include/force.h

   1 /*
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  35
  36 #ifndef _force_h
  37 #define _force_h
  38
  39
  40 #include "typedefs.h"
  41 #include "pbc.h"
  42 #include "network.h"
  43 #include "tgroup.h"
  44 #include "vsite.h"
  45 #include "genborn.h"
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51 static const char *sepdvdlformat="  %-30s V %12.5e  dVdl %12.5e\n";
  52
  53 void calc_vir(FILE *fplog,int nxf,rvec x[],rvec f[],tensor vir,
  54                      gmx_bool bScrewPBC,matrix box);
  55 /* Calculate virial for nxf atoms, and add it to vir */
  56
  57 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 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 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 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 void make_wall_tables(FILE *fplog,const output_env_t oenv,
  85                              const t_inputrec *ir,const char *tabfn,
  86                              const gmx_groups_t *groups,
  87                              t_forcerec *fr);
  88
  89 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 t_forcerec *mk_forcerec(void);
  95
  96 #define GMX_MAKETABLES_FORCEUSER  (1<<0)
  97 #define GMX_MAKETABLES_14ONLY     (1<<1)
  98
  99 t_forcetable make_tables(FILE *fp,const output_env_t oenv,
 100                                 const t_forcerec *fr, gmx_bool bVerbose,
 101                                 const char *fn, real rtab,int flags);
 102 /* Return tables for inner loops. When bVerbose the tables are printed
 103  * to .xvg files
 104  */
 105
 106 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 t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
 113                                   const t_forcerec *fr,
 114                                   const char *fn,
 115                                   real rtab);
 116
 117 /* Read a table for AdResS Thermo Force calculations */
 118 extern t_forcetable make_atf_table(FILE *out,const output_env_t oenv,
 119                                    const t_forcerec *fr,
 120                                    const char *fn,
 121                                    matrix box);
 122
 123 void pr_forcerec(FILE *fplog,t_forcerec *fr,t_commrec *cr);
 124
 125 void
 126 forcerec_set_ranges(t_forcerec *fr,
 127                     int ncg_home,int ncg_force,
 128                     int natoms_force,
 129                     int natoms_force_constr,int natoms_f_novirsum);
 130 /* Set the number of cg's and atoms for the force calculation */
 131
 132 gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
 133                              gmx_bool bPrintNote,t_commrec *cr,FILE *fp);
 134 /* Returns if we can use all-vs-all loops.
 135  * If bPrintNote==TRUE, prints a note, if necessary, to stderr
 136  * and fp (if !=NULL) on the master node.
 137  */
 138
 139 void init_forcerec(FILE       *fplog,
 140                           const output_env_t oenv,
 141                           t_forcerec *fr,
 142                           t_fcdata   *fcd,
 143                           const t_inputrec *ir,
 144                           const gmx_mtop_t *mtop,
 145                           const t_commrec  *cr,
 146                           matrix     box,
 147                           gmx_bool       bMolEpot,
 148                           const char *tabfn,
 149                           const char *tabafn,
 150                           const char *tabpfn,
 151                           const char *tabbfn,
 152                           gmx_bool       bNoSolvOpt,
 153                           real       print_force);
 154 /* The Force rec struct must be created with mk_forcerec
 155  * The gmx_booleans have the following meaning:
 156  * bSetQ:    Copy the charges [ only necessary when they change ]
 157  * bMolEpot: Use the free energy stuff per molecule
 158  * print_force >= 0: print forces for atoms with force >= print_force
 159  */
 160
 161 void init_enerdata(int ngener,int n_flambda,gmx_enerdata_t *enerd);
 162 /* Intializes the energy storage struct */
 163
 164 void destroy_enerdata(gmx_enerdata_t *enerd);
 165 /* Free all memory associated with enerd */
 166
 167 void reset_enerdata(t_grpopts *opts,
 168                            t_forcerec *fr,gmx_bool bNS,
 169                            gmx_enerdata_t *enerd,
 170                            gmx_bool bMaster);
 171 /* Resets the energy data, if bNS=TRUE also zeros the long-range part */
 172
 173 void sum_epot(t_grpopts *opts,gmx_enerdata_t *enerd);
 174 /* Locally sum the non-bonded potential energy terms */
 175
 176 void sum_dhdl(gmx_enerdata_t *enerd,double lambda,t_inputrec *ir);
 177 /* Sum the free energy contributions */
 178
