include/force.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _force_h
  37 #define _force_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43
  44 #include "typedefs.h"
  45 #include "pbc.h"
  46 #include "network.h"
  47 #include "tgroup.h"
  48 #include "vsite.h"
  49 #include "genborn.h"
  50
  51 static const char *sepdvdlformat="  %-30s V %12.5e  dVdl %12.5e\n";
  52
  53 extern void calc_vir(FILE *fplog,int nxf,rvec x[],rvec f[],tensor vir,
  54                      bool bScrewPBC,matrix box);
  55 /* Calculate virial for nxf atoms, and add it to vir */
  56
  57 extern void f_calc_vir(FILE *fplog,int i0,int i1,rvec x[],rvec f[],tensor vir,
  58                        t_graph *g,rvec shift_vec[]);
  59 /* Calculate virial taking periodicity into account */
  60
  61 extern real RF_excl_correction(FILE *fplog,
  62                                const t_forcerec *fr,t_graph *g,
  63                                const t_mdatoms *mdatoms,const t_blocka *excl,
  64                                rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
  65                                real lambda,real *dvdlambda);
  66 /* Calculate the reaction-field energy correction for this node:
  67  * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
  68  * and force correction for all excluded pairs, including self pairs.
  69  */
  70
  71 extern void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,
  72                        real Rc,real Temp,
  73                        real zsq,matrix box,
  74                        real *kappa,real *krf,real *crf);
  75 /* Determine the reaction-field constants */
  76
  77 extern void init_generalized_rf(FILE *fplog,
  78                                 const gmx_mtop_t *mtop,const t_inputrec *ir,
  79                                 t_forcerec *fr);
  80 /* Initialize the generalized reaction field parameters */
  81
  82
  83 /* In wall.c */
  84 extern void make_wall_tables(FILE *fplog,
  85                              const t_inputrec *ir,const char *tabfn,
  86                              const gmx_groups_t *groups,
  87                              t_forcerec *fr);
  88
  89 extern real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
  90                      rvec x[],rvec f[],real lambda,real Vlj[],t_nrnb *nrnb);
  91
  92
  93
  94 extern t_forcerec *mk_forcerec(void);
  95
  96 #define GMX_MAKETABLES_FORCEUSER  (1<<0)
  97 #define GMX_MAKETABLES_14ONLY     (1<<1)
  98
  99 extern t_forcetable make_tables(FILE *fp,const t_forcerec *fr,
 100                                 bool bVerbose,const char *fn,
 101                                 real rtab,int flags);
 102 /* Return tables for inner loops. When bVerbose the tables are printed
 103  * to .xvg files
 104  */
 105
 106 extern bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle);
 107 /* Return a table for bonded interactions,
 108  * angle should be: bonds 0, angles 1, dihedrals 2
 109  */
 110
 111 /* Return a table for GB calculations */
 112 extern t_forcetable make_gb_table(FILE *out,const t_forcerec *fr,
 113                                                                   const char *fn,
 114                                                                   real rtab);
 115
 116 extern void pr_forcerec(FILE *fplog,t_forcerec *fr,t_commrec *cr);
 117
 118 extern void
 119 forcerec_set_ranges(t_forcerec *fr,
 120                     int ncg_home,int ncg_force,
 121                     int natoms_force,int natoms_f_novirsum);
 122 /* Set the number of cg's and atoms for the force calculation */
 123
 124 extern void init_forcerec(FILE       *fplog,
 125                           t_forcerec *fr,
 126                           t_fcdata   *fcd,
 127                           const t_inputrec *ir,
 128                           const gmx_mtop_t *mtop,
 129                           const t_commrec  *cr,
 130                           matrix     box,
 131                           bool       bMolEpot,
 132                           const char *tabfn,
 133                           const char *tabpfn,
 134                           const char *tabbfn,
 135                           bool       bNoSolvOpt,
 136                           real       print_force);
 137 /* The Force rec struct must be created with mk_forcerec
 138  * The booleans have the following meaning:
 139  * bSetQ:    Copy the charges [ only necessary when they change ]
 140  * bMolEpot: Use the free energy stuff per molecule
 141  * print_force >= 0: print forces for atoms with force >= print_force
 142  */
 143
 144 extern void init_enerdata(int ngener,int n_flambda,gmx_enerdata_t *enerd);
 145 /* Intializes the energy storage struct */
 146
 147 extern void destroy_enerdata(gmx_enerdata_t *enerd);
 148 /* Free all memory associated with enerd */
 149
 150 extern void reset_enerdata(t_grpopts *opts,
 151                            t_forcerec *fr,bool bNS,
 152                            gmx_enerdata_t *enerd,
 153                            bool bMaster);
