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33 * GRoups of Organic Molecules in ACtion for Science
40 #include "nb_verlet.h"
41 #include "interaction_const.h"
48 } /* fixes auto-indentation problems */
51 /* Abstract type for PME that is defined only in the routine that use them. */
52 typedef struct gmx_pme *gmx_pme_t;
56 /* Structure describing the data in a single table */
59 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
60 enum gmx_table_format format; /* Interpolation type and data format */
62 real r; /* range of the table */
63 int n; /* n+1 is the number of table points */
64 real scale; /* distance (nm) between two table points */
65 real scale_exp; /* distance for exponential part of VdW table, not always used */
66 real * data; /* the actual table data */
68 /* Some information about the table layout. This can also be derived from the interpolation
69 * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
70 * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
71 * It is always true that stride = formatsize*ninteractions
73 int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
74 int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
75 int stride; /* Distance to next table point (number of fp variables per table point in total) */
80 t_forcetable table_elec;
81 t_forcetable table_vdw;
82 t_forcetable table_elec_vdw;
84 /* The actual neighbor lists, short and long range, see enum above
85 * for definition of neighborlist indices.
87 t_nblist nlist_sr[eNL_NR];
88 t_nblist nlist_lr[eNL_NR];
91 /* macros for the cginfo data in forcerec */
92 /* The maximum cg size in cginfo is 63
93 * because we only have space for 6 bits in cginfo,
94 * this cg size entry is actually only read with domain decomposition.
95 * But there is a smaller limit due to the t_excl data structure
96 * which is defined in nblist.h.
98 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~65535) | (gid) )
99 #define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
100 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
101 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
102 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
103 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
104 #define SET_CGINFO_SOLOPT(cgi, opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
105 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 3)
106 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
107 #define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
108 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1<<21))
109 #define GET_CGINFO_SETTLE(cgi) ( (cgi) & (1<<21))
110 /* This bit is only used with bBondComm in the domain decomposition */
111 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
112 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
113 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1<<23))
114 #define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
115 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
116 #define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
117 #define SET_CGINFO_NATOMS(cgi, opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
118 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>25) & 63)
121 /* Value to be used in mdrun for an infinite cut-off.
122 * Since we need to compare with the cut-off squared,
123 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
125 #define GMX_CUTOFF_INF 1E+18
127 /* enums for the neighborlist type */
129 enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
131 /* OOR is "one over r" -- standard coul */
133 enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
137 egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
138 egCOUL14, egLJ14, egGB, egNR
142 int nener; /* The number of energy group pairs */
143 real *ener[egNR]; /* Energy terms for each pair of groups */
147 real term[F_NRE]; /* The energies for all different interaction types */
148 gmx_grppairener_t grpp;
149 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
150 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
152 int fep_state; /*current fep state -- just for printing */
153 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
154 real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
155 gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
157 /* The idea is that dvdl terms with linear lambda dependence will be added
158 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
159 * should explicitly determine the energies at foreign lambda points
171 /* ewald table type */
172 typedef struct ewald_tab *ewald_tab_t;
177 unsigned red_mask; /* Mask for marking which parts of f are filled */
180 gmx_grppairener_t grpp;
187 interaction_const_t *ic;
189 /* Domain Decomposition */
199 const gmx_hw_info_t *hwinfo;
200 const gmx_gpu_opt_t *gpu_opt;
201 gmx_bool use_cpu_acceleration;
203 /* Interaction for calculated in kernels. In many cases this is similar to
204 * the electrostatics settings in the inputrecord, but the difference is that
205 * these variables always specify the actual interaction in the kernel - if
206 * we are tabulating reaction-field the inputrec will say reaction-field, but
207 * the kernel interaction will say cubic-spline-table. To be safe we also
208 * have a kernel-specific setting for the modifiers - if the interaction is
209 * tabulated we already included the inputrec modification there, so the kernel
210 * modification setting will say 'none' in that case.
