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.
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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 is 255, because we only have space for 8 bits in cginfo,
  72  * this cg size entry is actually only read with domain decomposition.
  73  */
  74 #define MAX_CHARGEGROUP_SIZE 256
  75 #define SET_CGINFO_GID(cgi,gid)      (cgi) = (((cgi)  &  ~65535)  |  (gid)   )
  76 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   65535)
  77 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  78 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  79 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  80 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  81 #define SET_CGINFO_SOLOPT(cgi,opt)   (cgi) = (((cgi)  & ~(15<<18)) | ((opt)<<18))
  82 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   15)
  83 /* This bit is only used with bBondComm in the domain decomposition */
  84 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  85 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  86 #define SET_CGINFO_NATOMS(cgi,opt)   (cgi) = (((cgi)  & ~(255<<23)) | ((opt)<<23))
  87 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>23)       &   255)
  88
  89
  90 /* Value to be used in mdrun for an infinite cut-off.
  91  * Since we need to compare with the cut-off squared,
  92  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
  93  */
  94 #define GMX_CUTOFF_INF 1E+18
  95
  96
  97 enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
  98        egCOUL14, egLJ14, egGB, egNR };
  99
 100 typedef struct {
 101   int  nener;        /* The number of energy group pairs     */
 102   real *ener[egNR];  /* Energy terms for each pair of groups */
 103 } gmx_grppairener_t;
 104
 105 typedef struct {
 106   real term[F_NRE];    /* The energies for all different interaction types */
 107   gmx_grppairener_t grpp;
 108   double dvdl_lin;     /* Contributions to dvdl with linear lam-dependence */
 109   double dvdl_nonlin;  /* Idem, but non-linear dependence                  */
 110   int    n_lambda;
 111   double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
 112 } gmx_enerdata_t;
 113 /* The idea is that dvdl terms with linear lambda dependence will be added
 114  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 115  * should explicitly determine the energies at foreign lambda points
 116  * when n_lambda > 0.
 117  */
 118
 119 typedef struct {
 120   int cg_start;
 121   int cg_end;
 122   int cg_mod;
 123   int *cginfo;
 124 } cginfo_mb_t;
 125
 126
 127 /* ewald table type */
 128 typedef struct ewald_tab *ewald_tab_t;
 129
 130 typedef struct {
 131   /* Domain Decomposition */
 132   gmx_bool bDomDec;
 133
 134   /* PBC stuff */
 135   int  ePBC;
 136   gmx_bool bMolPBC;
 137   int  rc_scaling;
 138   rvec posres_com;
 139   rvec posres_comB;
 140
 141   gmx_bool UseOptimizedKernels;
 142
 143   /* Use special N*N kernels? */
 144   gmx_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   gmx_bool bcoultab;
 188   gmx_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_def;
 206   real sc_sigma6_min;
 207   gmx_bool bSepDVDL;
 208
 209   /* NS Stuff */
 210   int  eeltype;
 211   int  vdwtype;
 212   int  cg0,hcg;
 213   /* solvent_opt contains the enum for the most common solvent
 214    * in the system, which will be optimized.
 215    * It can be set to esolNO to disable all water optimization */
 216   int  solvent_opt;
 217   int  nWatMol;
 218   gmx_bool bGrid;
 219   gmx_bool bExcl_IntraCGAll_InterCGNone;
 220   cginfo_mb_t *cginfo_mb;
 221   int  *cginfo;
 222   rvec *cg_cm;
 223   int  cg_nalloc;
 224   rvec *shift_vec;
 225
 226   /* The neighborlists including tables */
 227   int  nnblists;
 228   int  *gid2nblists;
 229   t_nblists *nblists;
 230
 231   /* The wall tables (if used) */
 232   int  nwall;
 233   t_forcetable **wall_tab;
 234
 235   /* This mask array of length nn determines whether or not this bit of the
 236    * neighbourlists should be computed. Usually all these are true of course,
 237    * but not when shells are used. During minimisation all the forces that
 238    * include shells are done, then after minimsation is converged the remaining
 239    * forces are computed.