 154 /* Resets the energy data, if bNS=TRUE also zeros the long-range part */
 155
 156 extern void sum_epot(t_grpopts *opts,gmx_enerdata_t *enerd);
 157 /* Locally sum the non-bonded potential energy terms */
 158
 159 extern void sum_dhdl(gmx_enerdata_t *enerd,double lambda,t_inputrec *ir);
 160 /* Sum the free energy contributions */
 161
 162 extern void update_forcerec(FILE *fplog,t_forcerec *fr,matrix box);
 163 /* Updates parameters in the forcerec that are time dependent */
 164
 165 /* Compute the average C6 and C12 params for LJ corrections */
 166 extern void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,
 167                              const gmx_mtop_t *mtop);
 168
 169 /* The state has changed */
 170 #define GMX_FORCE_STATECHANGED (1<<0)
 171 /* Do neighbor searching */
 172 #define GMX_FORCE_NS           (1<<1)
 173 /* Calculate bonded energies/forces */
 174 #define GMX_FORCE_DOLR         (1<<2)
 175 /* Calculate long-range energies/forces */
 176 #define GMX_FORCE_BONDED       (1<<3)
 177 /* Store long-range forces in a separate array */
 178 #define GMX_FORCE_SEPLRF       (1<<4)
 179 /* Calculate non-bonded energies/forces */
 180 #define GMX_FORCE_NONBONDED    (1<<5)
 181 /* Calculate forces (not only energies) */
 182 #define GMX_FORCE_FORCES       (1<<6)
 183 /* Calculate the virial */
 184 #define GMX_FORCE_VIRIAL       (1<<7)
 185 /* Calculate dHdl */
 186 #define GMX_FORCE_DHDL         (1<<8)
 187 /* Normally one want all energy terms and forces */
 188 #define GMX_FORCE_ALLFORCES    (GMX_FORCE_BONDED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
 189
 190 extern void do_force(FILE *log,t_commrec *cr,
 191                      t_inputrec *inputrec,
 192                      gmx_step_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 193                      gmx_localtop_t *top,
 194                      gmx_mtop_t *mtop,
 195                      gmx_groups_t *groups,
 196                      matrix box,rvec x[],history_t *hist,
 197                      rvec f[],
 198                      tensor vir_force,
 199                      t_mdatoms *mdatoms,
 200                      gmx_enerdata_t *enerd,t_fcdata *fcd,
 201                      real lambda,t_graph *graph,
 202                      t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
 203                      double t,FILE *field,gmx_edsam_t ed,
 204                      bool bBornRadii,
 205                      int flags);
 206 /* Communicate coordinates (if parallel).
 207  * Do neighbor searching (if necessary).
 208  * Calculate forces.
 209  * Communicate forces (if parallel).
 210  * Spread forces for vsites (if present).
 211  *
 212  * f is always required.
 213  */
 214
 215 extern void ns(FILE       *fplog,
 216                t_forcerec *fr,
 217                rvec       x[],
 218                matrix     box,
 219                gmx_groups_t *groups,
 220                t_grpopts  *opts,
 221                gmx_localtop_t *top,
 222                t_mdatoms  *md,
 223                t_commrec  *cr,
 224                t_nrnb     *nrnb,
 225                real       lambda,
 226                real       *dvdlambda,
 227                gmx_grppairener_t *grppener,
 228                bool       bFillGrid,
 229                bool       bDoLongRange,
 230                bool       bDoForces,
 231                rvec       *f);
 232 /* Call the neighborsearcher */
 233
 234 extern void do_force_lowlevel(FILE         *fplog,
 235                               gmx_step_t   step,
 236                               t_forcerec   *fr,
 237                               t_inputrec   *ir,
 238                               t_idef       *idef,
 239                               t_commrec    *cr,
 240                               t_nrnb       *nrnb,
 241                               gmx_wallcycle_t wcycle,
 242                               t_mdatoms    *md,
 243                               t_grpopts    *opts,
 244                               rvec         x[],
 245                               history_t    *hist,
 246                               rvec         f[],
 247                               gmx_enerdata_t *enerd,
 248                               t_fcdata     *fcd,
 249                               gmx_mtop_t     *mtop,
 250                               gmx_localtop_t *top,
 251                               gmx_genborn_t *born,
 252                               t_atomtypes  *atype,
 253                               bool         bBornRadii,
 254                               matrix       box,
 255                               real         lambda,
 256                               t_graph      *graph,
 257                               t_blocka     *excl,
 258                               rvec         mu_tot[2],
 259                               int          flags,
 260                               float        *cycles_pme);
 261 /* Call all the force routines */
 262
 263
 264 #endif  /* _force_h */