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 /* Abstract type for PME that is defined only in the routine that use them. */
  51 struct gmx_ns_t;
  52 struct gmx_pme_t;
  53 struct nonbonded_verlet_t;
  54 struct bonded_threading_t;
  55 class DispersionCorrection;
  56 struct t_forcetable;
  57 struct t_QMMMrec;
  58
  59 namespace gmx
  60 {
  61 class GpuBonded;
  62 class ForceProviders;
  63 class StatePropagatorDataGpu;
  64 class PmePpCommGpu;
  65 }
  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  */
  76 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
  77 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  78 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  79 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  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_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  83 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  84 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  85 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  86 /* This bit is only used with bBondComm in the domain decomposition */
  87 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  88 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  89 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  90 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  91 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  92 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  93
  94
  95 /* Value to be used in mdrun for an infinite cut-off.
  96  * Since we need to compare with the cut-off squared,
  97  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
  98  */
  99 #define GMX_CUTOFF_INF 1E+18
 100
 101 /* enums for the neighborlist type */
 102 enum {
 103     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 104 };
 105
 106 struct cginfo_mb_t
 107 {
 108     int  cg_start;
 109     int  cg_end;
 110     int  cg_mod;
 111     int *cginfo;
 112 };
 113
 114
 115 /* Forward declaration of type for managing Ewald tables */
 116 struct gmx_ewald_tab_t;
 117
 118 struct ewald_corr_thread_t;
 119
 120 struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
 121     // Declare an explicit constructor and destructor, so they can be
 122     // implemented in a single source file, so that not every source
 123     // file that includes this one needs to understand how to find the
 124     // destructors of the objects pointed to by unique_ptr members.
 125     t_forcerec();
 126     ~t_forcerec();
 127
 128     struct interaction_const_t *ic = nullptr;
 129
 130     /* PBC stuff */
 131     int                         ePBC = 0;
 132     //! Tells whether atoms inside a molecule can be in different periodic images,
 133     //  i.e. whether we need to take into account PBC when computing distances inside molecules.
 134     //  This determines whether PBC must be considered for e.g. bonded interactions.
 135     gmx_bool                    bMolPBC     = FALSE;
 136     int                         rc_scaling  = 0;
 137     rvec                        posres_com  = { 0 };
 138     rvec                        posres_comB = { 0 };
 139
 140     gmx_bool                    use_simd_kernels = FALSE;
 141
 142     /* Interaction for calculated in kernels. In many cases this is similar to
 143      * the electrostatics settings in the inputrecord, but the difference is that
 144      * these variables always specify the actual interaction in the kernel - if
 145      * we are tabulating reaction-field the inputrec will say reaction-field, but
 146      * the kernel interaction will say cubic-spline-table. To be safe we also
 147      * have a kernel-specific setting for the modifiers - if the interaction is
 148      * tabulated we already included the inputrec modification there, so the kernel
 149      * modification setting will say 'none' in that case.
 150      */
 151     int nbkernel_elec_interaction = 0;
 152     int nbkernel_vdw_interaction  = 0;
 153     int nbkernel_elec_modifier    = 0;
 154     int nbkernel_vdw_modifier     = 0;
 155
 156     /* Cut-Off stuff.
