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41 #include "../../topology/idef.h"
42 #include "nb_verlet.h"
43 #include "interaction_const.h"
50 } /* fixes auto-indentation problems */
53 /* Abstract type for PME that is defined only in the routine that use them. */
54 typedef struct gmx_pme *gmx_pme_t;
58 /* Structure describing the data in a single table */
61 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
62 enum gmx_table_format format; /* Interpolation type and data format */
64 real r; /* range of the table */
65 int n; /* n+1 is the number of table points */
66 real scale; /* distance (nm) between two table points */
67 real scale_exp; /* distance for exponential part of VdW table, not always used */
68 real * data; /* the actual table data */
70 /* Some information about the table layout. This can also be derived from the interpolation
71 * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
72 * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
73 * It is always true that stride = formatsize*ninteractions
75 int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
76 int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
77 int stride; /* Distance to next table point (number of fp variables per table point in total) */
82 t_forcetable table_elec;
83 t_forcetable table_vdw;
84 t_forcetable table_elec_vdw;
86 /* The actual neighbor lists, short and long range, see enum above
87 * for definition of neighborlist indices.
89 t_nblist nlist_sr[eNL_NR];
90 t_nblist nlist_lr[eNL_NR];
93 /* macros for the cginfo data in forcerec
95 * Since the tpx format support max 256 energy groups, we do the same here.
96 * Note that we thus have bits 8-14 still unused.
98 * The maximum cg size in cginfo is 63
99 * because we only have space for 6 bits in cginfo,
100 * this cg size entry is actually only read with domain decomposition.
101 * But there is a smaller limit due to the t_excl data structure
102 * which is defined in nblist.h.
104 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
105 #define GET_CGINFO_GID(cgi) ( (cgi) & 255)
106 #define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1<<15))
107 #define GET_CGINFO_FEP(cgi) ( (cgi) & (1<<15))
108 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
109 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
110 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
111 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
112 #define SET_CGINFO_SOLOPT(cgi, opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
113 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 3)
114 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
115 #define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
116 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1<<21))
117 #define GET_CGINFO_SETTLE(cgi) ( (cgi) & (1<<21))
118 /* This bit is only used with bBondComm in the domain decomposition */
119 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
120 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
121 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1<<23))
122 #define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
123 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
124 #define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
125 #define SET_CGINFO_NATOMS(cgi, opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
126 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>25) & 63)
129 /* Value to be used in mdrun for an infinite cut-off.
130 * Since we need to compare with the cut-off squared,
131 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
133 #define GMX_CUTOFF_INF 1E+18
135 /* enums for the neighborlist type */
137 enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
139 /* OOR is "one over r" -- standard coul */
141 enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
145 egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
146 egCOUL14, egLJ14, egGB, egNR
150 int nener; /* The number of energy group pairs */
151 real *ener[egNR]; /* Energy terms for each pair of groups */
155 real term[F_NRE]; /* The energies for all different interaction types */
156 gmx_grppairener_t grpp;
157 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
158 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
160 int fep_state; /*current fep state -- just for printing */
161 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
162 real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
163 gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
165 /* The idea is that dvdl terms with linear lambda dependence will be added
166 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
167 * should explicitly determine the energies at foreign lambda points
179 /* ewald table type */
180 typedef struct ewald_tab *ewald_tab_t;
185 unsigned red_mask; /* Mask for marking which parts of f are filled */
188 gmx_grppairener_t grpp;
197 interaction_const_t *ic;
199 /* Domain Decomposition */
209 const gmx_hw_info_t *hwinfo;
210 const gmx_gpu_opt_t *gpu_opt;
211 gmx_bool use_simd_kernels;
213 /* Interaction for calculated in kernels. In many cases this is similar to
214 * the electrostatics settings in the inputrecord, but the difference is that
215 * these variables always specify the actual interaction in the kernel - if
216 * we are tabulating reaction-field the inputrec will say reaction-field, but
217 * the kernel interaction will say cubic-spline-table. To be safe we also
218 * have a kernel-specific setting for the modifiers - if the interaction is
219 * tabulated we already included the inputrec modification there, so the kernel
220 * modification setting will say 'none' in that case.
