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 #ifdef __cplusplus
  51
  52 extern "C" {
  53
  54 struct t_mdatoms;
  55 struct t_commrec;
  56
  57 /*! \libinternal \brief
  58  * Interface for a component that provides forces during MD.
  59  *
  60  * This is typically part of a larger structure/class managing its own
  61  * data, such that it has the information on what to do stored locally.
  62  * \todo Implement returning of energy and dH/dlambda.
  63  * \inlibraryapi
  64  */
  65 struct IForceProvider
  66 {
  67     public:
  68         /*! \brief Compute forces
  69          *
  70          * \todo This is specific for electric fields and needs to be generalized.
  71          * \param[in]    cr      Communication record for parallel operations
  72          * \param[in]    mdatoms Atom information
  73          * \param[inout] force   The forces
  74          * \param[in]    t       The actual time in the simulation (ps)
  75          */
  76         virtual void calculateForces(const t_commrec  *cr,
  77                                      const t_mdatoms  *mdatoms,
  78                                      PaddedRVecVector *force,
  79                                      double            t) = 0;
  80
  81     protected:
  82         ~IForceProvider() {}
  83 };
  84 #endif
  85
  86 /* Abstract type for PME that is defined only in the routine that use them. */
  87 struct gmx_genborn_t;
  88 struct gmx_ns_t;
  89 struct gmx_pme_t;
  90 struct nonbonded_verlet_t;
  91 struct bonded_threading_t;
  92 struct t_forcetable;
  93 struct t_nblist;
  94 struct t_nblists;
  95 struct t_QMMMrec;
  96 struct gmx_hw_info_t;
  97 struct gmx_gpu_opt_t;
  98
  99 /* macros for the cginfo data in forcerec
 100  *
 101  * Since the tpx format support max 256 energy groups, we do the same here.
 102  * Note that we thus have bits 8-14 still unused.
 103  *
 104  * The maximum cg size in cginfo is 63
 105  * because we only have space for 6 bits in cginfo,
 106  * this cg size entry is actually only read with domain decomposition.
 107  * But there is a smaller limit due to the t_excl data structure
 108  * which is defined in nblist.h.
 109  */
 110 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
 111 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
 112 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
 113 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
 114 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
 115 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
 116 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
 117 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
 118 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
 119 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
 120 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
 121 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
 122 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
 123 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
 124 /* This bit is only used with bBondComm in the domain decomposition */
 125 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
 126 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
 127 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
 128 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
 129 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
 130 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
 131 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
 132 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
 133
 134
 135 /* Value to be used in mdrun for an infinite cut-off.
 136  * Since we need to compare with the cut-off squared,
 137  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 138  */
 139 #define GMX_CUTOFF_INF 1E+18
 140
 141 /* enums for the neighborlist type */
 142 enum {
 143     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 144 };
 145 /* OOR is "one over r" -- standard coul */
 146 enum {
 147     enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
 148 };
 149
 150 enum {
 151     egCOULSR, egLJSR, egBHAMSR,
 152     egCOUL14, egLJ14, egGB, egNR
 153 };
 154 extern const char *egrp_nm[egNR+1];
 155
 156 typedef struct gmx_grppairener_t {
 157     int   nener;      /* The number of energy group pairs     */
 158     real *ener[egNR]; /* Energy terms for each pair of groups */
 159 } gmx_grppairener_t;
 160
 161 typedef struct gmx_enerdata_t {
 162     real              term[F_NRE];         /* The energies for all different interaction types */
 163     gmx_grppairener_t grpp;
 164     double            dvdl_lin[efptNR];    /* Contributions to dvdl with linear lam-dependence */
 165     double            dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence                  */
 166     int               n_lambda;
 167     int               fep_state;           /*current fep state -- just for printing */
 168     double           *enerpart_lambda;     /* Partial energy for lambda and flambda[] */
 169     real              foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
 170     gmx_grppairener_t foreign_grpp;        /* alternate array for storing foreign lambda energies */
 171 } gmx_enerdata_t;
 172 /* The idea is that dvdl terms with linear lambda dependence will be added
 173  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 174  * should explicitly determine the energies at foreign lambda points
 175  * when n_lambda > 0.
 176  */
 177
 178 typedef struct {
 179     int  cg_start;
 180     int  cg_end;
 181     int  cg_mod;
 182     int *cginfo;
 183 } cginfo_mb_t;
 184
 185
 186 /* Forward declaration of type for managing Ewald tables */
 187 struct gmx_ewald_tab_t;
 188
 189 typedef struct ewald_corr_thread_t ewald_corr_thread_t;
 190
 191 typedef struct t_forcerec {
 192     interaction_const_t *ic;
 193
 194     /* Domain Decomposition */
 195     gmx_bool bDomDec;
 196
 197     /* PBC stuff */
 198     int                         ePBC;
 199     gmx_bool                    bMolPBC;
 200     int                         rc_scaling;
 201     rvec                        posres_com;
 202     rvec                        posres_comB;
 203
 204     const struct gmx_hw_info_t *hwinfo;
 205     const struct gmx_gpu_opt_t *gpu_opt;
 206     gmx_bool                    use_simd_kernels;
 207
 208     /* Interaction for calculated in kernels. In many cases this is similar to
 209      * the electrostatics settings in the inputrecord, but the difference is that
 210      * these variables always specify the actual interaction in the kernel - if
 211      * we are tabulating reaction-field the inputrec will say reaction-field, but
 212      * the kernel interaction will say cubic-spline-table. To be safe we also
 213      * have a kernel-specific setting for the modifiers - if the interaction is
 214      * tabulated we already included the inputrec modification there, so the kernel
 215      * modification setting will say 'none' in that case.
