src/gromacs/mdtypes/forcerec.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_MDTYPES_TYPES_FORCEREC_H
  38 #define GMX_MDTYPES_TYPES_FORCEREC_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/mdtypes/interaction_const.h"
  42 #include "gromacs/mdtypes/md_enums.h"
  43 #include "gromacs/topology/idef.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/real.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 struct gmx_genborn_t;
  56 struct gmx_ns_t;
  57 struct gmx_pme_t;
  58 struct nonbonded_verlet_t;
  59 struct bonded_threading_t;
  60 struct t_forcetable;
  61 struct t_nblist;
  62 struct t_nblists;
  63 struct t_QMMMrec;
  64 struct gmx_hw_info_t;
  65 struct gmx_gpu_opt_t;
  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  * But there is a smaller limit due to the t_excl data structure
  76  * which is defined in nblist.h.
  77  */
  78 #define SET_CGINFO_GID(cgi, gid)     (cgi) = (((cgi)  &  ~255) | (gid))
  79 #define GET_CGINFO_GID(cgi)        ( (cgi)            &   255)
  80 #define SET_CGINFO_FEP(cgi)          (cgi) =  ((cgi)  |  (1<<15))
  81 #define GET_CGINFO_FEP(cgi)        ( (cgi)            &  (1<<15))
  82 #define SET_CGINFO_EXCL_INTRA(cgi)   (cgi) =  ((cgi)  |  (1<<16))
  83 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi)            &  (1<<16))
  84 #define SET_CGINFO_EXCL_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<17))
  85 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi)            &  (1<<17))
  86 #define SET_CGINFO_SOLOPT(cgi, opt)  (cgi) = (((cgi)  & ~(3<<18)) | ((opt)<<18))
  87 #define GET_CGINFO_SOLOPT(cgi)     (((cgi)>>18)       &   3)
  88 #define SET_CGINFO_CONSTR(cgi)       (cgi) =  ((cgi)  |  (1<<20))
  89 #define GET_CGINFO_CONSTR(cgi)     ( (cgi)            &  (1<<20))
  90 #define SET_CGINFO_SETTLE(cgi)       (cgi) =  ((cgi)  |  (1<<21))
  91 #define GET_CGINFO_SETTLE(cgi)     ( (cgi)            &  (1<<21))
  92 /* This bit is only used with bBondComm in the domain decomposition */
  93 #define SET_CGINFO_BOND_INTER(cgi)   (cgi) =  ((cgi)  |  (1<<22))
  94 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi)            &  (1<<22))
  95 #define SET_CGINFO_HAS_VDW(cgi)      (cgi) =  ((cgi)  |  (1<<23))
  96 #define GET_CGINFO_HAS_VDW(cgi)    ( (cgi)            &  (1<<23))
  97 #define SET_CGINFO_HAS_Q(cgi)        (cgi) =  ((cgi)  |  (1<<24))
  98 #define GET_CGINFO_HAS_Q(cgi)      ( (cgi)            &  (1<<24))
  99 #define SET_CGINFO_NATOMS(cgi, opt)  (cgi) = (((cgi)  & ~(63<<25)) | ((opt)<<25))
 100 #define GET_CGINFO_NATOMS(cgi)     (((cgi)>>25)       &   63)
 101
 102
 103 /* Value to be used in mdrun for an infinite cut-off.
