src/gromacs/mdtypes/forcerec.h

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  37 #ifndef GMX_MDTYPES_TYPES_FORCEREC_H
  38 #define GMX_MDTYPES_TYPES_FORCEREC_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #ifdef __cplusplus
  42 #include "gromacs/math/paddedvector.h"
  43 #endif
  44 #include "gromacs/mdtypes/interaction_const.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/topology/idef.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 struct ForceProviders;
  51
  52 /* Abstract type for PME that is defined only in the routine that use them. */
  53 struct gmx_genborn_t;
  54 struct gmx_ns_t;
  55 struct gmx_pme_t;
  56 struct nonbonded_verlet_t;
  57 struct bonded_threading_t;
  58 struct t_forcetable;
  59 struct t_nblist;
  60 struct t_nblists;
  61 struct t_QMMMrec;
  62
  63 #ifdef __cplusplus
  64 extern "C" {
  65 #endif
  66
  67 /* macros for the cginfo data in forcerec
  68  *
  69  * Since the tpx format support max 256 energy groups, we do the same here.
  70  * Note that we thus have bits 8-14 still unused.
  71  *
  72  * The maximum cg size in cginfo is 63
  73  * because we only have space for 6 bits in cginfo,
  74  * this cg size entry is actually only read with domain decomposition.
  75  * But there is a smaller limit due to the t_excl data structure
  76  * which is defined in nblist.h.
  77  */
  78 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
  79 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  80 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  81 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  82 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  83 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  84 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  85 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  86 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  87 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  88 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  89 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  90 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  91 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  92 /* This bit is only used with bBondComm in the domain decomposition */
  93 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  94 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  95 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  96 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  97 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  98 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  99 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
 100 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
 101
 102
 103 /* Value to be used in mdrun for an infinite cut-off.
 104  * Since we need to compare with the cut-off squared,
 105  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 106  */
 107 #define GMX_CUTOFF_INF 1E+18
 108
 109 /* enums for the neighborlist type */
 110 enum {
 111     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 112 };
 113 /* OOR is "one over r" -- standard coul */
 114 enum {
 115     enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
 116 };
 117
 118 enum {
 119     egCOULSR, egLJSR, egBHAMSR,
 120     egCOUL14, egLJ14, egGB, egNR
 121 };
 122 extern const char *egrp_nm[egNR+1];
 123
 124 struct gmx_grppairener_t
 125 {
 126     int   nener;      /* The number of energy group pairs     */
 127     real *ener[egNR]; /* Energy terms for each pair of groups */
 128 };
 129
 130 struct gmx_enerdata_t
 131 {
 132     real                     term[F_NRE];         /* The energies for all different interaction types */
 133     struct gmx_grppairener_t grpp;
 134     double                   dvdl_lin[efptNR];    /* Contributions to dvdl with linear lam-dependence */
 135     double                   dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence                  */
 136     int                      n_lambda;
 137     int                      fep_state;           /*current fep state -- just for printing */
 138     double                  *enerpart_lambda;     /* Partial energy for lambda and flambda[] */
 139     real                     foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
 140     struct gmx_grppairener_t foreign_grpp;        /* alternate array for storing foreign lambda energies */
 141 };
 142 /* The idea is that dvdl terms with linear lambda dependence will be added
 143  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 144  * should explicitly determine the energies at foreign lambda points
 145  * when n_lambda > 0.
 146  */
 147
 148 struct cginfo_mb_t
 149 {
 150     int  cg_start;
 151     int  cg_end;
 152     int  cg_mod;
 153     int *cginfo;
 154 };
 155
 156
 157 /* Forward declaration of type for managing Ewald tables */
 158 struct gmx_ewald_tab_t;
 159
 160 struct ewald_corr_thread_t;
 161
 162 struct t_forcerec {
 163     struct interaction_const_t *ic;
 164
 165     /* Domain Decomposition */
 166     gmx_bool bDomDec;
 167
 168     /* PBC stuff */
 169     int                         ePBC;
 170     gmx_bool                    bMolPBC;
 171     int                         rc_scaling;
 172     rvec                        posres_com;
 173     rvec                        posres_comB;
 174
 175     gmx_bool                    use_simd_kernels;
 176
 177     /* Interaction for calculated in kernels. In many cases this is similar to
 178      * the electrostatics settings in the inputrecord, but the difference is that
 179      * these variables always specify the actual interaction in the kernel - if
 180      * we are tabulating reaction-field the inputrec will say reaction-field, but
 181      * the kernel interaction will say cubic-spline-table. To be safe we also
 182      * have a kernel-specific setting for the modifiers - if the interaction is
 183      * tabulated we already included the inputrec modification there, so the kernel
 184      * modification setting will say 'none' in that case.
