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 }
  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  */
  75 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
  76 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  77 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  78 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  79 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  80 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  81 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  82 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  83 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  84 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  85 /* This bit is only used with bBondComm in the domain decomposition */
  86 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  87 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  88 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  89 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  90 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  91 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  92
  93
  94 /* Value to be used in mdrun for an infinite cut-off.
  95  * Since we need to compare with the cut-off squared,
  96  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
  97  */
  98 #define GMX_CUTOFF_INF 1E+18
  99
 100 /* enums for the neighborlist type */
 101 enum {
 102     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 103 };
 104
 105 struct cginfo_mb_t
 106 {
 107     int  cg_start;
 108     int  cg_end;
 109     int  cg_mod;
 110     int *cginfo;
 111 };
 112
 113
 114 /* Forward declaration of type for managing Ewald tables */
 115 struct gmx_ewald_tab_t;
 116
 117 struct ewald_corr_thread_t;
 118
 119 struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
 120     struct interaction_const_t *ic = nullptr;
 121
 122     /* PBC stuff */
 123     int                         ePBC = 0;
 124     //! Tells whether atoms inside a molecule can be in different periodic images,
 125     //  i.e. whether we need to take into account PBC when computing distances inside molecules.
 126     //  This determines whether PBC must be considered for e.g. bonded interactions.
 127     gmx_bool                    bMolPBC     = FALSE;
 128     int                         rc_scaling  = 0;
 129     rvec                        posres_com  = { 0 };
 130     rvec                        posres_comB = { 0 };
 131
 132     gmx_bool                    use_simd_kernels = FALSE;
 133
 134     /* Interaction for calculated in kernels. In many cases this is similar to
 135      * the electrostatics settings in the inputrecord, but the difference is that
 136      * these variables always specify the actual interaction in the kernel - if
 137      * we are tabulating reaction-field the inputrec will say reaction-field, but
 138      * the kernel interaction will say cubic-spline-table. To be safe we also
 139      * have a kernel-specific setting for the modifiers - if the interaction is
 140      * tabulated we already included the inputrec modification there, so the kernel
 141      * modification setting will say 'none' in that case.
 142      */
 143     int nbkernel_elec_interaction = 0;
 144     int nbkernel_vdw_interaction  = 0;
 145     int nbkernel_elec_modifier    = 0;
 146     int nbkernel_vdw_modifier     = 0;
 147
 148     /* Cut-Off stuff.
 149      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 150      */
 151     real rlist = 0;
 152
 153     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 154     double qsum[2]   = { 0 };
 155     double q2sum[2]  = { 0 };
 156     double c6sum[2]  = { 0 };
 157     rvec   mu_tot[2] = { { 0 } };
 158
 159     /* Dispersion correction stuff */
 160     std::unique_ptr<DispersionCorrection> dispersionCorrection;
 161
 162     /* Fudge factors */
 163     real fudgeQQ = 0;
 164
 165     /* Table stuff */
 166     gmx_bool             bcoultab = FALSE;
 167     gmx_bool             bvdwtab  = FALSE;
 168
 169     t_forcetable        *pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 170
 171     /* Free energy */
 172     int      efep          = 0;
 173     real     sc_alphavdw   = 0;
 174     real     sc_alphacoul  = 0;
 175     int      sc_power      = 0;
 176     real     sc_r_power    = 0;
 177     real     sc_sigma6_def = 0;
 178     real     sc_sigma6_min = 0;
 179
 180     /* Information about atom properties for the molecule blocks in the system */
 181     struct cginfo_mb_t *cginfo_mb                    = nullptr;
 182     /* Information about atom properties for local and non-local atoms */
 183     std::vector<int>    cginfo;
 184
 185     rvec               *shift_vec                    = nullptr;
 186
 187     int                 cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
 188     gmx_bool            bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
 189
 190     /* The Nbnxm Verlet non-bonded machinery */
 191     std::unique_ptr<nonbonded_verlet_t> nbv;
 192
 193     /* The wall tables (if used) */
 194     int                    nwall    = 0;
 195     t_forcetable        ***wall_tab = nullptr;
 196
 197     /* The number of atoms participating in do_force_lowlevel */
 198     int natoms_force = 0;
 199     /* The number of atoms participating in force and constraints */
 200     int natoms_force_constr = 0;
 201     /* The allocation size of vectors of size natoms_force */
 202     int nalloc_force = 0;
 203
 204     /* Forces that should not enter into the coord x force virial summation:
 205      * PPPM/PME/Ewald/posres/ForceProviders
 206      */
 207     /* True when we have contributions that are directly added to the virial */
 208     bool                   haveDirectVirialContributions = false;
 209     /* Force buffer for force computation with direct virial contributions */
 210     std::vector<gmx::RVec> forceBufferForDirectVirialContributions;
 211
 212     /* Data for PPPM/PME/Ewald */
 213     struct gmx_pme_t *pmedata                = nullptr;
 214     int               ljpme_combination_rule = 0;
 215
 216     /* PME/Ewald stuff */
 217     struct gmx_ewald_tab_t *ewald_table = nullptr;
 218
 219     /* Shift force array for computing the virial, size SHIFTS */
 220     std::vector<gmx::RVec> shiftForces;
 221
 222     /* Non bonded Parameter lists */
 223     int      ntype        = 0; /* Number of atom types */
 224     gmx_bool bBHAM        = FALSE;
 225     real    *nbfp         = nullptr;
 226     real    *ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
 227
 228     /* Energy group pair flags */
 229     int *egp_flags = nullptr;
 230
 231     /* Shell molecular dynamics flexible constraints */
 232     real fc_stepsize = 0;
 233
 234     /* If > 0 signals Test Particle Insertion,
 235      * the value is the number of atoms of the molecule to insert
 236      * Only the energy difference due to the addition of the last molecule
 237      * should be calculated.
 238      */
 239     int n_tpi = 0;
 240
 241     /* QMMM stuff */
 242     gmx_bool          bQMMM = FALSE;
 243     struct t_QMMMrec *qr    = nullptr;
 244
 245     /* QM-MM neighborlists */
 246     struct t_nblist        *QMMMlist = nullptr;
 247
 248     /* Limit for printing large forces, negative is don't print */
 249     real print_force = 0;
 250
 251     /* User determined parameters, copied from the inputrec */
 252     int  userint1  = 0;
 253     int  userint2  = 0;
 254     int  userint3  = 0;
 255     int  userint4  = 0;
 256     real userreal1 = 0;
 257     real userreal2 = 0;
 258     real userreal3 = 0;
 259     real userreal4 = 0;
 260
 261     /* Pointer to struct for managing threading of bonded force calculation */
 262     struct bonded_threading_t *bondedThreading = nullptr;
 263
 264     /* TODO: Replace the pointer by an object once we got rid of C */
 265     gmx::GpuBonded *gpuBonded = nullptr;
 266
 267     /* Ewald correction thread local virial and energy data */
 268     int                         nthread_ewc = 0;
 269     struct ewald_corr_thread_t *ewc_t       = nullptr;
 270
 271     gmx::ForceProviders        *forceProviders = nullptr;
 272
 273     // The stateGpu object is created in runner, forcerec just keeps the copy of the pointer.
 274     // TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of
 275     //       general StatePropagatorData object that is passed around
 276     gmx::StatePropagatorDataGpu  *stateGpu = nullptr;
 277 };
 278
 279 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 280  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 281  * in the code, but beware if you are using these macros externally.
 282  */
 283 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 284 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 285 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 286 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 287 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 288
 289 #endif