 104  * Since we need to compare with the cut-off squared,
 105  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
 106  */
 107 #define GMX_CUTOFF_INF 1E+18
 108
 109 /* enums for the neighborlist type */
 110 enum {
 111     enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
 112 };
 113 /* OOR is "one over r" -- standard coul */
 114 enum {
 115     enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
 116 };
 117
 118 enum {
 119     egCOULSR, egLJSR, egBHAMSR,
 120     egCOUL14, egLJ14, egGB, egNR
 121 };
 122 extern const char *egrp_nm[egNR+1];
 123
 124 typedef struct gmx_grppairener_t {
 125     int   nener;      /* The number of energy group pairs     */
 126     real *ener[egNR]; /* Energy terms for each pair of groups */
 127 } gmx_grppairener_t;
 128
 129 typedef struct gmx_enerdata_t {
 130     real              term[F_NRE];         /* The energies for all different interaction types */
 131     gmx_grppairener_t grpp;
 132     double            dvdl_lin[efptNR];    /* Contributions to dvdl with linear lam-dependence */
 133     double            dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence                  */
 134     int               n_lambda;
 135     int               fep_state;           /*current fep state -- just for printing */
 136     double           *enerpart_lambda;     /* Partial energy for lambda and flambda[] */
 137     real              foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
 138     gmx_grppairener_t foreign_grpp;        /* alternate array for storing foreign lambda energies */
 139 } gmx_enerdata_t;
 140 /* The idea is that dvdl terms with linear lambda dependence will be added
 141  * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 142  * should explicitly determine the energies at foreign lambda points
 143  * when n_lambda > 0.
 144  */
 145
 146 typedef struct {
 147     int  cg_start;
 148     int  cg_end;
 149     int  cg_mod;
 150     int *cginfo;
 151 } cginfo_mb_t;
 152
 153
 154 /* Forward declaration of type for managing Ewald tables */
 155 struct gmx_ewald_tab_t;
 156
 157 typedef struct ewald_corr_thread_t ewald_corr_thread_t;
 158
 159 typedef struct t_forcerec {
 160     interaction_const_t *ic;
 161
 162     /* Domain Decomposition */
 163     gmx_bool bDomDec;
 164
 165     /* PBC stuff */
 166     int                         ePBC;
 167     gmx_bool                    bMolPBC;
 168     int                         rc_scaling;
 169     rvec                        posres_com;
 170     rvec                        posres_comB;
 171
 172     const struct gmx_hw_info_t *hwinfo;
 173     const struct gmx_gpu_opt_t *gpu_opt;
 174     gmx_bool                    use_simd_kernels;
 175
 176     /* Interaction for calculated in kernels. In many cases this is similar to
 177      * the electrostatics settings in the inputrecord, but the difference is that
 178      * these variables always specify the actual interaction in the kernel - if
 179      * we are tabulating reaction-field the inputrec will say reaction-field, but
 180      * the kernel interaction will say cubic-spline-table. To be safe we also
 181      * have a kernel-specific setting for the modifiers - if the interaction is
 182      * tabulated we already included the inputrec modification there, so the kernel
 183      * modification setting will say 'none' in that case.
 184      */
 185     int nbkernel_elec_interaction;
 186     int nbkernel_vdw_interaction;
 187     int nbkernel_elec_modifier;
 188     int nbkernel_vdw_modifier;
 189
 190     /* Use special N*N kernels? */
 191     gmx_bool bAllvsAll;
 192     /* Private work data */
 193     void    *AllvsAll_work;
 194     void    *AllvsAll_workgb;
 195
 196     /* Cut-Off stuff.