 216      */
 217     int nbkernel_elec_interaction;
 218     int nbkernel_vdw_interaction;
 219     int nbkernel_elec_modifier;
 220     int nbkernel_vdw_modifier;
 221
 222     /* Use special N*N kernels? */
 223     gmx_bool bAllvsAll;
 224     /* Private work data */
 225     void    *AllvsAll_work;
 226     void    *AllvsAll_workgb;
 227
 228     /* Cut-Off stuff.
 229      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 230      */
 231     real rlist;
 232
 233     /* Dielectric constant resp. multiplication factor for charges */
 234     real zsquare, temp;
 235     real epsilon_r, epsilon_rf, epsfac;
 236
 237     /* Constants for reaction fields */
 238     real kappa, k_rf, c_rf;
 239
 240     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 241     double qsum[2];
 242     double q2sum[2];
 243     double c6sum[2];
 244     rvec   mu_tot[2];
 245
 246     /* Dispersion correction stuff */
 247     int                  eDispCorr;
 248     int                  numAtomsForDispersionCorrection;
 249     struct t_forcetable *dispersionCorrectionTable;
 250
 251     /* The shift of the shift or user potentials */
 252     real enershiftsix;
 253     real enershifttwelve;
 254     /* Integrated differces for energy and virial with cut-off functions */
 255     real enerdiffsix;
 256     real enerdifftwelve;
 257     real virdiffsix;
 258     real virdifftwelve;
 259     /* Constant for long range dispersion correction (average dispersion)
 260      * for topology A/B ([0]/[1]) */
 261     real avcsix[2];
 262     /* Constant for long range repulsion term. Relative difference of about
 263      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 264      */
 265     real avctwelve[2];
 266
 267     /* Fudge factors */
 268     real fudgeQQ;
 269
 270     /* Table stuff */
 271     gmx_bool             bcoultab;
 272     gmx_bool             bvdwtab;
 273     /* The normal tables are in the nblists struct(s) below */
 274
 275     struct t_forcetable *pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 276
 277     /* PPPM & Shifting stuff */
 278     int   coulomb_modifier;
 279     real  rcoulomb_switch, rcoulomb;
 280     real *phi;
 281
 282     /* VdW stuff */
 283     int    vdw_modifier;
 284     double reppow;
 285     real   rvdw_switch, rvdw;
 286     real   bham_b_max;
 287
 288     /* Free energy */
 289     int      efep;
 290     real     sc_alphavdw;
 291     real     sc_alphacoul;
 292     int      sc_power;
 293     real     sc_r_power;
 294     real     sc_sigma6_def;
 295     real     sc_sigma6_min;
 296
 297     /* NS Stuff */
 298     int  eeltype;
 299     int  vdwtype;
 300     int  cg0, hcg;
 301     /* solvent_opt contains the enum for the most common solvent
 302      * in the system, which will be optimized.
 303      * It can be set to esolNO to disable all water optimization */
 304     int          solvent_opt;
 305     int          nWatMol;
 306     gmx_bool     bGrid;
 307     gmx_bool     bExcl_IntraCGAll_InterCGNone;
 308     cginfo_mb_t *cginfo_mb;
 309     int         *cginfo;
 310     rvec        *cg_cm;
 311     int          cg_nalloc;
 312     rvec        *shift_vec;
 313
 314     /* The neighborlists including tables */
 315     int                        nnblists;
 316     int                       *gid2nblists;
 317     struct t_nblists          *nblists;
 318
 319     int                        cutoff_scheme; /* group- or Verlet-style cutoff */
 320     gmx_bool                   bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 321     struct nonbonded_verlet_t *nbv;
 322
 323     /* The wall tables (if used) */
 324     int                    nwall;
 325     struct t_forcetable ***wall_tab;
 326
 327     /* The number of charge groups participating in do_force_lowlevel */
 328     int ncg_force;
 329     /* The number of atoms participating in do_force_lowlevel */
 330     int natoms_force;
 331     /* The number of atoms participating in force and constraints */
 332     int natoms_force_constr;
 333     /* The allocation size of vectors of size natoms_force */
 334     int nalloc_force;
 335
 336     /* Forces that should not enter into the virial summation:
 337      * PPPM/PME/Ewald/posres
 338      * If such forces are present in the system, bF_NoVirSum=TRUE.
