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 "gromacs/math/vectypes.h"
  41 #ifdef __cplusplus
  42 #include "gromacs/math/paddedvector.h"
  43 #endif
  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 #ifdef __cplusplus
  62 extern "C" {
  63 #endif
  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  * But there is a smaller limit due to the t_excl data structure
  74  * which is defined in nblist.h.
  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_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  81 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  82 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  83 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  84 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  85 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  86 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  87 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  88 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  89 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  90 /* This bit is only used with bBondComm in the domain decomposition */
  91 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  92 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  93 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  94 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  95 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  96 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  97 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
  98 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
  99
 100
 101 /* Value to be used in mdrun for an infinite cut-off.
 102  * Since we need to compare with the cut-off squared,
 103  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 104  */
 105 #define GMX_CUTOFF_INF 1E+18
 106
 107 /* enums for the neighborlist type */
 108 enum {
 109     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 110 };
 111
 112 struct cginfo_mb_t
 113 {
 114     int  cg_start;
 115     int  cg_end;
 116     int  cg_mod;
 117     int *cginfo;
 118 };
 119
 120
 121 /* Forward declaration of type for managing Ewald tables */
 122 struct gmx_ewald_tab_t;
 123
 124 struct ewald_corr_thread_t;
 125
 126 struct t_forcerec {
 127     struct interaction_const_t *ic;
 128
 129     /* PBC stuff */
 130     int                         ePBC;
 131     //! Whether PBC must be considered for bonded interactions.
 132     gmx_bool                    bMolPBC;
 133     int                         rc_scaling;
 134     rvec                        posres_com;
 135     rvec                        posres_comB;
 136
 137     gmx_bool                    use_simd_kernels;
 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;
 149     int nbkernel_vdw_interaction;
 150     int nbkernel_elec_modifier;
 151     int nbkernel_vdw_modifier;
 152
 153     /* Use special N*N kernels? */
 154     gmx_bool bAllvsAll;
 155     /* Private work data */
 156     void    *AllvsAll_work;
 157
 158     /* Cut-Off stuff.
 159      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 160      */
 161     real rlist;
 162
 163     /* Parameters for generalized reaction field */
 164     real zsquare, temp;
 165
 166     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 167     double qsum[2];
 168     double q2sum[2];
 169     double c6sum[2];
 170     rvec   mu_tot[2];
 171
 172     /* Dispersion correction stuff */
 173     int                  eDispCorr;
 174     int                  numAtomsForDispersionCorrection;
 175     struct t_forcetable *dispersionCorrectionTable;
 176
 177     /* The shift of the shift or user potentials */
 178     real enershiftsix;
 179     real enershifttwelve;
 180     /* Integrated differces for energy and virial with cut-off functions */
 181     real enerdiffsix;
 182     real enerdifftwelve;
 183     real virdiffsix;
 184     real virdifftwelve;
 185     /* Constant for long range dispersion correction (average dispersion)
 186      * for topology A/B ([0]/[1]) */
 187     real avcsix[2];
 188     /* Constant for long range repulsion term. Relative difference of about
 189      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 190      */
 191     real avctwelve[2];
 192
 193     /* Fudge factors */
 194     real fudgeQQ;
 195
 196     /* Table stuff */
 197     gmx_bool             bcoultab;
 198     gmx_bool             bvdwtab;
 199     /* The normal tables are in the nblists struct(s) below */
 200
 201     struct t_forcetable *pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 202
 203     /* Free energy */
 204     int      efep;
 205     real     sc_alphavdw;
 206     real     sc_alphacoul;
 207     int      sc_power;
 208     real     sc_r_power;
 209     real     sc_sigma6_def;
 210     real     sc_sigma6_min;
 211
 212     /* NS Stuff */
 213     int  cg0, hcg;
 214     /* solvent_opt contains the enum for the most common solvent
 215      * in the system, which will be optimized.
