*
* 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);
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