gromacs-dev 4.6.5-1build1 / usr / include / gromacs / pull_rotation.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2008, The GROMACS development team,
 * check out http://www.gromacs.org for more information.
 * Copyright (c) 2012,2013, by the GROMACS development team, led by
 * David van der Spoel, Berk Hess, 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 pull_rotation.h
 *
 *  @brief Enforced rotation of protein parts or other groups of particles.
 *
 *  This file contains routines that are used to enforce rotational motion
 *  upon a subgroup of particles.
 *
 */

#ifndef _pull_rotation_h
#define _pull_rotation_h
#include "visibility.h"
#include "vec.h"
#include "typedefs.h"


#ifdef __cplusplus
extern "C" {
#endif


/*! \brief Initialize 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 Flags             Flags passed over from main, used to determine
 *                          whether or not we are doing a rerun.
 */
GMX_LIBMD_EXPORT
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,
                     gmx_bool bVerbose, unsigned long Flags);


/*! \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
 * 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.
 */
extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot);


/*! \brief Calculation of the enforced rotation potential.
 *
 * 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)
 */
extern void do_rotation(t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
                        gmx_large_int_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);


/*! \brief Add the enforced rotation forces to the official force array.
 *
 * 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.
 */
extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t);


/*! \brief Close the enforced rotation output files.
 *
 * \param rot               Pointer to all the enforced rotation data.
 */
GMX_LIBMD_EXPORT
extern void finish_rot(t_rot *rot);


#ifdef __cplusplus
}
#endif


#endif