/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* 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.
-
+
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
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* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
* @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.
- *
+ * upon a subgroup of particles.
+ *
*/
#ifndef _pull_rotation_h
/*! \brief Initialize the enforced rotation groups.
- *
+ *
* This routine does the memory allocation for various helper arrays, opens
- * the output files etc.
+ * 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 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 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,
- gmx_bool bVerbose, unsigned long Flags);
+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.
* \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);
+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
+ * 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 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);
+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 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 fplog General output file, normally md.log.
* \param rot Pointer to all the enforced rotation data.
*/
-extern void finish_rot(FILE *fplog,t_rot *rot);
+extern void finish_rot(FILE *fplog, t_rot *rot);
#ifdef __cplusplus
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff