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 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55 static const char *sepdvdlformat="  %-30s V %12.5e  dVdl %12.5e\n";
  56
  57 extern void calc_vir(FILE *fplog,int nxf,rvec x[],rvec f[],tensor vir,
  58                      bool bScrewPBC,matrix box);
  59 /* Calculate virial for nxf atoms, and add it to vir */
  60
  61 extern void f_calc_vir(FILE *fplog,int i0,int i1,rvec x[],rvec f[],tensor vir,
  62                        t_graph *g,rvec shift_vec[]);
  63 /* Calculate virial taking periodicity into account */
  64
  65 extern real RF_excl_correction(FILE *fplog,
  66                                const t_forcerec *fr,t_graph *g,
  67                                const t_mdatoms *mdatoms,const t_blocka *excl,
  68                                rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
  69                                real lambda,real *dvdlambda);
  70 /* Calculate the reaction-field energy correction for this node:
  71  * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
  72  * and force correction for all excluded pairs, including self pairs.
  73  */
  74
  75 extern void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,
  76                        real Rc,real Temp,
  77                        real zsq,matrix box,
  78                        real *kappa,real *krf,real *crf);
  79 /* Determine the reaction-field constants */
  80
  81 extern void init_generalized_rf(FILE *fplog,
  82                                 const gmx_mtop_t *mtop,const t_inputrec *ir,
  83                                 t_forcerec *fr);
  84 /* Initialize the generalized reaction field parameters */
  85
  86
  87 /* In wall.c */
  88 extern void make_wall_tables(FILE *fplog,const output_env_t oenv,
  89                              const t_inputrec *ir,const char *tabfn,
  90                              const gmx_groups_t *groups,
  91                              t_forcerec *fr);
  92
  93 extern real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
  94                      rvec x[],rvec f[],real lambda,real Vlj[],t_nrnb *nrnb);
  95
  96
  97
  98 extern t_forcerec *mk_forcerec(void);
  99
 100 #define GMX_MAKETABLES_FORCEUSER  (1<<0)
 101 #define GMX_MAKETABLES_14ONLY     (1<<1)
 102
 103 extern t_forcetable make_tables(FILE *fp,const output_env_t oenv,
 104                                 const t_forcerec *fr, bool bVerbose,
 105                                 const char *fn, real rtab,int flags);
 106 /* Return tables for inner loops. When bVerbose the tables are printed
 107  * to .xvg files
 108  */
 109
 110 extern bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle);
 111 /* Return a table for bonded interactions,
 112  * angle should be: bonds 0, angles 1, dihedrals 2
 113  */
 114
 115 /* Return a table for GB calculations */
 116 extern t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
 117                                   const t_forcerec *fr,
 118                                   const char *fn,
 119                                   real rtab);
 120
 121 extern void pr_forcerec(FILE *fplog,t_forcerec *fr,t_commrec *cr);
 122
 123 extern void
 124 forcerec_set_ranges(t_forcerec *fr,
 125                     int ncg_home,int ncg_force,
 126                     int natoms_force,int natoms_f_novirsum);
 127 /* Set the number of cg's and atoms for the force calculation */
 128
 129 extern bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
 130                              bool bPrintNote,t_commrec *cr,FILE *fp);
 131 /* Returns if we can use all-vs-all loops.
 132  * If bPrintNote==TRUE, prints a note, if necessary, to stderr
 133  * and fp (if !=NULL) on the master node.