212 int nbkernel_elec_interaction;
213 int nbkernel_vdw_interaction;
214 int nbkernel_elec_modifier;
215 int nbkernel_vdw_modifier;
217 /* Use special N*N kernels? */
219 /* Private work data */
221 void *AllvsAll_workgb;
224 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
226 real rlist, rlistlong;
228 /* Dielectric constant resp. multiplication factor for charges */
230 real epsilon_r, epsilon_rf, epsfac;
232 /* Constants for reaction fields */
233 real kappa, k_rf, c_rf;
235 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
240 /* Dispersion correction stuff */
243 /* The shift of the shift or user potentials */
245 real enershifttwelve;
246 /* Integrated differces for energy and virial with cut-off functions */
251 /* Constant for long range dispersion correction (average dispersion)
252 * for topology A/B ([0]/[1]) */
254 /* Constant for long range repulsion term. Relative difference of about
255 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
265 /* The normal tables are in the nblists struct(s) below */
266 t_forcetable tab14; /* for 1-4 interactions only */
268 /* PPPM & Shifting stuff */
269 int coulomb_modifier;
270 real rcoulomb_switch, rcoulomb;
276 real rvdw_switch, rvdw;
293 /* solvent_opt contains the enum for the most common solvent
294 * in the system, which will be optimized.
295 * It can be set to esolNO to disable all water optimization */
299 gmx_bool bExcl_IntraCGAll_InterCGNone;
300 cginfo_mb_t *cginfo_mb;
306 /* The neighborlists including tables */
311 int cutoff_scheme; /* group- or Verlet-style cutoff */
312 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
313 nonbonded_verlet_t *nbv;
315 /* The wall tables (if used) */
317 t_forcetable **wall_tab;
319 /* The number of charge groups participating in do_force_lowlevel */
321 /* The number of atoms participating in do_force_lowlevel */
323 /* The number of atoms participating in force and constraints */
324 int natoms_force_constr;
325 /* The allocation size of vectors of size natoms_force */
328 /* Twin Range stuff, f_twin has size natoms_force */
333 /* Forces that should not enter into the virial summation:
334 * PPPM/PME/Ewald/posres
336 gmx_bool bF_NoVirSum;
338 int f_novirsum_nalloc;
339 rvec *f_novirsum_alloc;
340 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
341 * points to the normal force vectors wen pressure is not requested.
345 /* Long-range forces and virial for PPPM/PME/Ewald */
349 /* PME/Ewald stuff */
352 ewald_tab_t ewald_table;
356 rvec vir_diag_posres;
359 /* Non bonded Parameter lists */
360 int ntype; /* Number of atom types */
364 /* Energy group pair flags */
367 /* Shell molecular dynamics flexible constraints */
370 /* Generalized born implicit solvent */
372 /* Generalized born stuff */
373 real gb_epsilon_solvent;
374 /* Table data for GB */
376 /* VdW radius for each atomtype (dim is thus ntype) */
378 /* Effective radius (derived from effective volume) for each type */
380 /* Implicit solvent - surface tension for each atomtype */
381 real *atype_surftens;
382 /* Implicit solvent - radius for GB calculation */
383 real *atype_gb_radius;
384 /* Implicit solvent - overlap for HCT model */
386 /* Generalized born interaction data */
389 /* Table scale for GB */
391 /* Table range for GB */
393 /* GB neighborlists (the sr list will contain for each atom all other atoms
394 * (for use in the SA calculation) and the lr list will contain
395 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
401 /* Inverse square root of the Born radii for implicit solvent */
403 /* Derivatives of the potential with respect to the Born radii */
405 /* Derivatives of the Born radii with respect to coordinates */
408 int nalloc_dadx; /* Allocated size of dadx */
410 /* If > 0 signals Test Particle Insertion,
411 * the value is the number of atoms of the molecule to insert
412 * Only the energy difference due to the addition of the last molecule
413 * should be calculated.
417 /* Neighbor searching stuff */
424 /* QM-MM neighborlists */
427 /* Limit for printing large forces, negative is don't print */
430 /* coarse load balancing time measurement */
435 /* parameter needed for AdResS simulation */
437 gmx_bool badress_tf_full_box;
438 real adress_const_wf;
439 real adress_ex_width;
440 real adress_hy_width;
444 int n_adress_tf_grps;
445 int * adress_tf_table_index;
446 int *adress_group_explicit;
447 t_forcetable * atf_tabs;
448 real adress_ex_forcecap;
449 gmx_bool adress_do_hybridpairs;
451 /* User determined parameters, copied from the inputrec */
461 /* Thread local force and energy data */
462 /* FIXME move to bonded_thread_data_t */
468 /* Exclusion load distribution over the threads */
472 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
473 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
474 * in the code, but beware if you are using these macros externally.
476 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
477 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
478 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
479 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
480 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]