222 int nbkernel_elec_interaction;
223 int nbkernel_vdw_interaction;
224 int nbkernel_elec_modifier;
225 int nbkernel_vdw_modifier;
227 /* Use special N*N kernels? */
229 /* Private work data */
231 void *AllvsAll_workgb;
234 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
236 real rlist, rlistlong;
238 /* Dielectric constant resp. multiplication factor for charges */
240 real epsilon_r, epsilon_rf, epsfac;
242 /* Constants for reaction fields */
243 real kappa, k_rf, c_rf;
245 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
251 /* Dispersion correction stuff */
254 /* The shift of the shift or user potentials */
256 real enershifttwelve;
257 /* Integrated differces for energy and virial with cut-off functions */
262 /* Constant for long range dispersion correction (average dispersion)
263 * for topology A/B ([0]/[1]) */
265 /* Constant for long range repulsion term. Relative difference of about
266 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
276 /* The normal tables are in the nblists struct(s) below */
277 t_forcetable tab14; /* for 1-4 interactions only */
279 /* PPPM & Shifting stuff */
280 int coulomb_modifier;
281 real rcoulomb_switch, rcoulomb;
287 real rvdw_switch, rvdw;
304 /* solvent_opt contains the enum for the most common solvent
305 * in the system, which will be optimized.
306 * It can be set to esolNO to disable all water optimization */
310 gmx_bool bExcl_IntraCGAll_InterCGNone;
311 cginfo_mb_t *cginfo_mb;
317 /* The neighborlists including tables */
322 int cutoff_scheme; /* group- or Verlet-style cutoff */
323 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
324 nonbonded_verlet_t *nbv;
326 /* The wall tables (if used) */
328 t_forcetable **wall_tab;
330 /* The number of charge groups participating in do_force_lowlevel */
332 /* The number of atoms participating in do_force_lowlevel */
334 /* The number of atoms participating in force and constraints */
335 int natoms_force_constr;
336 /* The allocation size of vectors of size natoms_force */
339 /* Twin Range stuff, f_twin has size natoms_force */
344 /* Forces that should not enter into the virial summation:
345 * PPPM/PME/Ewald/posres
347 gmx_bool bF_NoVirSum;
349 int f_novirsum_nalloc;
350 rvec *f_novirsum_alloc;
351 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
352 * points to the normal force vectors wen pressure is not requested.
356 /* Long-range forces and virial for PPPM/PME/Ewald */
358 int ljpme_combination_rule;
362 /* PME/Ewald stuff */
366 ewald_tab_t ewald_table;
370 rvec vir_diag_posres;
373 /* Non bonded Parameter lists */
374 int ntype; /* Number of atom types */
377 real *ljpme_c6grid; /* C6-values used on grid in LJPME */
379 /* Energy group pair flags */
382 /* Shell molecular dynamics flexible constraints */
385 /* Generalized born implicit solvent */
387 /* Generalized born stuff */
388 real gb_epsilon_solvent;
389 /* Table data for GB */
391 /* VdW radius for each atomtype (dim is thus ntype) */
393 /* Effective radius (derived from effective volume) for each type */
395 /* Implicit solvent - surface tension for each atomtype */
396 real *atype_surftens;
397 /* Implicit solvent - radius for GB calculation */
398 real *atype_gb_radius;
399 /* Implicit solvent - overlap for HCT model */
401 /* Generalized born interaction data */
404 /* Table scale for GB */
406 /* Table range for GB */
408 /* GB neighborlists (the sr list will contain for each atom all other atoms
409 * (for use in the SA calculation) and the lr list will contain
410 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
416 /* Inverse square root of the Born radii for implicit solvent */
418 /* Derivatives of the potential with respect to the Born radii */
420 /* Derivatives of the Born radii with respect to coordinates */
423 int nalloc_dadx; /* Allocated size of dadx */
425 /* If > 0 signals Test Particle Insertion,
426 * the value is the number of atoms of the molecule to insert
427 * Only the energy difference due to the addition of the last molecule
428 * should be calculated.
432 /* Neighbor searching stuff */
439 /* QM-MM neighborlists */
442 /* Limit for printing large forces, negative is don't print */
445 /* coarse load balancing time measurement */
450 /* parameter needed for AdResS simulation */
452 gmx_bool badress_tf_full_box;
453 real adress_const_wf;
454 real adress_ex_width;
455 real adress_hy_width;
459 int n_adress_tf_grps;
460 int * adress_tf_table_index;
461 int *adress_group_explicit;
462 t_forcetable * atf_tabs;
463 real adress_ex_forcecap;
464 gmx_bool adress_do_hybridpairs;
466 /* User determined parameters, copied from the inputrec */
476 /* Thread local force and energy data */
477 /* FIXME move to bonded_thread_data_t */
483 /* Exclusion load distribution over the threads */
487 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
488 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
489 * in the code, but beware if you are using these macros externally.
491 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
492 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
493 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
494 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
495 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]