries in the fnm structure.
- * \param fnm The filenames struct containing also the names
- * of the rotation output files.
- * \param cr Pointer to MPI communication data.
- * \param x The positions of all MD particles.
- * \param box The simulation box.
- * \param mtop Molecular topology.
- * \param oenv Needed to open the rotation output xvgr file.
- * \param bVerbose Whether to print extra status information.
- * \param Flags Flags passed over from main, used to determine
- * whether or not we are doing a rerun.
+ * \param fplog General output file, normally md.log.
+ * \param ir Struct containing MD input parameters, among those
+ * also the enforced rotation parameters.
+ * \param nfile Number of entries in the fnm structure.
+ * \param fnm The filenames struct containing also the names
+ * of the rotation output files.
+ * \param cr Pointer to MPI communication data.
+ * \param x The positions of all MD particles.
+ * \param box The simulation box.
+ * \param mtop Molecular topology.
+ * \param oenv Needed to open the rotation output xvgr file.
+ * \param bVerbose Whether to print extra status information.
+ * \param Flags Flags passed over from main, used to determine
+ * whether or not we are doing a rerun.
*/
extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
/*! \brief Make a selection of the home atoms for all enforced rotation groups.
*
- * This routine is similar to dd_make_local_pull_groups, but works only with
+ * This routine is similar to \ref dd_make_local_pull_groups, but works only with
* domain decomposition. It should be called at every domain decomposition.
*
- * \param dd Structure containing domain decomposition data.
- * \param rot Pointer to all the enforced rotation data.
+ * \param dd Structure containing domain decomposition data.
+ * \param rot Pointer to all the enforced rotation data.
*/
extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot);
-/*! \brief Calculation of the enforced rotation potential.
+/*! \brief Calculates the enforced rotation potential(s).
*
* This is the main enforced rotation module which is called during every time
* step. Here the rotation potential as well as the resulting forces are
* calculated.
*
- * \param cr Pointer to MPI communication data.
- * \param ir Struct containing MD input parameters, among those
- * \param box Simulation box, needed to make group whole.
- * \param x The positions of all the local particles.
- * \param t Time.
- * \param step The time step.
- * \param wcycle During the potential calculation the wallcycles are
- * counted. Later they enter the dynamic load balancing.
- * \param bNS After domain decomposition / neighborsearching several
- * local arrays have to be updated (masses, shifts)
+ * \param cr Pointer to MPI communication data.
+ * \param ir Struct containing MD input parameters, among those
+ * \param box Simulation box, needed to make group whole.
+ * \param x The positions of all the local particles.
+ * \param t Time.
+ * \param step The time step.
+ * \param wcycle During the potential calculation the wallcycles are
+ * counted. Later they enter the dynamic load balancing.
+ * \param bNS After domain decomposition / neighbor searching several
+ * local arrays have to be updated (masses, shifts)
*/
extern void do_rotation(t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
gmx_int64_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);
*
* Adds the forces from enforced rotation potential to the local forces and
* sums up the contributions to the rotation potential from all the nodes. Since
- * this needs communication, this routine should be called after the SR forces
- * have been evaluated (in order not to spoil cycle counts).
- * This routine also outputs data to the various rotation output files (e.g.
- * the potential, the angle of the group, torques and more).
- *
- * \param rot Pointer to all the enforced rotation data.
- * \param f The local forces to which the rotational forces have
- * to be added.
- * \param cr Pointer to MPI communication data.
- * \param step The time step, used for output.
- * \param t Time, used for output.
+ * this needs communication, this routine should be called after the short range
+ * forces have been evaluated (in order not to spoil cycle counts).
+ * This routine also outputs data to the rotation output files (e.g.
+ * the potential, the angle of the group(s), and torques).
+ *
+ * \param rot Pointer to all the enforced rotation data.
+ * \param f The local forces to which the rotational forces have
+ * to be added.
+ * \param cr Pointer to MPI communication data.
+ * \param step The time step, used for output.
+ * \param t Time, used for output.
+ * \returns The potential energy of the rotation potentials.
*/
extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_int64_t step, real t);
/*! \brief Close the enforced rotation output files.
*
- * \param rot Pointer to all the enforced rotation data.
+ * \param rot Pointer to all the enforced rotation data.
*/
extern void finish_rot(t_rot *rot);
*
* 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
+ * Copyright (c) 2013,2014, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, 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.
#include "md_support.h"
#include "md_logging.h"
#include "network.h"
-#include "pull.h"
#include "xvgr.h"
#include "physics.h"
#include "names.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/pulling/pull.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, 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.
#include "md_logging.h"
#include "md_support.h"
#include "network.h"
-#include "pull.h"
-#include "pull_rotation.h"
#include "names.h"
#include "disre.h"
#include "orires.h"
#include "txtdump.h"
#include "gmx_detect_hardware.h"
#include "gmx_omp_nthreads.h"
-#include "pull_rotation.h"
#include "calc_verletbuf.h"
#include "gmx_fatal_collective.h"
#include "membed.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff