include/types/forcerec.h

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  38
  39 #include "ns.h"
  40 #include "genborn.h"
  41 #include "qmmmrec.h"
  42 #include "idef.h"
  43 #include "nb_verlet.h"
  44 #include "interaction_const.h"
  45 #include "hw_info.h"
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50 #if 0
  51 } /* fixes auto-indentation problems */
  52 #endif
  53
  54 /* Abstract type for PME that is defined only in the routine that use them. */
  55 typedef struct gmx_pme *gmx_pme_t;
  56
  57
  58
  59 /* Structure describing the data in a single table */
  60 typedef struct
  61 {
  62     enum gmx_table_interaction  interaction; /* Types of interactions stored in this table */
  63     enum gmx_table_format       format;      /* Interpolation type and data format */
  64
  65     real                        r;           /* range of the table */
  66     int                         n;           /* n+1 is the number of table points */
  67     real                        scale;       /* distance (nm) between two table points */
  68     real                        scale_exp;   /* distance for exponential part of VdW table, not always used */
  69     real *                      data;        /* the actual table data */
  70
  71     /* Some information about the table layout. This can also be derived from the interpolation
  72      * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
  73      * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
  74      * It is always true that stride = formatsize*ninteractions
  75      */
  76     int                         formatsize;    /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
  77     int                         ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
  78     int                         stride;        /* Distance to next table point (number of fp variables per table point in total) */
  79 } t_forcetable;
  80
  81 typedef struct
  82 {
  83     t_forcetable   table_elec;
  84     t_forcetable   table_vdw;
  85     t_forcetable   table_elec_vdw;
  86
  87     /* The actual neighbor lists, short and long range, see enum above
  88      * for definition of neighborlist indices.
  89      */
  90     t_nblist nlist_sr[eNL_NR];
  91     t_nblist nlist_lr[eNL_NR];
  92 } t_nblists;
  93
  94 /* macros for the cginfo data in forcerec */
  95 /* The maximum cg size in cginfo is 63
  96  * because we only have space for 6 bits in cginfo,
  97  * this cg size entry is actually only read with domain decomposition.
  98  * But there is a smaller limit due to the t_excl data structure
  99  * which is defined in nblist.h.
 100  */
 101 #define SET_CGINFO_GID(cgi, gid)      (cgi) = (((cgi)  &  ~65535)  |  (gid)   )
 102 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   65535)
 103 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
 104 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
 105 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
 106 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
 107 #define SET_CGINFO_SOLOPT(cgi, opt)   (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
 108 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
 109 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
 110 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
 111 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
 112 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
 113 /* This bit is only used with bBondComm in the domain decomposition */
 114 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
 115 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
 116 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
 117 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
 118 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
 119 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
 120 #define SET_CGINFO_NATOMS(cgi, opt)   (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
 121 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
 122
 123
 124 /* Value to be used in mdrun for an infinite cut-off.
 125  * Since we need to compare with the cut-off squared,
 126  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 127  */
 128 #define GMX_CUTOFF_INF 1E+18
 129
 130 /* enums for the neighborlist type */
 131 enum {
 132     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 133 };
 134 /* OOR is "one over r" -- standard coul */
 135 enum {
 136     enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
 137 };
 138
 139 enum {
 140     egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
 141     egCOUL14, egLJ14, egGB, egNR
 142 };
 143
 144 typedef struct {
 145     int   nener;      /* The number of energy group pairs     */
 146     real *ener[egNR]; /* Energy terms for each pair of groups */
 147 } gmx_grppairener_t;
 148
 149 typedef struct {
 150     real              term[F_NRE];         /* The energies for all different interaction types */
 151     gmx_grppairener_t grpp;
 152     double            dvdl_lin[efptNR];    /* Contributions to dvdl with linear lam-dependence */
 153     double            dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence                  */
 154     int               n_lambda;
 155     int               fep_state;           /*current fep state -- just for printing */
 156     double           *enerpart_lambda;     /* Partial energy for lambda and flambda[] */
 157     real              foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
 158     gmx_grppairener_t foreign_grpp;        /* alternate array for storing foreign lambda energies */
 159 } gmx_enerdata_t;
 160 /* The idea is that dvdl terms with linear lambda dependence will be added
 161  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 162  * should explicitly determine the energies at foreign lambda points
 163  * when n_lambda > 0.
 164  */
 165
 166 typedef struct {
 167     int  cg_start;
 168     int  cg_end;
 169     int  cg_mod;
 170     int *cginfo;
 171 } cginfo_mb_t;
 172
 173
 174 /* ewald table type */
 175 typedef struct ewald_tab *ewald_tab_t;
 176
 177 typedef struct {
 178     rvec             *f;
 179     int               f_nalloc;
 180     unsigned          red_mask; /* Mask for marking which parts of f are filled */
 181     rvec             *fshift;
 182     real              ener[F_NRE];
 183     gmx_grppairener_t grpp;
 184     real              Vcorr;
 185     real              dvdl[efptNR];
 186     tensor            vir;
 187 } f_thread_t;
 188
 189 typedef struct {
 190     interaction_const_t *ic;
 191
 192     /* Domain Decomposition */
 193     gmx_bool bDomDec;
 194
 195     /* PBC stuff */
 196     int                  ePBC;
 197     gmx_bool             bMolPBC;
 198     int                  rc_scaling;
 199     rvec                 posres_com;
 200     rvec                 posres_comB;
 201
 202     const gmx_hw_info_t *hwinfo;
 203     gmx_bool             use_cpu_acceleration;
 204
 205     /* Interaction for calculated in kernels. In many cases this is similar to
 206      * the electrostatics settings in the inputrecord, but the difference is that
 207      * these variables always specify the actual interaction in the kernel - if
 208      * we are tabulating reaction-field the inputrec will say reaction-field, but
 209      * the kernel interaction will say cubic-spline-table. To be safe we also
 210      * have a kernel-specific setting for the modifiers - if the interaction is
 211      * tabulated we already included the inputrec modification there, so the kernel
 212      * modification setting will say 'none' in that case.
 213      */
 214     int nbkernel_elec_interaction;
 215     int nbkernel_vdw_interaction;
 216     int nbkernel_elec_modifier;
 217     int nbkernel_vdw_modifier;
 218
 219     /* Use special N*N kernels? */
 220     gmx_bool bAllvsAll;
 221     /* Private work data */
 222     void    *AllvsAll_work;
 223     void    *AllvsAll_workgb;
 224
 225     /* Cut-Off stuff.
 226      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 227      */
 228     real rlist, rlistlong;
 229
 230     /* Dielectric constant resp. multiplication factor for charges */
 231     real zsquare, temp;
 232     real epsilon_r, epsilon_rf, epsfac;
 233
 234     /* Constants for reaction fields */
 235     real kappa, k_rf, c_rf;
 236
 237     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 238     double qsum[2];
 239     double q2sum[2];
 240     rvec   mu_tot[2];
 241
 242     /* Dispersion correction stuff */
 243     int  eDispCorr;
 244
 245     /* The shift of the shift or user potentials */
 246     real enershiftsix;
 247     real enershifttwelve;
 248     /* Integrated differces for energy and virial with cut-off functions */
 249     real enerdiffsix;
 250     real enerdifftwelve;
 251     real virdiffsix;
 252     real virdifftwelve;
 253     /* Constant for long range dispersion correction (average dispersion)
 254      * for topology A/B ([0]/[1]) */
 255     real avcsix[2];
 256     /* Constant for long range repulsion term. Relative difference of about
 257      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 258      */
 259     real avctwelve[2];
 260
 261     /* Fudge factors */
 262     real fudgeQQ;
 263
 264     /* Table stuff */
 265     gmx_bool     bcoultab;
 266     gmx_bool     bvdwtab;
 267     /* The normal tables are in the nblists struct(s) below */
 268     t_forcetable tab14; /* for 1-4 interactions only */
 269
 270     /* PPPM & Shifting stuff */
 271     int   coulomb_modifier;
 272     real  rcoulomb_switch, rcoulomb;
 273     real *phi;
 274
 275     /* VdW stuff */
 276     int    vdw_modifier;
 277     double reppow;
 278     real   rvdw_switch, rvdw;
 279     real   bham_b_max;
 280
 281     /* Free energy */
 282     int      efep;
 283     real     sc_alphavdw;
 284     real     sc_alphacoul;
 285     int      sc_power;
 286     real     sc_r_power;
 287     real     sc_sigma6_def;
 288     real     sc_sigma6_min;
 289     gmx_bool bSepDVDL;
 290
 291     /* NS Stuff */
 292     int  eeltype;
 293     int  vdwtype;
 294     int  cg0, hcg;
 295     /* solvent_opt contains the enum for the most common solvent
 296      * in the system, which will be optimized.
 297      * It can be set to esolNO to disable all water optimization */
 298     int          solvent_opt;
 299     int          nWatMol;
 300     gmx_bool     bGrid;
 301     gmx_bool     bExcl_IntraCGAll_InterCGNone;
 302     cginfo_mb_t *cginfo_mb;
 303     int         *cginfo;
 304     rvec        *cg_cm;
 305     int          cg_nalloc;
 306     rvec        *shift_vec;
 307
 308     /* The neighborlists including tables */
 309     int                 nnblists;
 310     int                *gid2nblists;
 311     t_nblists          *nblists;
 312
 313     int                 cutoff_scheme; /* group- or Verlet-style cutoff */
 314     gmx_bool            bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 315     nonbonded_verlet_t *nbv;
 316
 317     /* The wall tables (if used) */
 318     int            nwall;
 319     t_forcetable **wall_tab;
 320
 321     /* The number of charge groups participating in do_force_lowlevel */
 322     int ncg_force;
 323     /* The number of atoms participating in do_force_lowlevel */
 324     int natoms_force;
 325     /* The number of atoms participating in force and constraints */
 326     int natoms_force_constr;
 327     /* The allocation size of vectors of size natoms_force */
 328     int nalloc_force;
 329
 330     /* Twin Range stuff, f_twin has size natoms_force */
 331     gmx_bool bTwinRange;
 332     int      nlr;
 333     rvec    *f_twin;
 334
 335     /* Forces that should not enter into the virial summation:
 336      * PPPM/PME/Ewald/posres
 337      */
 338     gmx_bool bF_NoVirSum;
 339     int      f_novirsum_n;
 340     int      f_novirsum_nalloc;
 341     rvec    *f_novirsum_alloc;
 342     /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
 343      * points to the normal force vectors wen pressure is not requested.
