include/types/forcerec.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
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   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
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  35
  36 #include "ns.h"
  37 #include "genborn.h"
  38 #include "qmmmrec.h"
  39 #include "idef.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 /* Abstract type for PME that is defined only in the routine that use them. */
  46 typedef struct gmx_pme *gmx_pme_t;
  47
  48 typedef struct {
  49   real r;         /* range of the table */
  50   int  n;         /* n+1 is the number of points */
  51   real scale;     /* distance between two points */
  52   real scale_exp; /* distance for exponential Buckingham table */
  53   real *tab;      /* the actual tables, per point there are  4 numbers for
  54                    * Coulomb, dispersion and repulsion (in total 12 numbers)
  55                    */
  56 } t_forcetable;
  57
  58 typedef struct {
  59   t_forcetable tab;
  60   /* We duplicate tables for cache optimization purposes */
  61   real *coultab;      /* Coul only */
  62   real *vdwtab;       /* Vdw only   */
  63   /* The actual neighbor lists, short and long range, see enum above
  64    * for definition of neighborlist indices.
  65    */
  66   t_nblist nlist_sr[eNL_NR];
  67   t_nblist nlist_lr[eNL_NR];
  68 } t_nblists;
  69
  70 /* macros for the cginfo data in forcerec */
  71 /* The maximum cg size in cginfo is 255,
  72  * because we only have space for 8 bits in cginfo,
  73  * this cg size entry is actually only read with domain decomposition.
  74  * But there is a smaller limit due to the t_excl data structure
  75  * which is defined in nblist.h.
  76  */
  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   gmx_bool bDomDec;
 135
 136   /* PBC stuff */
 137   int  ePBC;
 138   gmx_bool bMolPBC;
 139   int  rc_scaling;
 140   rvec posres_com;
 141   rvec posres_comB;
 142
 143   gmx_bool UseOptimizedKernels;
 144
 145   /* Use special N*N kernels? */
 146   gmx_bool bAllvsAll;
 147   /* Private work data */
 148   void *AllvsAll_work;
 149   void *AllvsAll_workgb;
 150
 151   /* Cut-Off stuff.
 152    * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 153    */
 154   real rlist,rlistlong;
 155
 156   /* Dielectric constant resp. multiplication factor for charges */
 157   real zsquare,temp;
 158   real epsilon_r,epsilon_rf,epsfac;
 159
 160   /* Constants for reaction fields */
 161   real kappa,k_rf,c_rf;
 162
 163   /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 164   double qsum[2];
 165   rvec   mu_tot[2];
 166
 167   /* Dispersion correction stuff */
 168   int  eDispCorr;
 169   /* The shift of the shift or user potentials */
 170   real enershiftsix;
 171   real enershifttwelve;
 172   /* Integrated differces for energy and virial with cut-off functions */
 173   real enerdiffsix;
 174   real enerdifftwelve;
 175   real virdiffsix;
 176   real virdifftwelve;
 177   /* Constant for long range dispersion correction (average dispersion)
 178    * for topology A/B ([0]/[1]) */
 179   real avcsix[2];
 180   /* Constant for long range repulsion term. Relative difference of about
 181    * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 182    */
 183   real avctwelve[2];
 184
 185   /* Fudge factors */
 186   real fudgeQQ;
 187
 188   /* Table stuff */
 189   gmx_bool bcoultab;
 190   gmx_bool bvdwtab;
 191   /* The normal tables are in the nblists struct(s) below */
 192   t_forcetable tab14; /* for 1-4 interactions only */
 193
 194   /* PPPM & Shifting stuff */
 195   real rcoulomb_switch,rcoulomb;
 196   real *phi;
 197
 198   /* VdW stuff */
 199   double reppow;
 200   real rvdw_switch,rvdw;
 201   real bham_b_max;
 202
 203   /* Free energy ? */
 204   int  efep;
 205   real sc_alpha;
 206   int  sc_power;
 207   real sc_sigma6_def;
 208   real sc_sigma6_min;
 209   gmx_bool bSepDVDL;
 210
 211   /* NS Stuff */
 212   int  eeltype;
 213   int  vdwtype;
 214   int  cg0,hcg;
 215   /* solvent_opt contains the enum for the most common solvent
 216    * in the system, which will be optimized.
 217    * It can be set to esolNO to disable all water optimization */
 218   int  solvent_opt;
 219   int  nWatMol;
 220   gmx_bool bGrid;
 221   gmx_bool bExcl_IntraCGAll_InterCGNone;
 222   cginfo_mb_t *cginfo_mb;
 223   int  *cginfo;
 224   rvec *cg_cm;
 225   int  cg_nalloc;
 226   rvec *shift_vec;
 227
 228   /* The neighborlists including tables */
 229   int  nnblists;
 230   int  *gid2nblists;
 231   t_nblists *nblists;
 232
 233   /* The wall tables (if used) */
 234   int  nwall;
 235   t_forcetable **wall_tab;
 236
 237   /* This mask array of length nn determines whether or not this bit of the
 238    * neighbourlists should be computed. Usually all these are true of course,
 239    * but not when shells are used. During minimisation all the forces that
 240    * include shells are done, then after minimsation is converged the remaining
 241    * forces are computed.