 339      */
 340     gmx_bool          bF_NoVirSum;
 341 #ifdef __cplusplus
 342     /* TODO: Replace the pointer by an object once we got rid of C */
 343     PaddedRVecVector *forceBufferNoVirialSummation;
 344 #else
 345     void             *forceBufferNoVirialSummation_dummy;
 346 #endif
 347     /* Pointer that points to forceNoVirialSummation when virial is calcaluted,
 348      * points to the normal force vector when the virial is not requested
 349      * or when bF_NoVirSum == FALSE.
 350      */
 351 #ifdef __cplusplus
 352     PaddedRVecVector *f_novirsum;
 353 #else
 354     void             *f_novirsum_xdummy;
 355 #endif
 356
 357     /* Long-range forces and virial for PPPM/PME/Ewald */
 358     struct gmx_pme_t *pmedata;
 359     int               ljpme_combination_rule;
 360     tensor            vir_el_recip;
 361     tensor            vir_lj_recip;
 362
 363     /* PME/Ewald stuff */
 364     gmx_bool                bEwald;
 365     real                    ewaldcoeff_q;
 366     real                    ewaldcoeff_lj;
 367     struct gmx_ewald_tab_t *ewald_table;
 368
 369     /* Virial Stuff */
 370     rvec *fshift;
 371     rvec  vir_diag_posres;
 372     dvec  vir_wall_z;
 373
 374     /* Non bonded Parameter lists */
 375     int      ntype; /* Number of atom types */
 376     gmx_bool bBHAM;
 377     real    *nbfp;
 378     real    *ljpme_c6grid; /* C6-values used on grid in LJPME */
 379
 380     /* Energy group pair flags */
 381     int *egp_flags;
 382
 383     /* Shell molecular dynamics flexible constraints */
 384     real fc_stepsize;
 385
 386     /* Generalized born implicit solvent */
 387     gmx_bool              bGB;
 388     /* Generalized born stuff */
 389     real                  gb_epsilon_solvent;
 390     /* Table data for GB */
 391     struct t_forcetable  *gbtab;
 392     /* VdW radius for each atomtype (dim is thus ntype) */
 393     real                 *atype_radius;
 394     /* Effective radius (derived from effective volume) for each type */
 395     real                 *atype_vol;
 396     /* Implicit solvent - surface tension for each atomtype */
 397     real                 *atype_surftens;
 398     /* Implicit solvent - radius for GB calculation */
 399     real                 *atype_gb_radius;
 400     /* Implicit solvent - overlap for HCT model */
 401     real                 *atype_S_hct;
 402     /* Generalized born interaction data */
 403     struct gmx_genborn_t *born;
 404
 405     /* Table scale for GB */
 406     real gbtabscale;
 407     /* Table range for GB */
 408     real gbtabr;
 409     /* GB neighborlists (the sr list will contain for each atom all other atoms
 410      * (for use in the SA calculation) and the lr list will contain
 411      * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 412      */
 413     struct t_nblist *gblist_sr;
 414     struct t_nblist *gblist_lr;
 415     struct t_nblist *gblist;
 416
 417     /* Inverse square root of the Born radii for implicit solvent */
 418     real *invsqrta;
 419     /* Derivatives of the potential with respect to the Born radii */
 420     real *dvda;
 421     /* Derivatives of the Born radii with respect to coordinates */
 422     real *dadx;
 423     real *dadx_rawptr;
 424     int   nalloc_dadx; /* Allocated size of dadx */
 425
 426     /* If > 0 signals Test Particle Insertion,
 427      * the value is the number of atoms of the molecule to insert
 428      * Only the energy difference due to the addition of the last molecule
 429      * should be calculated.
 430      */
 431     gmx_bool n_tpi;
 432
 433     /* Neighbor searching stuff */
 434     struct gmx_ns_t *ns;
 435
 436     /* QMMM stuff */
 437     gmx_bool          bQMMM;
 438     struct t_QMMMrec *qr;
 439
 440     /* QM-MM neighborlists */
 441     struct t_nblist        *QMMMlist;
 442
 443     /* Limit for printing large forces, negative is don't print */
 444     real print_force;
 445
 446     /* coarse load balancing time measurement */
 447     double t_fnbf;
 448     double t_wait;
 449     int    timesteps;
 450
 451     /* User determined parameters, copied from the inputrec */
 452     int  userint1;
 453     int  userint2;
 454     int  userint3;
 455     int  userint4;
 456     real userreal1;
 457     real userreal2;
 458     real userreal3;
 459     real userreal4;
 460
 461     /* Pointer to struct for managing threading of bonded force calculation */
 462     struct bonded_threading_t *bonded_threading;
 463
 464     /* Ewald correction thread local virial and energy data */
 465     int                    nthread_ewc;
 466     ewald_corr_thread_t   *ewc_t;
 467
 468     struct IForceProvider *efield;
 469 } t_forcerec;
 470
 471 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 472  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 473  * in the code, but beware if you are using these macros externally.
 474  */
 475 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 476 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 477 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 478 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 479 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 480
 481 #ifdef __cplusplus
 482 }
 483 #endif
 484 #endif