 197      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 198      */
 199     real rlist;
 200
 201     /* Dielectric constant resp. multiplication factor for charges */
 202     real zsquare, temp;
 203     real epsilon_r, epsilon_rf, epsfac;
 204
 205     /* Constants for reaction fields */
 206     real kappa, k_rf, c_rf;
 207
 208     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 209     double qsum[2];
 210     double q2sum[2];
 211     double c6sum[2];
 212     rvec   mu_tot[2];
 213
 214     /* Dispersion correction stuff */
 215     int  eDispCorr;
 216     int  numAtomsForDispersionCorrection;
 217     /* The shift of the shift or user potentials */
 218     real enershiftsix;
 219     real enershifttwelve;
 220     /* Integrated differces for energy and virial with cut-off functions */
 221     real enerdiffsix;
 222     real enerdifftwelve;
 223     real virdiffsix;
 224     real virdifftwelve;
 225     /* Constant for long range dispersion correction (average dispersion)
 226      * for topology A/B ([0]/[1]) */
 227     real avcsix[2];
 228     /* Constant for long range repulsion term. Relative difference of about
 229      * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
 230      */
 231     real avctwelve[2];
 232
 233     /* Fudge factors */
 234     real fudgeQQ;
 235
 236     /* Table stuff */
 237     gmx_bool             bcoultab;
 238     gmx_bool             bvdwtab;
 239     /* The normal tables are in the nblists struct(s) below */
 240     struct t_forcetable *tab14; /* for 1-4 interactions only */
 241
 242     /* PPPM & Shifting stuff */
 243     int   coulomb_modifier;
 244     real  rcoulomb_switch, rcoulomb;
 245     real *phi;
 246
 247     /* VdW stuff */
 248     int    vdw_modifier;
 249     double reppow;
 250     real   rvdw_switch, rvdw;
 251     real   bham_b_max;
 252
 253     /* Free energy */
 254     int      efep;
 255     real     sc_alphavdw;
 256     real     sc_alphacoul;
 257     int      sc_power;
 258     real     sc_r_power;
 259     real     sc_sigma6_def;
 260     real     sc_sigma6_min;
 261
 262     /* NS Stuff */
 263     int  eeltype;
 264     int  vdwtype;
 265     int  cg0, hcg;
 266     /* solvent_opt contains the enum for the most common solvent
 267      * in the system, which will be optimized.
 268      * It can be set to esolNO to disable all water optimization */
 269     int          solvent_opt;
 270     int          nWatMol;
 271     gmx_bool     bGrid;
 272     gmx_bool     bExcl_IntraCGAll_InterCGNone;
 273     cginfo_mb_t *cginfo_mb;
 274     int         *cginfo;
 275     rvec        *cg_cm;
 276     int          cg_nalloc;
 277     rvec        *shift_vec;
 278
 279     /* The neighborlists including tables */
 280     int                               nnblists;
 281     int                              *gid2nblists;
 282     struct t_nblists                 *nblists;
 283
 284     int                               cutoff_scheme; /* group- or Verlet-style cutoff */
 285     gmx_bool                          bNonbonded;    /* true if nonbonded calculations are *not* turned off */
 286     struct nonbonded_verlet_t        *nbv;
 287
 288     /* The wall tables (if used). A 2D array of pointers to tables. */
 289     int                    nwall;
 290     struct t_forcetable ***wall_tab;
 291
 292     /* The number of charge groups participating in do_force_lowlevel */
 293     int ncg_force;
 294     /* The number of atoms participating in do_force_lowlevel */
 295     int natoms_force;
 296     /* The number of atoms participating in force and constraints */
 297     int natoms_force_constr;
 298     /* The allocation size of vectors of size natoms_force */
 299     int nalloc_force;
 300
 301     /* Forces that should not enter into the virial summation:
 302      * PPPM/PME/Ewald/posres
 303      */
 304     gmx_bool bF_NoVirSum;
 305     int      f_novirsum_n;
 306     int      f_novirsum_nalloc;
 307     rvec    *f_novirsum_alloc;
 308     /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
 309      * points to the normal force vectors wen pressure is not requested.