 179 void update_forcerec(FILE *fplog,t_forcerec *fr,matrix box);
 180 /* Updates parameters in the forcerec that are time dependent */
 181
 182 /* Compute the average C6 and C12 params for LJ corrections */
 183 void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,
 184                              const gmx_mtop_t *mtop);
 185
 186 /* The state has changed */
 187 #define GMX_FORCE_STATECHANGED (1<<0)
 188 /* The box might have changed */
 189 #define GMX_FORCE_DYNAMICBOX   (1<<1)
 190 /* Do neighbor searching */
 191 #define GMX_FORCE_NS           (1<<2)
 192 /* Calculate bonded energies/forces */
 193 #define GMX_FORCE_DOLR         (1<<3)
 194 /* Calculate long-range energies/forces */
 195 #define GMX_FORCE_BONDED       (1<<4)
 196 /* Store long-range forces in a separate array */
 197 #define GMX_FORCE_SEPLRF       (1<<5)
 198 /* Calculate non-bonded energies/forces */
 199 #define GMX_FORCE_NONBONDED    (1<<6)
 200 /* Calculate forces (not only energies) */
 201 #define GMX_FORCE_FORCES       (1<<7)
 202 /* Calculate the virial */
 203 #define GMX_FORCE_VIRIAL       (1<<8)
 204 /* Calculate dHdl */
 205 #define GMX_FORCE_DHDL         (1<<9)
 206 /* Normally one want all energy terms and forces */
 207 #define GMX_FORCE_ALLFORCES    (GMX_FORCE_BONDED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
 208
 209 void do_force(FILE *log,t_commrec *cr,
 210                      t_inputrec *inputrec,
 211                      gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 212                      gmx_localtop_t *top,
 213                      gmx_mtop_t *mtop,
 214                      gmx_groups_t *groups,
 215                      matrix box,rvec x[],history_t *hist,
 216                      rvec f[],
 217                      tensor vir_force,
 218                      t_mdatoms *mdatoms,
 219                      gmx_enerdata_t *enerd,t_fcdata *fcd,
 220                      real lambda,t_graph *graph,
 221                      t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
 222                      double t,FILE *field,gmx_edsam_t ed,
 223                      gmx_bool bBornRadii,
 224                      int flags);
 225 /* Communicate coordinates (if parallel).
 226  * Do neighbor searching (if necessary).
 227  * Calculate forces.
 228  * Communicate forces (if parallel).
 229  * Spread forces for vsites (if present).
 230  *
 231  * f is always required.
 232  */
 233
 234 void ns(FILE       *fplog,
 235                t_forcerec *fr,
 236                rvec       x[],
 237                matrix     box,
 238                gmx_groups_t *groups,
 239                t_grpopts  *opts,
 240                gmx_localtop_t *top,
 241                t_mdatoms  *md,
 242                t_commrec  *cr,
 243                t_nrnb     *nrnb,
 244                real       lambda,
 245                real       *dvdlambda,
 246                gmx_grppairener_t *grppener,
 247                gmx_bool       bFillGrid,
 248                gmx_bool       bDoLongRange,
 249                gmx_bool       bDoForces,
 250                rvec       *f);
 251 /* Call the neighborsearcher */
 252
 253 void do_force_lowlevel(FILE         *fplog,
 254                               gmx_large_int_t   step,
 255                               t_forcerec   *fr,
 256                               t_inputrec   *ir,
 257                               t_idef       *idef,
 258                               t_commrec    *cr,
 259                               t_nrnb       *nrnb,
 260                               gmx_wallcycle_t wcycle,
 261                               t_mdatoms    *md,
 262                               t_grpopts    *opts,
 263                               rvec         x[],
 264                               history_t    *hist,
 265                               rvec         f[],
 266                               gmx_enerdata_t *enerd,
 267                               t_fcdata     *fcd,
 268                               gmx_mtop_t     *mtop,
 269                               gmx_localtop_t *top,
 270                               gmx_genborn_t *born,
 271                               t_atomtypes  *atype,
 272                               gmx_bool         bBornRadii,
 273                               matrix       box,
 274                               real         lambda,
 275                               t_graph      *graph,
 276                               t_blocka     *excl,
 277                               rvec         mu_tot[2],
 278                               int          flags,
 279                               float        *cycles_pme);
 280 /* Call all the force routines */
 281
 282 #ifdef __cplusplus
 283 }
 284 #endif
 285
 286 #endif  /* _force_h */