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43 #include "nb_verlet.h"
44 #include "interaction_const.h"
51 } /* fixes auto-indentation problems */
54 /* Abstract type for PME that is defined only in the routine that use them. */
55 typedef struct gmx_pme *gmx_pme_t;
59 /* Structure describing the data in a single table */
62 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
63 enum gmx_table_format format; /* Interpolation type and data format */
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 */
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
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) */
83 t_forcetable table_elec;
84 t_forcetable table_vdw;
85 t_forcetable table_elec_vdw;
87 /* The actual neighbor lists, short and long range, see enum above
88 * for definition of neighborlist indices.
90 t_nblist nlist_sr[eNL_NR];
91 t_nblist nlist_lr[eNL_NR];
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.
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)
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).
128 #define GMX_CUTOFF_INF 1E+18
130 /* enums for the neighborlist type */
132 enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
134 /* OOR is "one over r" -- standard coul */
136 enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
140 egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
141 egCOUL14, egLJ14, egGB, egNR
145 int nener; /* The number of energy group pairs */
146 real *ener[egNR]; /* Energy terms for each pair of groups */
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 */
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 */
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
174 /* ewald table type */
175 typedef struct ewald_tab *ewald_tab_t;
180 unsigned red_mask; /* Mask for marking which parts of f are filled */
183 gmx_grppairener_t grpp;
190 interaction_const_t *ic;
192 /* Domain Decomposition */
202 const gmx_hw_info_t *hwinfo;
203 const gmx_gpu_opt_t *gpu_opt;
204 gmx_bool use_cpu_acceleration;
206 /* Interaction for calculated in kernels. In many cases this is similar to
207 * the electrostatics settings in the inputrecord, but the difference is that
208 * these variables always specify the actual interaction in the kernel - if
209 * we are tabulating reaction-field the inputrec will say reaction-field, but
210 * the kernel interaction will say cubic-spline-table. To be safe we also
211 * have a kernel-specific setting for the modifiers - if the interaction is
212 * tabulated we already included the inputrec modification there, so the kernel
213 * modification setting will say 'none' in that case.
215 int nbkernel_elec_interaction;
216 int nbkernel_vdw_interaction;
217 int nbkernel_elec_modifier;
218 int nbkernel_vdw_modifier;
220 /* Use special N*N kernels? */
222 /* Private work data */
224 void *AllvsAll_workgb;
227 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
229 real rlist, rlistlong;
231 /* Dielectric constant resp. multiplication factor for charges */
233 real epsilon_r, epsilon_rf, epsfac;
235 /* Constants for reaction fields */
236 real kappa, k_rf, c_rf;
238 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
243 /* Dispersion correction stuff */
246 /* The shift of the shift or user potentials */
248 real enershifttwelve;
249 /* Integrated differces for energy and virial with cut-off functions */
254 /* Constant for long range dispersion correction (average dispersion)
255 * for topology A/B ([0]/[1]) */
257 /* Constant for long range repulsion term. Relative difference of about
258 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
268 /* The normal tables are in the nblists struct(s) below */
269 t_forcetable tab14; /* for 1-4 interactions only */
271 /* PPPM & Shifting stuff */
272 int coulomb_modifier;
273 real rcoulomb_switch, rcoulomb;
279 real rvdw_switch, rvdw;
296 /* solvent_opt contains the enum for the most common solvent
297 * in the system, which will be optimized.
298 * It can be set to esolNO to disable all water optimization */
302 gmx_bool bExcl_IntraCGAll_InterCGNone;
303 cginfo_mb_t *cginfo_mb;
309 /* The neighborlists including tables */
314 int cutoff_scheme; /* group- or Verlet-style cutoff */
315 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
316 nonbonded_verlet_t *nbv;
318 /* The wall tables (if used) */
320 t_forcetable **wall_tab;
322 /* The number of charge groups participating in do_force_lowlevel */
324 /* The number of atoms participating in do_force_lowlevel */
326 /* The number of atoms participating in force and constraints */
327 int natoms_force_constr;
328 /* The allocation size of vectors of size natoms_force */
331 /* Twin Range stuff, f_twin has size natoms_force */
336 /* Forces that should not enter into the virial summation:
337 * PPPM/PME/Ewald/posres
339 gmx_bool bF_NoVirSum;
341 int f_novirsum_nalloc;
342 rvec *f_novirsum_alloc;
343 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
344 * points to the normal force vectors wen pressure is not requested.
348 /* Long-range forces and virial for PPPM/PME/Ewald */
352 /* PME/Ewald stuff */
355 ewald_tab_t ewald_table;
359 rvec vir_diag_posres;
362 /* Non bonded Parameter lists */
363 int ntype; /* Number of atom types */
367 /* Energy group pair flags */
370 /* xmdrun flexible constraints */
373 /* Generalized born implicit solvent */
375 /* Generalized born stuff */
376 real gb_epsilon_solvent;
377 /* Table data for GB */
379 /* VdW radius for each atomtype (dim is thus ntype) */
381 /* Effective radius (derived from effective volume) for each type */
383 /* Implicit solvent - surface tension for each atomtype */
384 real *atype_surftens;
385 /* Implicit solvent - radius for GB calculation */
386 real *atype_gb_radius;
387 /* Implicit solvent - overlap for HCT model */
389 /* Generalized born interaction data */
392 /* Table scale for GB */
394 /* Table range for GB */
396 /* GB neighborlists (the sr list will contain for each atom all other atoms
397 * (for use in the SA calculation) and the lr list will contain
398 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
404 /* Inverse square root of the Born radii for implicit solvent */
406 /* Derivatives of the potential with respect to the Born radii */
408 /* Derivatives of the Born radii with respect to coordinates */
411 int nalloc_dadx; /* Allocated size of dadx */
413 /* If > 0 signals Test Particle Insertion,
414 * the value is the number of atoms of the molecule to insert
415 * Only the energy difference due to the addition of the last molecule
416 * should be calculated.
420 /* Neighbor searching stuff */
427 /* QM-MM neighborlists */
430 /* Limit for printing large forces, negative is don't print */
433 /* coarse load balancing time measurement */
438 /* parameter needed for AdResS simulation */
440 gmx_bool badress_tf_full_box;
441 real adress_const_wf;
442 real adress_ex_width;
443 real adress_hy_width;
447 int n_adress_tf_grps;
448 int * adress_tf_table_index;
449 int *adress_group_explicit;
450 t_forcetable * atf_tabs;
451 real adress_ex_forcecap;
452 gmx_bool adress_do_hybridpairs;
454 /* User determined parameters, copied from the inputrec */
464 /* Thread local force and energy data */
465 /* FIXME move to bonded_thread_data_t */
471 /* Exclusion load distribution over the threads */
475 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
476 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
477 * in the code, but beware if you are using these macros externally.
479 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
480 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
481 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
482 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
483 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]