 240    */
 241   /* gmx_bool *bMask; */
 242
 243   /* The number of charge groups participating in do_force_lowlevel */
 244   int ncg_force;
 245   /* The number of atoms participating in do_force_lowlevel */
 246   int natoms_force;
 247   /* The number of atoms participating in force and constraints */
 248   int natoms_force_constr;
 249   /* The allocation size of vectors of size natoms_force */
 250   int nalloc_force;
 251
 252   /* Twin Range stuff, f_twin has size natoms_force */
 253   gmx_bool bTwinRange;
 254   int  nlr;
 255   rvec *f_twin;
 256
 257   /* Forces that should not enter into the virial summation:
 258    * PPPM/PME/Ewald/posres
 259    */
 260   gmx_bool bF_NoVirSum;
 261   int  f_novirsum_n;
 262   int  f_novirsum_nalloc;
 263   rvec *f_novirsum_alloc;
 264   /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
 265    * points to the normal force vectors wen pressure is not requested.
 266    */
 267   rvec *f_novirsum;
 268
 269   /* Long-range forces and virial for PPPM/PME/Ewald */
 270   gmx_pme_t pmedata;
 271   tensor    vir_el_recip;
 272
 273   /* PME/Ewald stuff */
 274   gmx_bool bEwald;
 275   real ewaldcoeff;
 276   ewald_tab_t ewald_table;
 277
 278   /* Virial Stuff */
 279   rvec *fshift;
 280   rvec vir_diag_posres;
 281   dvec vir_wall_z;
 282
 283   /* Non bonded Parameter lists */
 284   int  ntype; /* Number of atom types */
 285   gmx_bool bBHAM;
 286   real *nbfp;
 287
 288   /* Energy group pair flags */
 289   int *egp_flags;
 290
 291   /* xmdrun flexible constraints */
 292   real fc_stepsize;
 293
 294   /* Generalized born implicit solvent */
 295   gmx_bool bGB;
 296   /* Generalized born stuff */
 297   real gb_epsilon_solvent;
 298   /* Table data for GB */
 299   t_forcetable gbtab;
 300   /* VdW radius for each atomtype (dim is thus ntype) */
 301   real *atype_radius;
 302   /* Effective radius (derived from effective volume) for each type */
 303   real *atype_vol;
 304   /* Implicit solvent - surface tension for each atomtype */
 305   real *atype_surftens;
 306   /* Implicit solvent - radius for GB calculation */
 307   real *atype_gb_radius;
 308   /* Implicit solvent - overlap for HCT model */
 309   real *atype_S_hct;
 310   /* Generalized born interaction data */
 311   gmx_genborn_t *born;
 312
 313   /* Table scale for GB */
 314   real gbtabscale;
 315   /* Table range for GB */
 316   real gbtabr;
 317   /* GB neighborlists (the sr list will contain for each atom all other atoms
 318    * (for use in the SA calculation) and the lr list will contain
 319    * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 320    */
 321   t_nblist gblist_sr;
 322   t_nblist gblist_lr;
 323   t_nblist gblist;
 324
 325   /* Inverse square root of the Born radii for implicit solvent */
 326   real *invsqrta;
 327   /* Derivatives of the potential with respect to the Born radii */
 328   real *dvda;
 329   /* Derivatives of the Born radii with respect to coordinates */
 330   real *dadx;
 331   real *dadx_rawptr;
 332   int   nalloc_dadx; /* Allocated size of dadx */
 333
 334   /* If > 0 signals Test Particle Insertion,
 335    * the value is the number of atoms of the molecule to insert
 336    * Only the energy difference due to the addition of the last molecule
 337    * should be calculated.
 338    */
 339   gmx_bool n_tpi;
 340
 341   /* Neighbor searching stuff */
 342   gmx_ns_t ns;
 343
 344   /* QMMM stuff */
 345   gmx_bool         bQMMM;
 346   t_QMMMrec    *qr;
 347
 348   /* QM-MM neighborlists */
 349   t_nblist QMMMlist;
 350
 351   /* Limit for printing large forces, negative is don't print */
 352   real print_force;
 353
 354   /* coarse load balancing time measurement */
 355   double t_fnbf;
 356   double t_wait;
 357   int timesteps;
 358
 359   /* User determined parameters, copied from the inputrec */
 360   int  userint1;
 361   int  userint2;
 362   int  userint3;
 363   int  userint4;
 364   real userreal1;
 365   real userreal2;
 366   real userreal3;
 367   real userreal4;
 368 } t_forcerec;
 369
 370 #define C6(nbfp,ntp,ai,aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 371 #define C12(nbfp,ntp,ai,aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 372 #define BHAMC(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 373 #define BHAMA(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 374 #define BHAMB(nbfp,ntp,ai,aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 375
 376 #ifdef __cplusplus
 377 }
 378 #endif
 379