 344      */
 345     rvec *f_novirsum;
 346
 347     /* Long-range forces and virial for PPPM/PME/Ewald */
 348     gmx_pme_t pmedata;
 349     tensor    vir_el_recip;
 350
 351     /* PME/Ewald stuff */
 352     gmx_bool    bEwald;
 353     real        ewaldcoeff;
 354     ewald_tab_t ewald_table;
 355
 356     /* Virial Stuff */
 357     rvec *fshift;
 358     rvec  vir_diag_posres;
 359     dvec  vir_wall_z;
 360
 361     /* Non bonded Parameter lists */
 362     int      ntype; /* Number of atom types */
 363     gmx_bool bBHAM;
 364     real    *nbfp;
 365
 366     /* Energy group pair flags */
 367     int *egp_flags;
 368
 369     /* xmdrun flexible constraints */
 370     real fc_stepsize;
 371
 372     /* Generalized born implicit solvent */
 373     gmx_bool       bGB;
 374     /* Generalized born stuff */
 375     real           gb_epsilon_solvent;
 376     /* Table data for GB */
 377     t_forcetable   gbtab;
 378     /* VdW radius for each atomtype (dim is thus ntype) */
 379     real          *atype_radius;
 380     /* Effective radius (derived from effective volume) for each type */
 381     real          *atype_vol;
 382     /* Implicit solvent - surface tension for each atomtype */
 383     real          *atype_surftens;
 384     /* Implicit solvent - radius for GB calculation */
 385     real          *atype_gb_radius;
 386     /* Implicit solvent - overlap for HCT model */
 387     real          *atype_S_hct;
 388     /* Generalized born interaction data */
 389     gmx_genborn_t *born;
 390
 391     /* Table scale for GB */
 392     real gbtabscale;
 393     /* Table range for GB */
 394     real gbtabr;
 395     /* GB neighborlists (the sr list will contain for each atom all other atoms
 396      * (for use in the SA calculation) and the lr list will contain
 397      * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 398      */
 399     t_nblist gblist_sr;
 400     t_nblist gblist_lr;
 401     t_nblist gblist;
 402
 403     /* Inverse square root of the Born radii for implicit solvent */
 404     real *invsqrta;
 405     /* Derivatives of the potential with respect to the Born radii */
 406     real *dvda;
 407     /* Derivatives of the Born radii with respect to coordinates */
 408     real *dadx;
 409     real *dadx_rawptr;
 410     int   nalloc_dadx; /* Allocated size of dadx */
 411
 412     /* If > 0 signals Test Particle Insertion,
 413      * the value is the number of atoms of the molecule to insert
 414      * Only the energy difference due to the addition of the last molecule
 415      * should be calculated.
 416      */
 417     gmx_bool n_tpi;
 418
 419     /* Neighbor searching stuff */
 420     gmx_ns_t ns;
 421
 422     /* QMMM stuff */
 423     gmx_bool         bQMMM;
 424     t_QMMMrec       *qr;
 425
 426     /* QM-MM neighborlists */
 427     t_nblist QMMMlist;
 428
 429     /* Limit for printing large forces, negative is don't print */
 430     real print_force;
 431
 432     /* coarse load balancing time measurement */
 433     double t_fnbf;
 434     double t_wait;
 435     int    timesteps;
 436
 437     /* parameter needed for AdResS simulation */
 438     int             adress_type;
 439     gmx_bool        badress_tf_full_box;
 440     real            adress_const_wf;
 441     real            adress_ex_width;
 442     real            adress_hy_width;
 443     int             adress_icor;
 444     int             adress_site;
 445     rvec            adress_refs;
 446     int             n_adress_tf_grps;
 447     int           * adress_tf_table_index;
 448     int            *adress_group_explicit;
 449     t_forcetable *  atf_tabs;
 450     real            adress_ex_forcecap;
 451     gmx_bool        adress_do_hybridpairs;
 452
 453     /* User determined parameters, copied from the inputrec */
 454     int  userint1;
 455     int  userint2;
 456     int  userint3;
 457     int  userint4;
 458     real userreal1;
 459     real userreal2;
 460     real userreal3;
 461     real userreal4;
 462
 463     /* Thread local force and energy data */
 464     /* FIXME move to bonded_thread_data_t */
 465     int         nthreads;
 466     int         red_ashift;
 467     int         red_nblock;
 468     f_thread_t *f_t;
 469
 470     /* Exclusion load distribution over the threads */
 471     int  *excl_load;
 472 } t_forcerec;
 473
 474 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 475  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 476  * in the code, but beware if you are using these macros externally.
 477  */
 478 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 479 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 480 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 481 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 482 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 483
 484 #ifdef __cplusplus
 485 }
 486 #endif