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 <memory>
  42 #include <vector>
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/mdtypes/interaction_const.h"
  46 #include "gromacs/mdtypes/md_enums.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_ns_t;
  54 struct gmx_pme_t;
  55 struct nonbonded_verlet_t;
  56 struct bonded_threading_t;
  57 struct t_forcetable;
  58 struct t_QMMMrec;
  59
  60 namespace gmx
  61 {
  62 class GpuBonded;
  63 }
  64
  65 /* macros for the cginfo data in forcerec
  66  *
  67  * Since the tpx format support max 256 energy groups, we do the same here.
  68  * Note that we thus have bits 8-14 still unused.
  69  *
  70  * The maximum cg size in cginfo is 63
  71  * because we only have space for 6 bits in cginfo,
  72  * this cg size entry is actually only read with domain decomposition.
  73  */
  74 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
  75 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  76 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  77 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  78 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  79 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  80 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  81 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  82 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  83 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  84 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  85 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  86 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  87 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  88 /* This bit is only used with bBondComm in the domain decomposition */
  89 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  90 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  91 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  92 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  93 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  94 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  95 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
  96 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
  97
  98
  99 /* Value to be used in mdrun for an infinite cut-off.
 100  * Since we need to compare with the cut-off squared,
 101  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 102  */
 103 #define GMX_CUTOFF_INF 1E+18
 104
 105 /* enums for the neighborlist type */
 106 enum {
 107     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 108 };
 109
 110 struct cginfo_mb_t
 111 {
 112     int  cg_start;
 113     int  cg_end;
 114     int  cg_mod;
 115     int *cginfo;
 116 };
 117
 118
 119 /* Forward declaration of type for managing Ewald tables */
 120 struct gmx_ewald_tab_t;
 121
 122 struct ewald_corr_thread_t;
 123
 124 struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
 125     struct interaction_const_t *ic = nullptr;
 126
 127     /* PBC stuff */
 128     int                         ePBC = 0;
 129     //! Tells whether atoms inside a molecule can be in different periodic images,
 130     //  i.e. whether we need to take into account PBC when computing distances inside molecules.
 131     //  This determines whether PBC must be considered for e.g. bonded interactions.
 132     gmx_bool                    bMolPBC     = FALSE;
 133     int                         rc_scaling  = 0;
 134     rvec                        posres_com  = { 0 };
 135     rvec                        posres_comB = { 0 };
 136
 137     gmx_bool                    use_simd_kernels = FALSE;
 138
 139     /* Interaction for calculated in kernels. In many cases this is similar to
 140      * the electrostatics settings in the inputrecord, but the difference is that
 141      * these variables always specify the actual interaction in the kernel - if
 142      * we are tabulating reaction-field the inputrec will say reaction-field, but
 143      * the kernel interaction will say cubic-spline-table. To be safe we also
 144      * have a kernel-specific setting for the modifiers - if the interaction is
 145      * tabulated we already included the inputrec modification there, so the kernel
 146      * modification setting will say 'none' in that case.
 147      */
 148     int nbkernel_elec_interaction = 0;
 149     int nbkernel_vdw_interaction  = 0;
 150     int nbkernel_elec_modifier    = 0;
 151     int nbkernel_vdw_modifier     = 0;
 152
 153     /* Cut-Off stuff.
 154      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 155      */
 156     real rlist = 0;
 157
 158     /* Parameters for generalized reaction field */
 159     real zsquare = 0;
 160     real temp    = 0;
 161
 162     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 163     double qsum[2]   = { 0 };
 164     double q2sum[2]  = { 0 };
 165     double c6sum[2]  = { 0 };
 166     rvec   mu_tot[2] = { { 0 } };
 167
 168     /* Dispersion correction stuff */
 169     int                  eDispCorr = 0;
 170     int                  numAtomsForDispersionCorrection = 0;
 171     struct t_forcetable *dispersionCorrectionTable       = nullptr;
 172
 173     /* The shift of the shift or user potentials */
 174     real enershiftsix    = 0;
 175     real enershifttwelve = 0;
 176     /* Integrated differces for energy and virial with cut-off functions */
 177     real enerdiffsix    = 0;
 178     real enerdifftwelve = 0;
 179     real virdiffsix     = 0;
 180     real virdifftwelve  = 0;
 181     /* Constant for long range dispersion correction (average dispersion)
 182      * for topology A/B ([0]/[1]) */
 183     real avcsix[2] = { 0 };
 184     /* Constant for long range repulsion term. Relative difference of about
 185      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 186      */
 187     real avctwelve[2] = { 0 };
 188
 189     /* Fudge factors */
 190     real fudgeQQ = 0;
 191
 192     /* Table stuff */
 193     gmx_bool             bcoultab = FALSE;
 194     gmx_bool             bvdwtab  = FALSE;
 195
 196     struct t_forcetable *pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 197
 198     /* Free energy */
 199     int      efep          = 0;
 200     real     sc_alphavdw   = 0;
 201     real     sc_alphacoul  = 0;
 202     int      sc_power      = 0;
 203     real     sc_r_power    = 0;
 204     real     sc_sigma6_def = 0;
 205     real     sc_sigma6_min = 0;
 206
 207     /* NS Stuff */
 208     int  cg0 = 0;
 209     int  hcg = 0;
 210     /* solvent_opt contains the enum for the most common solvent
 211      * in the system, which will be optimized.
