include/pull.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team,
   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38
  39 #ifndef _pull_h
  40 #define _pull_h
  41 #include "visibility.h"
  42 #include "vec.h"
  43 #include "typedefs.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49
  50 /* This file contains datatypes and function declarations necessary
  51    for mdrun to interface with the pull code */
  52
  53 /* Get the distance to the reference and deviation for pull group g */
  54 GMX_LIBMD_EXPORT
  55 void get_pullgrp_distance(t_pull *pull,t_pbc *pbc,int g,double t,
  56                                  dvec dr,dvec dev);
  57
  58 /* Set the all the pull forces to zero */
  59 void clear_pull_forces(t_pull *pull);
  60
  61 /* Determine the COM pull forces and add them to f, return the potential */
  62 real pull_potential(int ePull,t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  63                            t_commrec *cr, double t, real lambda,
  64                            rvec *x, rvec *f, tensor vir, real *dvdlambda);
  65
  66 /* Constrain the coordinates xp in the directions in x
  67  * and also constrain v when v!=NULL.
  68  */
  69 void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  70                             t_commrec *cr, double dt, double t,
  71                             rvec *x, rvec *xp, rvec *v, tensor vir);
  72
  73 /* Make a selection of the home atoms for all pull groups.
  74  * Should be called at every domain decomposition.
  75  */
  76 GMX_LIBMD_EXPORT
  77 void dd_make_local_pull_groups(gmx_domdec_t *dd,
  78                                       t_pull *pull,t_mdatoms *md);
  79
  80 /* get memory and initialize the fields of pull that still need it, and
  81    do runtype specific initialization */
  82 GMX_LIBMD_EXPORT
  83 void init_pull(FILE *fplog,
  84                       t_inputrec *ir, /* the inputrec */
  85                       int nfile,
  86                       const t_filenm fnm[], /* standard filename struct */
  87                       gmx_mtop_t *mtop, /* the topology of the whole system */
  88                       t_commrec * cr, /* struct for communication info */
  89                       const output_env_t oenv,  /* output options */
  90                       real lambda, /* FEP lambda */
  91                       gmx_bool bOutFile,   /* open output files */
  92                       unsigned long Flags);
  93
  94 /* Close the pull output files */
  95 GMX_LIBMD_EXPORT
  96 void finish_pull(FILE *fplog,t_pull *pull);
  97
  98 /* Print the pull output (x and/or f) */
  99 GMX_LIBMD_EXPORT
 100 void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
 101
 102 /* In pullutil.c */
 103
 104 /* Calculates centers of mass all pull groups */
 105 GMX_LIBMD_EXPORT
 106 void pull_calc_coms(t_commrec *cr,
 107                            t_pull *pull,   /* the pull group */
 108                            t_mdatoms *md,  /* all atoms */
 109                            t_pbc *pbc,
 110                            double t,       /* only used for cylinder ref. */
 111                            rvec x[],       /* local coordinates */
 112                            rvec *xp        /* updated x, can be NULL */
 113                            );
 114
 115 #ifdef __cplusplus
 116 }
 117 #endif
 118
 119 #endif