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