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33 * GRoups of Organic Molecules in ACtion for Science
45 /* Abstract type for PME that is defined only in the routine that use them. */
46 typedef struct gmx_pme *gmx_pme_t;
49 real r; /* range of the table */
50 int n; /* n+1 is the number of points */
51 real scale; /* distance between two points */
52 real scale_exp; /* distance for exponential Buckingham table */
53 real *tab; /* the actual tables, per point there are 4 numbers for
54 * Coulomb, dispersion and repulsion (in total 12 numbers)
60 /* We duplicate tables for cache optimization purposes */
61 real *coultab; /* Coul only */
62 real *vdwtab; /* Vdw only */
63 /* The actual neighbor lists, short and long range, see enum above
64 * for definition of neighborlist indices.
66 t_nblist nlist_sr[eNL_NR];
67 t_nblist nlist_lr[eNL_NR];
70 /* macros for the cginfo data in forcerec */
71 /* The maximum cg size in cginfo is 255,
72 * because we only have space for 8 bits in cginfo,
73 * this cg size entry is actually only read with domain decomposition.
74 * But there is a smaller limit due to the t_excl data structure
75 * which is defined in nblist.h.
77 #define SET_CGINFO_GID(cgi,gid) (cgi) = (((cgi) & ~65535) | (gid) )
78 #define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
79 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
80 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
81 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
82 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
83 #define SET_CGINFO_SOLOPT(cgi,opt) (cgi) = (((cgi) & ~(15<<18)) | ((opt)<<18))
84 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 15)
85 /* This bit is only used with bBondComm in the domain decomposition */
86 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
87 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
88 #define SET_CGINFO_NATOMS(cgi,opt) (cgi) = (((cgi) & ~(255<<23)) | ((opt)<<23))
89 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>23) & 255)
92 /* Value to be used in mdrun for an infinite cut-off.
93 * Since we need to compare with the cut-off squared,
94 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
96 #define GMX_CUTOFF_INF 1E+18
98 /* enums for the neighborlist type */
99 enum { enbvdwNONE,enbvdwLJ,enbvdwBHAM,enbvdwTAB,enbvdwNR};
100 /* OOR is "one over r" -- standard coul */
101 enum { enbcoulNONE,enbcoulOOR,enbcoulRF,enbcoulTAB,enbcoulGB,enbcoulFEWALD,enbcoulNR};
103 enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
104 egCOUL14, egLJ14, egGB, egNR };
107 int nener; /* The number of energy group pairs */
108 real *ener[egNR]; /* Energy terms for each pair of groups */
112 real term[F_NRE]; /* The energies for all different interaction types */
113 gmx_grppairener_t grpp;
114 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
115 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
117 int fep_state; /*current fep state -- just for printing */
118 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
120 /* The idea is that dvdl terms with linear lambda dependence will be added
121 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
122 * should explicitly determine the energies at foreign lambda points
134 /* ewald table type */
135 typedef struct ewald_tab *ewald_tab_t;
138 /* Domain Decomposition */
148 gmx_bool UseOptimizedKernels;
150 /* Use special N*N kernels? */
152 /* Private work data */
154 void *AllvsAll_workgb;
157 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
159 real rlist,rlistlong;
161 /* Dielectric constant resp. multiplication factor for charges */
163 real epsilon_r,epsilon_rf,epsfac;
165 /* Constants for reaction fields */
166 real kappa,k_rf,c_rf;
168 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
172 /* Dispersion correction stuff */
174 /* The shift of the shift or user potentials */
176 real enershifttwelve;
177 /* Integrated differces for energy and virial with cut-off functions */
182 /* Constant for long range dispersion correction (average dispersion)
183 * for topology A/B ([0]/[1]) */
185 /* Constant for long range repulsion term. Relative difference of about
186 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
196 /* The normal tables are in the nblists struct(s) below */
197 t_forcetable tab14; /* for 1-4 interactions only */
199 /* PPPM & Shifting stuff */
200 real rcoulomb_switch,rcoulomb;
205 real rvdw_switch,rvdw;
222 /* solvent_opt contains the enum for the most common solvent
223 * in the system, which will be optimized.
224 * It can be set to esolNO to disable all water optimization */
228 cginfo_mb_t *cginfo_mb;
234 /* The neighborlists including tables */
239 /* The wall tables (if used) */
241 t_forcetable **wall_tab;
243 /* This mask array of length nn determines whether or not this bit of the
244 * neighbourlists should be computed. Usually all these are true of course,
245 * but not when shells are used. During minimisation all the forces that
246 * include shells are done, then after minimsation is converged the remaining
247 * forces are computed.
249 /* gmx_bool *bMask; */
251 /* The number of charge groups participating in do_force_lowlevel */
253 /* The number of atoms participating in do_force_lowlevel */
255 /* The number of atoms participating in force and constraints */
256 int natoms_force_constr;
257 /* The allocation size of vectors of size natoms_force */
260 /* Twin Range stuff, f_twin has size natoms_force */
265 /* Forces that should not enter into the virial summation:
266 * PPPM/PME/Ewald/posres
268 gmx_bool bF_NoVirSum;
270 int f_novirsum_nalloc;
271 rvec *f_novirsum_alloc;
272 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
273 * points to the normal force vectors wen pressure is not requested.
277 /* Long-range forces and virial for PPPM/PME/Ewald */
281 /* PME/Ewald stuff */
284 ewald_tab_t ewald_table;
288 rvec vir_diag_posres;
291 /* Non bonded Parameter lists */
292 int ntype; /* Number of atom types */
296 /* Energy group pair flags */
299 /* xmdrun flexible constraints */
302 /* Generalized born implicit solvent */
304 /* Generalized born stuff */
305 real gb_epsilon_solvent;
306 /* Table data for GB */
308 /* VdW radius for each atomtype (dim is thus ntype) */
310 /* Effective radius (derived from effective volume) for each type */
312 /* Implicit solvent - surface tension for each atomtype */
313 real *atype_surftens;
314 /* Implicit solvent - radius for GB calculation */
315 real *atype_gb_radius;
316 /* Implicit solvent - overlap for HCT model */
318 /* Generalized born interaction data */
321 /* Table scale for GB */
323 /* Table range for GB */
325 /* GB neighborlists (the sr list will contain for each atom all other atoms
326 * (for use in the SA calculation) and the lr list will contain
327 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
333 /* Inverse square root of the Born radii for implicit solvent */
335 /* Derivatives of the potential with respect to the Born radii */
337 /* Derivatives of the Born radii with respect to coordinates */
340 int nalloc_dadx; /* Allocated size of dadx */
342 /* If > 0 signals Test Particle Insertion,
343 * the value is the number of atoms of the molecule to insert
344 * Only the energy difference due to the addition of the last molecule
345 * should be calculated.
349 /* Neighbor searching stuff */
356 /* QM-MM neighborlists */
359 /* Limit for printing large forces, negative is don't print */
362 /* coarse load balancing time measurement */
367 /* parameter needed for AdResS simulation */
369 gmx_bool badress_tf_full_box;
370 real adress_const_wf;
371 real adress_ex_width;
372 real adress_hy_width;
376 int n_adress_tf_grps;
377 int * adress_tf_table_index;
378 int *adress_group_explicit;
379 t_forcetable * atf_tabs;
380 real adress_ex_forcecap;
381 gmx_bool adress_do_hybridpairs;
383 /* User determined parameters, copied from the inputrec */
394 #define C6(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))]
395 #define C12(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
396 #define BHAMC(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))]
397 #define BHAMA(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
398 #define BHAMB(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]