include/types/forcerec.h

   1 /*
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   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   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
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "ns.h"
  40 #include "genborn.h"
  41 #include "qmmmrec.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 /* Abstract type for PME that is defined only in the routine that use them. */
  48 typedef struct gmx_pme *gmx_pme_t;
  49
  50 typedef struct {
  51   real r;         /* range of the table */
  52   int  n;         /* n+1 is the number of points */
  53   real scale;     /* distance between two points */
  54   real scale_exp; /* distance for exponential Buckingham table */
  55   real *tab;      /* the actual tables, per point there are  4 numbers for
  56                    * Coulomb, dispersion and repulsion (in total 12 numbers)
  57                    */
  58 } t_forcetable;
  59
  60 typedef struct {
  61   t_forcetable tab;
  62   /* We duplicate tables for cache optimization purposes */
  63   real *coultab;      /* Coul only */
  64   real *vdwtab;       /* Vdw only   */
  65   /* The actual neighbor lists, short and long range, see enum above
  66    * for definition of neighborlist indices.
  67    */
  68   t_nblist nlist_sr[eNL_NR];
  69   t_nblist nlist_lr[eNL_NR];
  70 } t_nblists;
  71
  72 /* macros for the cginfo data in forcerec */
  73 /* The maximum cg size is 255, because we only have space for 8 bits in cginfo,
  74  * this cg size entry is actually only read with domain decomposition.
  75  */
  76 #define MAX_CHARGEGROUP_SIZE 256
  77 #define SET_CGINFO_GID(cgi,gid)      (cgi) = (((cgi)  &  ~65535)  |  (gid)   )
  78 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   65535)
  79 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  80 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  81 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  82 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  83 #define SET_CGINFO_SOLOPT(cgi,opt)   (cgi) = (((cgi)  & ~(15<<18)) | ((opt)<<18))
  84 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   15)
  85 /* This bit is only used with bBondComm in the domain decomposition */
  86 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  87 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  88 #define SET_CGINFO_NATOMS(cgi,opt)   (cgi) = (((cgi)  & ~(255<<23)) | ((opt)<<23))
  89 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>23)       &   255)
  90
  91
  92 /* Value to be used in mdrun for an infinite cut-off.
  93  * Since we need to compare with the cut-off squared,
  94  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
  95  */
  96 #define GMX_CUTOFF_INF 1E+18
  97
  98
  99 enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
 100        egCOUL14, egLJ14, egGB, egNR };
 101
 102 typedef struct {
 103   int  nener;        /* The number of energy group pairs     */
 104   real *ener[egNR];  /* Energy terms for each pair of groups */
 105 } gmx_grppairener_t;
 106
 107 typedef struct {
 108   real term[F_NRE];    /* The energies for all different interaction types */
 109   gmx_grppairener_t grpp;
 110   double dvdl_lin;     /* Contributions to dvdl with linear lam-dependence */
 111   double dvdl_nonlin;  /* Idem, but non-linear dependence                  */
 112   int    n_lambda;
 113   double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
 114 } gmx_enerdata_t;
 115 /* The idea is that dvdl terms with linear lambda dependence will be added
 116  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 117  * should explicitly determine the energies at foreign lambda points
 118  * when n_lambda > 0.
 119  */
 120
 121 typedef struct {
 122   int cg_start;
 123   int cg_end;
 124   int cg_mod;
 125   int *cginfo;
 126 } cginfo_mb_t;
 127
 128
 129 /* ewald table type */
 130 typedef struct ewald_tab *ewald_tab_t;
 131
 132 typedef struct {
 133   /* Domain Decomposition */
 134   bool bDomDec;
 135
 136   /* PBC stuff */
 137   int  ePBC;
 138   bool bMolPBC;
 139   int  rc_scaling;
 140   rvec posres_com;
 141   rvec posres_comB;
 142
 143   /* Use special N*N kernels? */
 144   bool bAllvsAll;
 145   /* Private work data */
 146   void *AllvsAll_work;
 147   void *AllvsAll_workgb;
 148
 149   /* Cut-Off stuff.