 310      */
 311     rvec *f_novirsum;
 312
 313     /* Long-range forces and virial for PPPM/PME/Ewald */
 314     struct gmx_pme_t *pmedata;
 315     int               ljpme_combination_rule;
 316     tensor            vir_el_recip;
 317     tensor            vir_lj_recip;
 318
 319     /* PME/Ewald stuff */
 320     gmx_bool                bEwald;
 321     real                    ewaldcoeff_q;
 322     real                    ewaldcoeff_lj;
 323     struct gmx_ewald_tab_t *ewald_table;
 324
 325     /* Virial Stuff */
 326     rvec *fshift;
 327     rvec  vir_diag_posres;
 328     dvec  vir_wall_z;
 329
 330     /* Non bonded Parameter lists */
 331     int      ntype; /* Number of atom types */
 332     gmx_bool bBHAM;
 333     real    *nbfp;
 334     real    *ljpme_c6grid; /* C6-values used on grid in LJPME */
 335
 336     /* Energy group pair flags */
 337     int *egp_flags;
 338
 339     /* Shell molecular dynamics flexible constraints */
 340     real fc_stepsize;
 341
 342     /* Generalized born implicit solvent */
 343     gmx_bool              bGB;
 344     /* Generalized born stuff */
 345     real                  gb_epsilon_solvent;
 346     /* Table data for GB */
 347     struct t_forcetable  *gbtab;
 348     /* VdW radius for each atomtype (dim is thus ntype) */
 349     real                 *atype_radius;
 350     /* Effective radius (derived from effective volume) for each type */
 351     real                 *atype_vol;
 352     /* Implicit solvent - surface tension for each atomtype */
 353     real                 *atype_surftens;
 354     /* Implicit solvent - radius for GB calculation */
 355     real                 *atype_gb_radius;
 356     /* Implicit solvent - overlap for HCT model */
 357     real                 *atype_S_hct;
 358     /* Generalized born interaction data */
 359     struct gmx_genborn_t *born;
 360
 361     /* Table scale for GB */
 362     real gbtabscale;
 363     /* Table range for GB */
 364     real gbtabr;
 365     /* GB neighborlists (the sr list will contain for each atom all other atoms
 366      * (for use in the SA calculation) and the lr list will contain
 367      * for each atom all atoms 1-4 or greater (for use in the GB calculation)
 368      */
 369     struct t_nblist *gblist_sr;
 370     struct t_nblist *gblist_lr;
 371     struct t_nblist *gblist;
 372
 373     /* Inverse square root of the Born radii for implicit solvent */
 374     real *invsqrta;
 375     /* Derivatives of the potential with respect to the Born radii */
 376     real *dvda;
 377     /* Derivatives of the Born radii with respect to coordinates */
 378     real *dadx;
 379     real *dadx_rawptr;
 380     int   nalloc_dadx; /* Allocated size of dadx */
 381
 382     /* If > 0 signals Test Particle Insertion,
 383      * the value is the number of atoms of the molecule to insert
 384      * Only the energy difference due to the addition of the last molecule
 385      * should be calculated.
 386      */
 387     gmx_bool n_tpi;
 388
 389     /* Neighbor searching stuff */
 390     struct gmx_ns_t *ns;
 391
 392     /* QMMM stuff */
 393     gmx_bool          bQMMM;
 394     struct t_QMMMrec *qr;
 395
 396     /* QM-MM neighborlists */
 397     struct t_nblist        *QMMMlist;
 398
 399     /* Limit for printing large forces, negative is don't print */
 400     real print_force;
 401
 402     /* coarse load balancing time measurement */
 403     double t_fnbf;
 404     double t_wait;
 405     int    timesteps;
 406
 407     /* User determined parameters, copied from the inputrec */
 408     int  userint1;
 409     int  userint2;
 410     int  userint3;
 411     int  userint4;
 412     real userreal1;
 413     real userreal2;
 414     real userreal3;
 415     real userreal4;
 416
 417     /* Pointer to struct for managing threading of bonded force calculation */
 418     struct bonded_threading_t *bonded_threading;
 419
 420     /* Ewald correction thread local virial and energy data */
 421     int                  nthread_ewc;
 422     ewald_corr_thread_t *ewc_t;
 423     /* Ewald charge correction load distribution over the threads */
 424     int                 *excl_load;
 425 } t_forcerec;
 426
 427 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 428  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 429  * in the code, but beware if you are using these macros externally.
 430  */
 431 #define C6(nbfp, ntp, ai, aj)     (nbfp)[2*((ntp)*(ai)+(aj))]
 432 #define C12(nbfp, ntp, ai, aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]
 433 #define BHAMC(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))]
 434 #define BHAMA(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+1]
 435 #define BHAMB(nbfp, ntp, ai, aj)  (nbfp)[3*((ntp)*(ai)+(aj))+2]
 436
 437 #ifdef __cplusplus
 438 }
 439 #endif
 440 #endif