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 <array>
  41 #include <vector>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/mdtypes/interaction_const.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48
  49 struct ForceProviders;
  50
  51 /* Abstract type for PME that is defined only in the routine that use them. */
  52 struct gmx_ns_t;
  53 struct gmx_pme_t;
  54 struct nonbonded_verlet_t;
  55 struct bonded_threading_t;
  56 struct t_forcetable;
  57 struct t_nblist;
  58 struct t_nblists;
  59 struct t_QMMMrec;
  60
  61 namespace gmx
  62 {
  63 class GpuBonded;
  64 }
  65
  66 /* macros for the cginfo data in forcerec
  67  *
  68  * Since the tpx format support max 256 energy groups, we do the same here.
  69  * Note that we thus have bits 8-14 still unused.
  70  *
  71  * The maximum cg size in cginfo is 63
  72  * because we only have space for 6 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)  &  ~255) | (gid))
  78 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  79 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  80 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  81 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  82 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  83 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  84 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  85 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  86 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  87 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  88 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  89 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  90 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  91 /* This bit is only used with bBondComm in the domain decomposition */
  92 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  93 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  94 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  95 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  96 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  97 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  98 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
  99 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
 100
 101
 102 /* Value to be used in mdrun for an infinite cut-off.
 103  * Since we need to compare with the cut-off squared,
 104  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 105  */
 106 #define GMX_CUTOFF_INF 1E+18
 107
 108 /* enums for the neighborlist type */
 109 enum {
 110     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 111 };
 112
 113 struct cginfo_mb_t
 114 {
 115     int  cg_start;
 116     int  cg_end;
 117     int  cg_mod;
 118     int *cginfo;
 119 };
 120
 121
 122 /* Forward declaration of type for managing Ewald tables */
 123 struct gmx_ewald_tab_t;
 124
 125 struct ewald_corr_thread_t;
 126
 127 struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
 128     struct interaction_const_t *ic;
 129
 130     /* PBC stuff */
 131     int                         ePBC;
 132     //! Whether PBC must be considered for bonded interactions.
 133     gmx_bool                    bMolPBC;
 134     int                         rc_scaling;
 135     rvec                        posres_com;
 136     rvec                        posres_comB;
 137
 138     gmx_bool                    use_simd_kernels;
 139
 140     /* Interaction for calculated in kernels. In many cases this is similar to
 141      * the electrostatics settings in the inputrecord, but the difference is that
 142      * these variables always specify the actual interaction in the kernel - if
 143      * we are tabulating reaction-field the inputrec will say reaction-field, but
 144      * the kernel interaction will say cubic-spline-table. To be safe we also
 145      * have a kernel-specific setting for the modifiers - if the interaction is
 146      * tabulated we already included the inputrec modification there, so the kernel
 147      * modification setting will say 'none' in that case.
 148      */
 149     int nbkernel_elec_interaction;
 150     int nbkernel_vdw_interaction;
 151     int nbkernel_elec_modifier;
 152     int nbkernel_vdw_modifier;
 153
 154     /* Use special N*N kernels? */
 155     gmx_bool bAllvsAll;
 156     /* Private work data */
 157     void    *AllvsAll_work;
 158
 159     /* Cut-Off stuff.