 150    * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 151    */
 152   real rlist,rlistlong;
 153
 154   /* Dielectric constant resp. multiplication factor for charges */
 155   real zsquare,temp;
 156   real epsilon_r,epsilon_rf,epsfac;
 157
 158   /* Constants for reaction fields */
 159   real kappa,k_rf,c_rf;
 160
 161   /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 162   double qsum[2];
 163   rvec   mu_tot[2];
 164
 165   /* Dispersion correction stuff */
 166   int  eDispCorr;
 167   /* The shift of the shift or user potentials */
 168   real enershiftsix;
 169   real enershifttwelve;
 170   /* Integrated differces for energy and virial with cut-off functions */
 171   real enerdiffsix;
 172   real enerdifftwelve;
 173   real virdiffsix;
 174   real virdifftwelve;
 175   /* Constant for long range dispersion correction (average dispersion)
 176    * for topology A/B ([0]/[1]) */
 177   real avcsix[2];
 178   /* Constant for long range repulsion term. Relative difference of about
 179    * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 180    */
 181   real avctwelve[2];
 182
 183   /* Fudge factors */
 184   real fudgeQQ;
 185
 186   /* Table stuff */
 187   bool bcoultab;
 188   bool bvdwtab;
 189   /* The normal tables are in the nblists struct(s) below */
 190   t_forcetable tab14; /* for 1-4 interactions only */
 191
 192   /* PPPM & Shifting stuff */
 193   real rcoulomb_switch,rcoulomb;
 194   real *phi;
 195
 196   /* VdW stuff */
 197   double reppow;
 198   real rvdw_switch,rvdw;
 199   real bham_b_max;
 200
 201   /* Free energy ? */
 202   int  efep;
 203   real sc_alpha;
 204   int  sc_power;
 205   real sc_sigma6;
 206   bool bSepDVDL;
 207
 208   /* NS Stuff */
 209   int  eeltype;
 210   int  vdwtype;
 211   int  cg0,hcg;
 212   /* solvent_opt contains the enum for the most common solvent
 213    * in the system, which will be optimized.
 214    * It can be set to esolNO to disable all water optimization */
 215   int  solvent_opt;
 216   int  nWatMol;
 217   bool bGrid;
 218   cginfo_mb_t *cginfo_mb;
 219   int  *cginfo;
 220   rvec *cg_cm;
 221   int  cg_nalloc;
 222   rvec *shift_vec;
 223
 224   /* The neighborlists including tables */
 225   int  nnblists;
 226   int  *gid2nblists;
 227   t_nblists *nblists;
 228
 229   /* The wall tables (if used) */
 230   int  nwall;
 231   t_forcetable **wall_tab;
 232
 233   /* This mask array of length nn determines whether or not this bit of the
 234    * neighbourlists should be computed. Usually all these are true of course,
 235    * but not when shells are used. During minimisation all the forces that
 236    * include shells are done, then after minimsation is converged the remaining
 237    * forces are computed.
 238    */
 239   /* bool *bMask; */
 240
 241   /* The number of charge groups participating in do_force_lowlevel */
 242   int ncg_force;
 243   /* The number of atoms participating in do_force_lowlevel */
 244   int natoms_force;
 245   /* The allocation size of vectors of size natoms_force */
 246   int nalloc_force;
 247
 248   /* Twin Range stuff, f_twin has size natoms_force */
 249   bool bTwinRange;
 250   int  nlr;
 251   rvec *f_twin;
 252
 253   /* Forces that should not enter into the virial summation:
 254    * PPPM/PME/Ewald/posres
 255    */
 256   bool bF_NoVirSum;
 257   int  f_novirsum_n;
 258   int  f_novirsum_nalloc;
 259   rvec *f_novirsum_alloc;
 260   /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
 261    * points to the normal force vectors wen pressure is not requested.