 185      */
 186     int nbkernel_elec_interaction;
 187     int nbkernel_vdw_interaction;
 188     int nbkernel_elec_modifier;
 189     int nbkernel_vdw_modifier;
 190
 191     /* Use special N*N kernels? */
 192     gmx_bool bAllvsAll;
 193     /* Private work data */
 194     void    *AllvsAll_work;
 195     void    *AllvsAll_workgb;
 196
 197     /* Cut-Off stuff.
 198      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 199      */
 200     real rlist;
 201
 202     /* Dielectric constant resp. multiplication factor for charges */
 203     real zsquare, temp;
 204     real epsilon_r, epsilon_rf, epsfac;
 205
 206     /* Constants for reaction fields */
 207     real kappa, k_rf, c_rf;
 208
 209     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 210     double qsum[2];
 211     double q2sum[2];
 212     double c6sum[2];
 213     rvec   mu_tot[2];
 214
 215     /* Dispersion correction stuff */
 216     int                  eDispCorr;
 217     int                  numAtomsForDispersionCorrection;
 218     struct t_forcetable *dispersionCorrectionTable;
 219
 220     /* The shift of the shift or user potentials */
 221     real enershiftsix;
 222     real enershifttwelve;
 223     /* Integrated differces for energy and virial with cut-off functions */
 224     real enerdiffsix;
 225     real enerdifftwelve;
 226     real virdiffsix;
 227     real virdifftwelve;
 228     /* Constant for long range dispersion correction (average dispersion)
 229      * for topology A/B ([0]/[1]) */
 230     real avcsix[2];
 231     /* Constant for long range repulsion term. Relative difference of about
 232      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 233      */
 234     real avctwelve[2];
 235
 236     /* Fudge factors */
 237     real fudgeQQ;
 238
 239     /* Table stuff */
 240     gmx_bool             bcoultab;
 241     gmx_bool             bvdwtab;
 242     /* The normal tables are in the nblists struct(s) below */
 243
 244     struct t_forcetable *pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 245
 246     /* PPPM & Shifting stuff */
 247     int   coulomb_modifier;
 248     real  rcoulomb_switch, rcoulomb;
 249     real *phi;
 250
 251     /* VdW stuff */
 252     int    vdw_modifier;
 253     double reppow;
 254     real   rvdw_switch, rvdw;
 255     real   bham_b_max;
 256
 257     /* Free energy */
 258     int      efep;
 259     real     sc_alphavdw;
 260     real     sc_alphacoul;
 261     int      sc_power;
 262     real     sc_r_power;
 263     real     sc_sigma6_def;
 264     real     sc_sigma6_min;
 265
 266     /* NS Stuff */
 267     int  eeltype;
 268     int  vdwtype;
 269     int  cg0, hcg;
 270     /* solvent_opt contains the enum for the most common solvent
 271      * in the system, which will be optimized.
 272      * It can be set to esolNO to disable all water optimization */
 273     int                 solvent_opt;
 274     int                 nWatMol;
 275     gmx_bool            bGrid;
 276     gmx_bool            bExcl_IntraCGAll_InterCGNone;
 277     struct cginfo_mb_t *cginfo_mb;
 278     int                *cginfo;
 279     rvec               *cg_cm;
 280     int                 cg_nalloc;
 281     rvec               *shift_vec;
 282
 283     /* The neighborlists including tables */
 284     int                        nnblists;
 285     int                       *gid2nblists;
 286     struct t_nblists          *nblists;
 287
 288     int                        cutoff_scheme; /* group- or Verlet-style cutoff */
 289     gmx_bool                   bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 290     struct nonbonded_verlet_t *nbv;
 291
 292     /* The wall tables (if used) */
 293     int                    nwall;
 294     struct t_forcetable ***wall_tab;
 295
 296     /* The number of charge groups participating in do_force_lowlevel */
 297     int ncg_force;
 298     /* The number of atoms participating in do_force_lowlevel */
 299     int natoms_force;
 300     /* The number of atoms participating in force and constraints */
 301     int natoms_force_constr;
 302     /* The allocation size of vectors of size natoms_force */
 303     int nalloc_force;
 304
 305     /* Forces that should not enter into the virial summation:
 306      * PPPM/PME/Ewald/posres
 307      * If such forces are present in the system, bF_NoVirSum=TRUE.
 308      */
 309     gmx_bool          bF_NoVirSum;
 310 #ifdef __cplusplus
 311     /* TODO: Replace the pointer by an object once we got rid of C */
 312     PaddedRVecVector *forceBufferNoVirialSummation;
 313 #else
 314     void             *forceBufferNoVirialSummation_dummy;
 315 #endif
 316     /* Pointer that points to forceNoVirialSummation when virial is calcaluted,
 317      * points to the normal force vector when the virial is not requested
 318      * or when bF_NoVirSum == FALSE.