 242    */
 243   /* gmx_bool *bMask; */
 244
 245   /* The number of charge groups participating in do_force_lowlevel */
 246   int ncg_force;
 247   /* The number of atoms participating in do_force_lowlevel */
 248   int natoms_force;
 249   /* The number of atoms participating in force and constraints */
 250   int natoms_force_constr;
 251   /* The allocation size of vectors of size natoms_force */
 252   int nalloc_force;
 253
 254   /* Twin Range stuff, f_twin has size natoms_force */
 255   gmx_bool bTwinRange;
 256   int  nlr;
 257   rvec *f_twin;
 258
 259   /* Forces that should not enter into the virial summation:
 260    * PPPM/PME/Ewald/posres
 261    */
 262   gmx_bool bF_NoVirSum;
 263   int  f_novirsum_n;
 264   int  f_novirsum_nalloc;
 265   rvec *f_novirsum_alloc;
 266   /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
 267    * points to the normal force vectors wen pressure is not requested.
 268    */
 269   rvec *f_novirsum;
 270
 271   /* Long-range forces and virial for PPPM/PME/Ewald */
 272   gmx_pme_t pmedata;
 273   tensor    vir_el_recip;
 274
 275   /* PME/Ewald stuff */
 276   gmx_bool bEwald;
 277   real ewaldcoeff;
 278   ewald_tab_t ewald_table;
 279
 280   /* Virial Stuff */
 281   rvec *fshift;
 282   rvec vir_diag_posres;
 283   dvec vir_wall_z;
 284
 285   /* Non bonded Parameter lists */
 286   int  ntype; /* Number of atom types */
 287   gmx_bool bBHAM;
 288   real *nbfp;
 289
 290   /* Energy group pair flags */
 291   int *egp_flags;
 292
 293   /* xmdrun flexible constraints */
 294   real fc_stepsize;
 295
 296   /* Generalized born implicit solvent */
 297   gmx_bool bGB;
 298   /* Generalized born stuff */
 299   real gb_epsilon_solvent;
 300   /* Table data for GB */
 301   t_forcetable gbtab;
 302   /* VdW radius for each atomtype (dim is thus ntype) */
 303   real *atype_radius;
 304   /* Effective radius (derived from effective volume) for each type */
 305   real *atype_vol;
 306   /* Implicit solvent - surface tension for each atomtype */
 307   real *atype_surftens;
 308   /* Implicit solvent - radius for GB calculation */
 309   real *atype_gb_radius;
 310   /* Implicit solvent - overlap for HCT model */
 311   real *atype_S_hct;
 312   /* Generalized born interaction data */
 313   gmx_genborn_t *born;
 314
 315   /* Table scale for GB */
 316   real gbtabscale;
 317   /* Table range for GB */
 318   real gbtabr;
 319   /* GB neighborlists (the sr list will contain for each atom all other atoms
 320    * (for use in the SA calculation) and the lr list will contain
 321    * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 322    */
 323   t_nblist gblist_sr;
 324   t_nblist gblist_lr;
 325   t_nblist gblist;
 326
 327   /* Inverse square root of the Born radii for implicit solvent */
 328   real *invsqrta;
 329   /* Derivatives of the potential with respect to the Born radii */
 330   real *dvda;
 331   /* Derivatives of the Born radii with respect to coordinates */
 332   real *dadx;
 333   real *dadx_rawptr;
 334   int   nalloc_dadx; /* Allocated size of dadx */
 335
 336   /* If > 0 signals Test Particle Insertion,
 337    * the value is the number of atoms of the molecule to insert
 338    * Only the energy difference due to the addition of the last molecule
 339    * should be calculated.
 340    */
 341   gmx_bool n_tpi;
 342
 343   /* Neighbor searching stuff */
 344   gmx_ns_t ns;
 345
 346   /* QMMM stuff */
 347   gmx_bool         bQMMM;
 348   t_QMMMrec    *qr;
 349
 350   /* QM-MM neighborlists */
 351   t_nblist QMMMlist;
 352
 353   /* Limit for printing large forces, negative is don't print */
 354   real print_force;
 355
 356   /* coarse load balancing time measurement */
 357   double t_fnbf;
 358   double t_wait;
 359   int timesteps;
 360
 361   /* parameter needed for AdResS simulation */
 362   int  adress_type;
 363   gmx_bool badress_tf_full_box;
 364   real adress_const_wf;
 365   real adress_ex_width;
 366   real adress_hy_width;
 367   int  adress_icor;
 368   int  adress_site;
 369   rvec adress_refs;
 370   int n_adress_tf_grps;
 371   int * adress_tf_table_index;
 372   int *adress_group_explicit;
 373   t_forcetable *  atf_tabs;
 374   real adress_ex_forcecap;
 375   gmx_bool adress_do_hybridpairs;
 376
 377   /* User determined parameters, copied from the inputrec */
 378   int  userint1;
 379   int  userint2;
 380   int  userint3;
 381   int  userint4;
 382   real userreal1;
 383   real userreal2;
 384   real userreal3;
 385   real userreal4;
 386 } t_forcerec;
 387
 388 #define C6(nbfp,ntp,ai,aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 389 #define C12(nbfp,ntp,ai,aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 390 #define BHAMC(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 391 #define BHAMA(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 392 #define BHAMB(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 393
 394 #ifdef __cplusplus
 395 }
 396 #endif
 397