 134  */
 135
 136 extern void init_forcerec(FILE       *fplog,
 137                           const output_env_t oenv,
 138                           t_forcerec *fr,
 139                           t_fcdata   *fcd,
 140                           const t_inputrec *ir,
 141                           const gmx_mtop_t *mtop,
 142                           const t_commrec  *cr,
 143                           matrix     box,
 144                           bool       bMolEpot,
 145                           const char *tabfn,
 146                           const char *tabpfn,
 147                           const char *tabbfn,
 148                           bool       bNoSolvOpt,
 149                           real       print_force);
 150 /* The Force rec struct must be created with mk_forcerec
 151  * The booleans have the following meaning:
 152  * bSetQ:    Copy the charges [ only necessary when they change ]
 153  * bMolEpot: Use the free energy stuff per molecule
 154  * print_force >= 0: print forces for atoms with force >= print_force
 155  */
 156
 157 extern void init_enerdata(int ngener,int n_flambda,gmx_enerdata_t *enerd);
 158 /* Intializes the energy storage struct */
 159
 160 extern void destroy_enerdata(gmx_enerdata_t *enerd);
 161 /* Free all memory associated with enerd */
 162
 163 extern void reset_enerdata(t_grpopts *opts,
 164                            t_forcerec *fr,bool bNS,
 165                            gmx_enerdata_t *enerd,
 166                            bool bMaster);
 167 /* Resets the energy data, if bNS=TRUE also zeros the long-range part */
 168
 169 extern void sum_epot(t_grpopts *opts,gmx_enerdata_t *enerd);
 170 /* Locally sum the non-bonded potential energy terms */
 171
 172 extern void sum_dhdl(gmx_enerdata_t *enerd,double lambda,t_inputrec *ir);
 173 /* Sum the free energy contributions */
 174
 175 extern void update_forcerec(FILE *fplog,t_forcerec *fr,matrix box);
 176 /* Updates parameters in the forcerec that are time dependent */
 177
 178 /* Compute the average C6 and C12 params for LJ corrections */
 179 extern void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,
 180                              const gmx_mtop_t *mtop);
 181
 182 /* The state has changed */
 183 #define GMX_FORCE_STATECHANGED (1<<0)
 184 /* The box might have changed */
 185 #define GMX_FORCE_DYNAMICBOX   (1<<1)
 186 /* Do neighbor searching */
 187 #define GMX_FORCE_NS           (1<<2)
 188 /* Calculate bonded energies/forces */
 189 #define GMX_FORCE_DOLR         (1<<3)
 190 /* Calculate long-range energies/forces */
 191 #define GMX_FORCE_BONDED       (1<<4)
 192 /* Store long-range forces in a separate array */
 193 #define GMX_FORCE_SEPLRF       (1<<5)
 194 /* Calculate non-bonded energies/forces */
 195 #define GMX_FORCE_NONBONDED    (1<<6)
 196 /* Calculate forces (not only energies) */
 197 #define GMX_FORCE_FORCES       (1<<7)
 198 /* Calculate the virial */
 199 #define GMX_FORCE_VIRIAL       (1<<8)
 200 /* Calculate dHdl */
 201 #define GMX_FORCE_DHDL         (1<<9)
 202 /* Normally one want all energy terms and forces */
 203 #define GMX_FORCE_ALLFORCES    (GMX_FORCE_BONDED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
 204
 205 extern void do_force(FILE *log,t_commrec *cr,
 206                      t_inputrec *inputrec,
 207                      gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 208                      gmx_localtop_t *top,
 209                      gmx_mtop_t *mtop,
 210                      gmx_groups_t *groups,
 211                      matrix box,rvec x[],history_t *hist,
 212                      rvec f[],
 213                      tensor vir_force,
 214                      t_mdatoms *mdatoms,
 215                      gmx_enerdata_t *enerd,t_fcdata *fcd,
 216                      real lambda,t_graph *graph,
 217                      t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
 218                      double t,FILE *field,gmx_edsam_t ed,
 219                      bool bBornRadii,
 220                      int flags);
 221 /* Communicate coordinates (if parallel).
 222  * Do neighbor searching (if necessary).
 223  * Calculate forces.
 224  * Communicate forces (if parallel).
 225  * Spread forces for vsites (if present).
 226  *
 227  * f is always required.
 228  */
 229
 230 extern void ns(FILE       *fplog,
 231                t_forcerec *fr,
 232                rvec       x[],
 233                matrix     box,
 234                gmx_groups_t *groups,
 235                t_grpopts  *opts,
 236                gmx_localtop_t *top,
 237                t_mdatoms  *md,
 238                t_commrec  *cr,
 239                t_nrnb     *nrnb,
 240                real       lambda,
 241                real       *dvdlambda,
 242                gmx_grppairener_t *grppener,
 243                bool       bFillGrid,
 244                bool       bDoLongRange,
 245                bool       bDoForces,
 246                rvec       *f);
 247 /* Call the neighborsearcher */
 248
 249 extern void do_force_lowlevel(FILE         *fplog,
 250                               gmx_large_int_t   step,
 251                               t_forcerec   *fr,
 252                               t_inputrec   *ir,
 253                               t_idef       *idef,
 254                               t_commrec    *cr,
 255                               t_nrnb       *nrnb,
 256                               gmx_wallcycle_t wcycle,
 257                               t_mdatoms    *md,
 258                               t_grpopts    *opts,
 259                               rvec         x[],
 260                               history_t    *hist,
 261                               rvec         f[],
 262                               gmx_enerdata_t *enerd,
 263                               t_fcdata     *fcd,
 264                               gmx_mtop_t     *mtop,
 265                               gmx_localtop_t *top,
 266                               gmx_genborn_t *born,
 267                               t_atomtypes  *atype,
 268                               bool         bBornRadii,
 269                               matrix       box,
 270                               real         lambda,
 271                               t_graph      *graph,
 272                               t_blocka     *excl,
 273                               rvec         mu_tot[2],
 274                               int          flags,
 275                               float        *cycles_pme);
 276 /* Call all the force routines */
 277
 278 #ifdef __cplusplus
 279 }
 280 #endif
 281
 282 #endif  /* _force_h */