 262    */
 263   rvec *f_novirsum;
 264
 265   /* Long-range forces and virial for PPPM/PME/Ewald */
 266   gmx_pme_t pmedata;
 267   tensor    vir_el_recip;
 268
 269   /* PME/Ewald stuff */
 270   bool bEwald;
 271   real ewaldcoeff;
 272   ewald_tab_t ewald_table;
 273
 274   /* Virial Stuff */
 275   rvec *fshift;
 276   rvec vir_diag_posres;
 277   dvec vir_wall_z;
 278
 279   /* Non bonded Parameter lists */
 280   int  ntype; /* Number of atom types */
 281   bool bBHAM;
 282   real *nbfp;
 283
 284   /* Energy group pair flags */
 285   int *egp_flags;
 286
 287   /* xmdrun flexible constraints */
 288   real fc_stepsize;
 289
 290   /* Generalized born implicit solvent */
 291   bool bGB;
 292   /* Generalized born stuff */
 293   real gb_epsilon_solvent;
 294   /* Table data for GB */
 295   t_forcetable gbtab;
 296   /* VdW radius for each atomtype (dim is thus ntype) */
 297   real *atype_radius;
 298   /* Effective radius (derived from effective volume) for each type */
 299   real *atype_vol;
 300   /* Implicit solvent - surface tension for each atomtype */
 301   real *atype_surftens;
 302   /* Implicit solvent - radius for GB calculation */
 303   real *atype_gb_radius;
 304   /* Implicit solvent - overlap for HCT model */
 305   real *atype_S_hct;
 306   /* Generalized born interaction data */
 307   gmx_genborn_t *born;
 308
 309   /* Table scale for GB */
 310   real gbtabscale;
 311   /* Table range for GB */
 312   real gbtabr;
 313   /* GB neighborlists (the sr list will contain for each atom all other atoms
 314    * (for use in the SA calculation) and the lr list will contain
 315    * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 316    */
 317   t_nblist gblist_sr;
 318   t_nblist gblist_lr;
 319   t_nblist gblist;
 320
 321   /* Inverse square root of the Born radii for implicit solvent */
 322   real *invsqrta;
 323   /* Derivatives of the potential with respect to the Born radii */
 324   real *dvda;
 325   /* Derivatives of the Born radii with respect to coordinates */
 326   real *dadx;
 327   real *dadx_rawptr;
 328   int   nalloc_dadx; /* Allocated size of dadx */
 329
 330   /* If > 0 signals Test Particle Insertion,
 331    * the value is the number of atoms of the molecule to insert
 332    * Only the energy difference due to the addition of the last molecule
 333    * should be calculated.
 334    */
 335   bool n_tpi;
 336
 337   /* Neighbor searching stuff */
 338   gmx_ns_t ns;
 339
 340   /* QMMM stuff */
 341   bool         bQMMM;
 342   t_QMMMrec    *qr;
 343
 344   /* QM-MM neighborlists */
 345   t_nblist QMMMlist;
 346
 347   /* Limit for printing large forces, negative is don't print */
 348   real print_force;
 349
 350   /* coarse load balancing time measurement */
 351   double t_fnbf;
 352   double t_wait;
 353   int timesteps;
 354
 355   /* User determined parameters, copied from the inputrec */
 356   int  userint1;
 357   int  userint2;
 358   int  userint3;
 359   int  userint4;
 360   real userreal1;
 361   real userreal2;
 362   real userreal3;
 363   real userreal4;
 364 } t_forcerec;
 365
 366 #define C6(nbfp,ntp,ai,aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 367 #define C12(nbfp,ntp,ai,aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 368 #define BHAMC(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 369 #define BHAMA(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 370 #define BHAMB(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 371
 372 #ifdef __cplusplus
 373 }
 374 #endif
 375