 160      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 161      */
 162     real rlist;
 163
 164     /* Parameters for generalized reaction field */
 165     real zsquare, temp;
 166
 167     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 168     double qsum[2];
 169     double q2sum[2];
 170     double c6sum[2];
 171     rvec   mu_tot[2];
 172
 173     /* Dispersion correction stuff */
 174     int                  eDispCorr;
 175     int                  numAtomsForDispersionCorrection;
 176     struct t_forcetable *dispersionCorrectionTable;
 177
 178     /* The shift of the shift or user potentials */
 179     real enershiftsix;
 180     real enershifttwelve;
 181     /* Integrated differces for energy and virial with cut-off functions */
 182     real enerdiffsix;
 183     real enerdifftwelve;
 184     real virdiffsix;
 185     real virdifftwelve;
 186     /* Constant for long range dispersion correction (average dispersion)
 187      * for topology A/B ([0]/[1]) */
 188     real avcsix[2];
 189     /* Constant for long range repulsion term. Relative difference of about
 190      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 191      */
 192     real avctwelve[2];
 193
 194     /* Fudge factors */
 195     real fudgeQQ;
 196
 197     /* Table stuff */
 198     gmx_bool             bcoultab;
 199     gmx_bool             bvdwtab;
 200     /* The normal tables are in the nblists struct(s) below */
 201
 202     struct t_forcetable *pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 203
 204     /* Free energy */
 205     int      efep;
 206     real     sc_alphavdw;
 207     real     sc_alphacoul;
 208     int      sc_power;
 209     real     sc_r_power;
 210     real     sc_sigma6_def;
 211     real     sc_sigma6_min;
 212
 213     /* NS Stuff */
 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     struct 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     struct t_nblists          *nblists;
 232
 233     int                        cutoff_scheme; /* group- or Verlet-style cutoff */
 234     gmx_bool                   bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 235     struct nonbonded_verlet_t *nbv;
 236
 237     /* The wall tables (if used) */
 238     int                    nwall;
 239     struct t_forcetable ***wall_tab;
 240
 241     /* The number of charge groups participating in do_force_lowlevel */
 242     int ncg_force;
 243     /* The number of atoms participating in do_force_lowlevel */
 244     int natoms_force;
 245     /* The number of atoms participating in force and constraints */
 246     int natoms_force_constr;
 247     /* The allocation size of vectors of size natoms_force */
 248     int nalloc_force;
 249
 250     /* Forces that should not enter into the coord x force virial summation:
 251      * PPPM/PME/Ewald/posres/ForceProviders
 252      */
 253     /* True when we have contributions that are directly added to the virial */
 254     gmx_bool                 haveDirectVirialContributions;
 255     /* TODO: Replace the pointer by an object once we got rid of C */
 256     std::vector<gmx::RVec>  *forceBufferForDirectVirialContributions;
 257
 258     /* Data for PPPM/PME/Ewald */
 259     struct gmx_pme_t *pmedata;
 260     int               ljpme_combination_rule;
 261
 262     /* PME/Ewald stuff */
 263     struct gmx_ewald_tab_t *ewald_table;
 264
 265     /* Shift force array for computing the virial */
 266     rvec *fshift;
 267
 268     /* Non bonded Parameter lists */
 269     int      ntype; /* Number of atom types */
 270     gmx_bool bBHAM;
 271     real    *nbfp;
 272     real    *ljpme_c6grid; /* C6-values used on grid in LJPME */
 273
 274     /* Energy group pair flags */
 275     int *egp_flags;
 276
 277     /* Shell molecular dynamics flexible constraints */
 278     real fc_stepsize;
 279
 280     /* If > 0 signals Test Particle Insertion,
 281      * the value is the number of atoms of the molecule to insert
 282      * Only the energy difference due to the addition of the last molecule
 283      * should be calculated.
 284      */
 285     int n_tpi;
 286
 287     /* Neighbor searching stuff */
 288     struct gmx_ns_t *ns;
 289
 290     /* QMMM stuff */
 291     gmx_bool          bQMMM;
 292     struct t_QMMMrec *qr;
 293
 294     /* QM-MM neighborlists */
 295     struct t_nblist        *QMMMlist;
 296
 297     /* Limit for printing large forces, negative is don't print */
 298     real print_force;
 299
 300     /* coarse load balancing time measurement */
 301     double t_fnbf;
 302     double t_wait;
 303     int    timesteps;
 304
 305     /* User determined parameters, copied from the inputrec */
 306     int  userint1;
 307     int  userint2;
 308     int  userint3;
 309     int  userint4;
 310     real userreal1;
 311     real userreal2;
 312     real userreal3;
 313     real userreal4;
 314
 315     /* Pointer to struct for managing threading of bonded force calculation */
 316     struct bonded_threading_t *bondedThreading;
 317
 318     /* TODO: Replace the pointer by an object once we got rid of C */
 319     gmx::GpuBonded *gpuBonded;
 320
 321     /* Ewald correction thread local virial and energy data */
 322     int                         nthread_ewc;
 323     struct ewald_corr_thread_t *ewc_t;
 324
 325     struct ForceProviders      *forceProviders;
 326 };
 327
 328 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 329  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 330  * in the code, but beware if you are using these macros externally.
 331  */
 332 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 333 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 334 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 335 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 336 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 337
 338 #endif