 157      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 158      */
 159     real rlist = 0;
 160
 161     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 162     double qsum[2]   = { 0 };
 163     double q2sum[2]  = { 0 };
 164     double c6sum[2]  = { 0 };
 165     rvec   mu_tot[2] = { { 0 } };
 166
 167     /* Dispersion correction stuff */
 168     std::unique_ptr<DispersionCorrection> dispersionCorrection;
 169
 170     /* Fudge factors */
 171     real fudgeQQ = 0;
 172
 173     /* Table stuff */
 174     gmx_bool             bcoultab = FALSE;
 175     gmx_bool             bvdwtab  = FALSE;
 176
 177     t_forcetable        *pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 178
 179     /* Free energy */
 180     int      efep          = 0;
 181     real     sc_alphavdw   = 0;
 182     real     sc_alphacoul  = 0;
 183     int      sc_power      = 0;
 184     real     sc_r_power    = 0;
 185     real     sc_sigma6_def = 0;
 186     real     sc_sigma6_min = 0;
 187
 188     /* Information about atom properties for the molecule blocks in the system */
 189     struct cginfo_mb_t *cginfo_mb                    = nullptr;
 190     /* Information about atom properties for local and non-local atoms */
 191     std::vector<int>    cginfo;
 192
 193     rvec               *shift_vec                    = nullptr;
 194
 195     int                 cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
 196     gmx_bool            bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
 197
 198     /* The Nbnxm Verlet non-bonded machinery */
 199     std::unique_ptr<nonbonded_verlet_t> nbv;
 200
 201     /* The wall tables (if used) */
 202     int                    nwall    = 0;
 203     t_forcetable        ***wall_tab = nullptr;
 204
 205     /* The number of atoms participating in do_force_lowlevel */
 206     int natoms_force = 0;
 207     /* The number of atoms participating in force and constraints */
 208     int natoms_force_constr = 0;
 209     /* The allocation size of vectors of size natoms_force */
 210     int nalloc_force = 0;
 211
 212     /* Forces that should not enter into the coord x force virial summation:
 213      * PPPM/PME/Ewald/posres/ForceProviders
 214      */
 215     /* True when we have contributions that are directly added to the virial */
 216     bool                   haveDirectVirialContributions = false;
 217     /* Force buffer for force computation with direct virial contributions */
 218     std::vector<gmx::RVec> forceBufferForDirectVirialContributions;
 219
 220     /* Data for PPPM/PME/Ewald */
 221     struct gmx_pme_t *pmedata                = nullptr;
 222     int               ljpme_combination_rule = 0;
 223
 224     /* PME/Ewald stuff */
 225     struct gmx_ewald_tab_t *ewald_table = nullptr;
 226
 227     /* Shift force array for computing the virial, size SHIFTS */
 228     std::vector<gmx::RVec> shiftForces;
 229
 230     /* Non bonded Parameter lists */
 231     int      ntype        = 0; /* Number of atom types */
 232     gmx_bool bBHAM        = FALSE;
 233     real    *nbfp         = nullptr;
 234     real    *ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
 235
 236     /* Energy group pair flags */
 237     int *egp_flags = nullptr;
 238
 239     /* Shell molecular dynamics flexible constraints */
 240     real fc_stepsize = 0;
 241
 242     /* If > 0 signals Test Particle Insertion,
 243      * the value is the number of atoms of the molecule to insert
 244      * Only the energy difference due to the addition of the last molecule
 245      * should be calculated.
 246      */
 247     int n_tpi = 0;
 248
 249     /* QMMM stuff */
 250     gmx_bool          bQMMM = FALSE;
 251     struct t_QMMMrec *qr    = nullptr;
 252
 253     /* QM-MM neighborlists */
 254     struct t_nblist        *QMMMlist = nullptr;
 255
 256     /* Limit for printing large forces, negative is don't print */
 257     real print_force = 0;
 258
 259     /* User determined parameters, copied from the inputrec */
 260     int  userint1  = 0;
 261     int  userint2  = 0;
 262     int  userint3  = 0;
 263     int  userint4  = 0;
 264     real userreal1 = 0;
 265     real userreal2 = 0;
 266     real userreal3 = 0;
 267     real userreal4 = 0;
 268
 269     /* Pointer to struct for managing threading of bonded force calculation */
 270     struct bonded_threading_t *bondedThreading = nullptr;
 271
 272     /* TODO: Replace the pointer by an object once we got rid of C */
 273     gmx::GpuBonded *gpuBonded = nullptr;
 274
 275     /* Ewald correction thread local virial and energy data */
 276     int                         nthread_ewc = 0;
 277     struct ewald_corr_thread_t *ewc_t       = nullptr;
 278
 279     gmx::ForceProviders        *forceProviders = nullptr;
 280
 281     // The stateGpu object is created in runner, forcerec just keeps the copy of the pointer.
 282     // TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of
 283     //       general StatePropagatorData object that is passed around
 284     gmx::StatePropagatorDataGpu  *stateGpu = nullptr;
 285
 286     /* For PME-PP GPU communication */
 287     std::unique_ptr<gmx::PmePpCommGpu> pmePpCommGpu;
 288 };
 289
 290 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 291  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 292  * in the code, but beware if you are using these macros externally.
 293  */
 294 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 295 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 296 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 297 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 298 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 299
 300 #endif