 319      */
 320 #ifdef __cplusplus
 321     PaddedRVecVector *f_novirsum;
 322 #else
 323     void             *f_novirsum_xdummy;
 324 #endif
 325
 326     /* Long-range forces and virial for PPPM/PME/Ewald */
 327     struct gmx_pme_t *pmedata;
 328     int               ljpme_combination_rule;
 329     tensor            vir_el_recip;
 330     tensor            vir_lj_recip;
 331
 332     /* PME/Ewald stuff */
 333     gmx_bool                bEwald;
 334     real                    ewaldcoeff_q;
 335     real                    ewaldcoeff_lj;
 336     struct gmx_ewald_tab_t *ewald_table;
 337
 338     /* Virial Stuff */
 339     rvec *fshift;
 340     rvec  vir_diag_posres;
 341     dvec  vir_wall_z;
 342
 343     /* Non bonded Parameter lists */
 344     int      ntype; /* Number of atom types */
 345     gmx_bool bBHAM;
 346     real    *nbfp;
 347     real    *ljpme_c6grid; /* C6-values used on grid in LJPME */
 348
 349     /* Energy group pair flags */
 350     int *egp_flags;
 351
 352     /* Shell molecular dynamics flexible constraints */
 353     real fc_stepsize;
 354
 355     /* Generalized born implicit solvent */
 356     gmx_bool              bGB;
 357     /* Generalized born stuff */
 358     real                  gb_epsilon_solvent;
 359     /* Table data for GB */
 360     struct t_forcetable  *gbtab;
 361     /* VdW radius for each atomtype (dim is thus ntype) */
 362     real                 *atype_radius;
 363     /* Effective radius (derived from effective volume) for each type */
 364     real                 *atype_vol;
 365     /* Implicit solvent - surface tension for each atomtype */
 366     real                 *atype_surftens;
 367     /* Implicit solvent - radius for GB calculation */
 368     real                 *atype_gb_radius;
 369     /* Implicit solvent - overlap for HCT model */
 370     real                 *atype_S_hct;
 371     /* Generalized born interaction data */
 372     struct gmx_genborn_t *born;
 373
 374     /* Table scale for GB */
 375     real gbtabscale;
 376     /* Table range for GB */
 377     real gbtabr;
 378     /* GB neighborlists (the sr list will contain for each atom all other atoms
 379      * (for use in the SA calculation) and the lr list will contain
 380      * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 381      */
 382     struct t_nblist *gblist_sr;
 383     struct t_nblist *gblist_lr;
 384     struct t_nblist *gblist;
 385
 386     /* Inverse square root of the Born radii for implicit solvent */
 387     real *invsqrta;
 388     /* Derivatives of the potential with respect to the Born radii */
 389     real *dvda;
 390     /* Derivatives of the Born radii with respect to coordinates */
 391     real *dadx;
 392     real *dadx_rawptr;
 393     int   nalloc_dadx; /* Allocated size of dadx */
 394
 395     /* If > 0 signals Test Particle Insertion,
 396      * the value is the number of atoms of the molecule to insert
 397      * Only the energy difference due to the addition of the last molecule
 398      * should be calculated.
 399      */
 400     gmx_bool n_tpi;
 401
 402     /* Neighbor searching stuff */
 403     struct gmx_ns_t *ns;
 404
 405     /* QMMM stuff */
 406     gmx_bool          bQMMM;
 407     struct t_QMMMrec *qr;
 408
 409     /* QM-MM neighborlists */
 410     struct t_nblist        *QMMMlist;
 411
 412     /* Limit for printing large forces, negative is don't print */
 413     real print_force;
 414
 415     /* coarse load balancing time measurement */
 416     double t_fnbf;
 417     double t_wait;
 418     int    timesteps;
 419
 420     /* User determined parameters, copied from the inputrec */
 421     int  userint1;
 422     int  userint2;
 423     int  userint3;
 424     int  userint4;
 425     real userreal1;
 426     real userreal2;
 427     real userreal3;
 428     real userreal4;
 429
 430     /* Pointer to struct for managing threading of bonded force calculation */
 431     struct bonded_threading_t *bonded_threading;
 432
 433     /* Ewald correction thread local virial and energy data */
 434     int                         nthread_ewc;
 435     struct ewald_corr_thread_t *ewc_t;
 436
 437     struct ForceProviders      *forceProviders;
 438 };
 439
 440 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 441  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 442  * in the code, but beware if you are using these macros externally.
 443  */
 444 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 445 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 446 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 447 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 448 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 449
 450 #ifdef __cplusplus
 451 }
 452 #endif
 453
 454 #endif