 216      * It can be set to esolNO to disable all water optimization */
 217     int                 solvent_opt;
 218     int                 nWatMol;
 219     gmx_bool            bGrid;
 220     gmx_bool            bExcl_IntraCGAll_InterCGNone;
 221     struct cginfo_mb_t *cginfo_mb;
 222     int                *cginfo;
 223     rvec               *cg_cm;
 224     int                 cg_nalloc;
 225     rvec               *shift_vec;
 226
 227     /* The neighborlists including tables */
 228     int                        nnblists;
 229     int                       *gid2nblists;
 230     struct t_nblists          *nblists;
 231
 232     int                        cutoff_scheme; /* group- or Verlet-style cutoff */
 233     gmx_bool                   bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 234     struct nonbonded_verlet_t *nbv;
 235
 236     /* The wall tables (if used) */
 237     int                    nwall;
 238     struct t_forcetable ***wall_tab;
 239
 240     /* The number of charge groups participating in do_force_lowlevel */
 241     int ncg_force;
 242     /* The number of atoms participating in do_force_lowlevel */
 243     int natoms_force;
 244     /* The number of atoms participating in force and constraints */
 245     int natoms_force_constr;
 246     /* The allocation size of vectors of size natoms_force */
 247     int nalloc_force;
 248
 249     /* Forces that should not enter into the coord x force virial summation:
 250      * PPPM/PME/Ewald/posres/ForceProviders
 251      */
 252     /* True when we have contributions that are directly added to the virial */
 253     gmx_bool          haveDirectVirialContributions;
 254 #ifdef __cplusplus
 255     /* TODO: Replace the pointer by an object once we got rid of C */
 256     std::vector<gmx::RVec>  *forceBufferForDirectVirialContributions;
 257 #else
 258     void                    *forceBufferForDirectVirialContributions_dummy;
 259 #endif
 260
 261     /* Data for PPPM/PME/Ewald */
 262     struct gmx_pme_t *pmedata;
 263     int               ljpme_combination_rule;
 264
 265     /* PME/Ewald stuff */
 266     struct gmx_ewald_tab_t *ewald_table;
 267
 268     /* Virial Stuff */
 269     rvec *fshift;
 270     dvec  vir_wall_z;
 271
 272     /* Non bonded Parameter lists */
 273     int      ntype; /* Number of atom types */
 274     gmx_bool bBHAM;
 275     real    *nbfp;
 276     real    *ljpme_c6grid; /* C6-values used on grid in LJPME */
 277
 278     /* Energy group pair flags */
 279     int *egp_flags;
 280
 281     /* Shell molecular dynamics flexible constraints */
 282     real fc_stepsize;
 283
 284     /* If > 0 signals Test Particle Insertion,
 285      * the value is the number of atoms of the molecule to insert
 286      * Only the energy difference due to the addition of the last molecule
 287      * should be calculated.
 288      */
 289     int n_tpi;
 290
 291     /* Neighbor searching stuff */
 292     struct gmx_ns_t *ns;
 293
 294     /* QMMM stuff */
 295     gmx_bool          bQMMM;
 296     struct t_QMMMrec *qr;
 297
 298     /* QM-MM neighborlists */
 299     struct t_nblist        *QMMMlist;
 300
 301     /* Limit for printing large forces, negative is don't print */
 302     real print_force;
 303
 304     /* coarse load balancing time measurement */
 305     double t_fnbf;
 306     double t_wait;
 307     int    timesteps;
 308
 309     /* User determined parameters, copied from the inputrec */
 310     int  userint1;
 311     int  userint2;
 312     int  userint3;
 313     int  userint4;
 314     real userreal1;
 315     real userreal2;
 316     real userreal3;
 317     real userreal4;
 318
 319     /* Pointer to struct for managing threading of bonded force calculation */
 320     struct bonded_threading_t *bondedThreading;
 321
 322     /* Ewald correction thread local virial and energy data */
 323     int                         nthread_ewc;
 324     struct ewald_corr_thread_t *ewc_t;
 325
 326     struct ForceProviders      *forceProviders;
 327 };
 328
 329 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 330  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 331  * in the code, but beware if you are using these macros externally.
 332  */
 333 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 334 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 335 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 336 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 337 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 338
 339 #ifdef __cplusplus
 340 }
 341 #endif
 342
 343 #endif