 212      * It can be set to esolNO to disable all water optimization */
 213     int                 solvent_opt                  = 0;
 214     int                 nWatMol                      = 0;
 215     gmx_bool            bGrid                        = FALSE;
 216     gmx_bool            bExcl_IntraCGAll_InterCGNone = FALSE;
 217     struct cginfo_mb_t *cginfo_mb                    = nullptr;
 218     int                *cginfo                       = nullptr;
 219     rvec               *cg_cm                        = nullptr;
 220     int                 cg_nalloc                    = 0;
 221     rvec               *shift_vec                    = nullptr;
 222
 223     int                 cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
 224     gmx_bool            bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
 225
 226     /* The Nbnxm Verlet non-bonded machinery */
 227     std::unique_ptr<nonbonded_verlet_t> nbv;
 228
 229     /* The wall tables (if used) */
 230     int                    nwall    = 0;
 231     struct t_forcetable ***wall_tab = nullptr;
 232
 233     /* The number of charge groups participating in do_force_lowlevel */
 234     int ncg_force = 0;
 235     /* The number of atoms participating in do_force_lowlevel */
 236     int natoms_force = 0;
 237     /* The number of atoms participating in force and constraints */
 238     int natoms_force_constr = 0;
 239     /* The allocation size of vectors of size natoms_force */
 240     int nalloc_force = 0;
 241
 242     /* Forces that should not enter into the coord x force virial summation:
 243      * PPPM/PME/Ewald/posres/ForceProviders
 244      */
 245     /* True when we have contributions that are directly added to the virial */
 246     gmx_bool                 haveDirectVirialContributions = FALSE;
 247     /* TODO: Replace the pointer by an object once we got rid of C */
 248     std::vector<gmx::RVec>  *forceBufferForDirectVirialContributions = nullptr;
 249
 250     /* Data for PPPM/PME/Ewald */
 251     struct gmx_pme_t *pmedata                = nullptr;
 252     int               ljpme_combination_rule = 0;
 253
 254     /* PME/Ewald stuff */
 255     struct gmx_ewald_tab_t *ewald_table = nullptr;
 256
 257     /* Shift force array for computing the virial */
 258     rvec *fshift = nullptr;
 259
 260     /* Non bonded Parameter lists */
 261     int      ntype        = 0; /* Number of atom types */
 262     gmx_bool bBHAM        = FALSE;
 263     real    *nbfp         = nullptr;
 264     real    *ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
 265
 266     /* Energy group pair flags */
 267     int *egp_flags = nullptr;
 268
 269     /* Shell molecular dynamics flexible constraints */
 270     real fc_stepsize = 0;
 271
 272     /* If > 0 signals Test Particle Insertion,
 273      * the value is the number of atoms of the molecule to insert
 274      * Only the energy difference due to the addition of the last molecule
 275      * should be calculated.
 276      */
 277     int n_tpi = 0;
 278
 279     /* QMMM stuff */
 280     gmx_bool          bQMMM = FALSE;
 281     struct t_QMMMrec *qr    = nullptr;
 282
 283     /* QM-MM neighborlists */
 284     struct t_nblist        *QMMMlist = nullptr;
 285
 286     /* Limit for printing large forces, negative is don't print */
 287     real print_force = 0;
 288
 289     /* User determined parameters, copied from the inputrec */
 290     int  userint1  = 0;
 291     int  userint2  = 0;
 292     int  userint3  = 0;
 293     int  userint4  = 0;
 294     real userreal1 = 0;
 295     real userreal2 = 0;
 296     real userreal3 = 0;
 297     real userreal4 = 0;
 298
 299     /* Pointer to struct for managing threading of bonded force calculation */
 300     struct bonded_threading_t *bondedThreading = nullptr;
 301
 302     /* TODO: Replace the pointer by an object once we got rid of C */
 303     gmx::GpuBonded *gpuBonded = nullptr;
 304
 305     /* Ewald correction thread local virial and energy data */
 306     int                         nthread_ewc = 0;
 307     struct ewald_corr_thread_t *ewc_t       = nullptr;
 308
 309     struct ForceProviders      *forceProviders = nullptr;
 310 };
 311
 312 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 313  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 314  * in the code, but beware if you are using these macros externally.
 315  */
 316 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 317 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 318 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 319 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 320 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 321
 322 #endif