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 class DispersionCorrection;
  58 struct t_forcetable;
  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  */
  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_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  80 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  81 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  82 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  83 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  84 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  85 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  86 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  87 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  88 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  89 /* This bit is only used with bBondComm in the domain decomposition */
  90 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  91 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  92 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  93 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  94 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  95 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  96 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
  97 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
  98
  99
 100 /* Value to be used in mdrun for an infinite cut-off.
 101  * Since we need to compare with the cut-off squared,
 102  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 103  */
 104 #define GMX_CUTOFF_INF 1E+18
 105
 106 /* enums for the neighborlist type */
 107 enum {
 108     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 109 };
 110
 111 struct cginfo_mb_t
 112 {
 113     int  cg_start;
 114     int  cg_end;
 115     int  cg_mod;
 116     int *cginfo;
 117 };
 118
 119
 120 /* Forward declaration of type for managing Ewald tables */
 121 struct gmx_ewald_tab_t;
 122
 123 struct ewald_corr_thread_t;
 124
 125 struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
 126     struct interaction_const_t *ic = nullptr;
 127
 128     /* PBC stuff */
 129     int                         ePBC = 0;
 130     //! Tells whether atoms inside a molecule can be in different periodic images,
 131     //  i.e. whether we need to take into account PBC when computing distances inside molecules.
 132     //  This determines whether PBC must be considered for e.g. bonded interactions.
 133     gmx_bool                    bMolPBC     = FALSE;
 134     int                         rc_scaling  = 0;
 135     rvec                        posres_com  = { 0 };
 136     rvec                        posres_comB = { 0 };
 137
 138     gmx_bool                    use_simd_kernels = FALSE;
 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 = 0;
 150     int nbkernel_vdw_interaction  = 0;
 151     int nbkernel_elec_modifier    = 0;
 152     int nbkernel_vdw_modifier     = 0;
 153
 154     /* Cut-Off stuff.
 155      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 156      */
 157     real rlist = 0;
 158
 159     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 160     double qsum[2]   = { 0 };
 161     double q2sum[2]  = { 0 };
 162     double c6sum[2]  = { 0 };
 163     rvec   mu_tot[2] = { { 0 } };
 164
 165     /* Dispersion correction stuff */
 166     std::unique_ptr<DispersionCorrection> dispersionCorrection;
 167
 168     /* Fudge factors */
 169     real fudgeQQ = 0;
 170
 171     /* Table stuff */
 172     gmx_bool             bcoultab = FALSE;
 173     gmx_bool             bvdwtab  = FALSE;
 174
 175     t_forcetable        *pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 176
 177     /* Free energy */
 178     int      efep          = 0;
 179     real     sc_alphavdw   = 0;
 180     real     sc_alphacoul  = 0;
 181     int      sc_power      = 0;
 182     real     sc_r_power    = 0;
 183     real     sc_sigma6_def = 0;
 184     real     sc_sigma6_min = 0;
 185
 186     /* NS Stuff */
 187     int  cg0 = 0;
 188     int  hcg = 0;
 189     /* solvent_opt contains the enum for the most common solvent
 190      * in the system, which will be optimized.
 191      * It can be set to esolNO to disable all water optimization */
 192     int                 solvent_opt                  = 0;
 193     int                 nWatMol                      = 0;
 194     gmx_bool            bExcl_IntraCGAll_InterCGNone = FALSE;
 195     struct cginfo_mb_t *cginfo_mb                    = nullptr;
 196     std::vector<int>    cginfo;
 197     rvec               *shift_vec                    = nullptr;
 198
 199     int                 cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
 200     gmx_bool            bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
 201
 202     /* The Nbnxm Verlet non-bonded machinery */
 203     std::unique_ptr<nonbonded_verlet_t> nbv;
 204
 205     /* The wall tables (if used) */
 206     int                    nwall    = 0;
 207     t_forcetable        ***wall_tab = nullptr;
 208
 209     /* The number of charge groups participating in do_force_lowlevel */
 210     int ncg_force = 0;
 211     /* The number of atoms participating in do_force_lowlevel */
 212     int natoms_force = 0;
 213     /* The number of atoms participating in force and constraints */
 214     int natoms_force_constr = 0;
 215     /* The allocation size of vectors of size natoms_force */
 216     int nalloc_force = 0;
 217
 218     /* Forces that should not enter into the coord x force virial summation:
 219      * PPPM/PME/Ewald/posres/ForceProviders
 220      */
 221     /* True when we have contributions that are directly added to the virial */
 222     bool                   haveDirectVirialContributions = false;
 223     /* Force buffer for force computation with direct virial contributions */
 224     std::vector<gmx::RVec> forceBufferForDirectVirialContributions;
 225
 226     /* Data for PPPM/PME/Ewald */
 227     struct gmx_pme_t *pmedata                = nullptr;
 228     int               ljpme_combination_rule = 0;
 229
 230     /* PME/Ewald stuff */
 231     struct gmx_ewald_tab_t *ewald_table = nullptr;
 232
 233     /* Shift force array for computing the virial, size SHIFTS */
 234     std::vector<gmx::RVec> shiftForces;
 235
 236     /* Non bonded Parameter lists */
 237     int      ntype        = 0; /* Number of atom types */
 238     gmx_bool bBHAM        = FALSE;
 239     real    *nbfp         = nullptr;
 240     real    *ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
 241
 242     /* Energy group pair flags */
 243     int *egp_flags = nullptr;
 244
 245     /* Shell molecular dynamics flexible constraints */
 246     real fc_stepsize = 0;
 247
 248     /* If > 0 signals Test Particle Insertion,
 249      * the value is the number of atoms of the molecule to insert
 250      * Only the energy difference due to the addition of the last molecule
 251      * should be calculated.
 252      */
 253     int n_tpi = 0;
 254
 255     /* QMMM stuff */
 256     gmx_bool          bQMMM = FALSE;
 257     struct t_QMMMrec *qr    = nullptr;
 258
 259     /* QM-MM neighborlists */
 260     struct t_nblist        *QMMMlist = nullptr;
 261
 262     /* Limit for printing large forces, negative is don't print */
 263     real print_force = 0;
 264
 265     /* User determined parameters, copied from the inputrec */
 266     int  userint1  = 0;
 267     int  userint2  = 0;
 268     int  userint3  = 0;
 269     int  userint4  = 0;
 270     real userreal1 = 0;
 271     real userreal2 = 0;
 272     real userreal3 = 0;
 273     real userreal4 = 0;
 274
 275     /* Pointer to struct for managing threading of bonded force calculation */
 276     struct bonded_threading_t *bondedThreading = nullptr;
 277
 278     /* TODO: Replace the pointer by an object once we got rid of C */
 279     gmx::GpuBonded *gpuBonded = nullptr;
 280
 281     /* Ewald correction thread local virial and energy data */
 282     int                         nthread_ewc = 0;
 283     struct ewald_corr_thread_t *ewc_t       = nullptr;
 284
 285     struct ForceProviders      *forceProviders = nullptr;
 286 };
 287
 288 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 289  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 290  * in the code, but beware if you are using these macros externally.
 291  */
 292 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 293 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 294 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 295 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 296 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 297
 298 #endif