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33 * GRoups of Organic Molecules in ACtion for Science
40 #include "../gmx_detectcpu.h"
46 /* Abstract type for PME that is defined only in the routine that use them. */
47 typedef struct gmx_pme *gmx_pme_t;
50 real r; /* range of the table */
51 int n; /* n+1 is the number of points */
52 real scale; /* distance between two points */
53 real scale_exp; /* distance for exponential Buckingham table */
54 real *tab; /* the actual tables, per point there are 4 numbers for
55 * Coulomb, dispersion and repulsion (in total 12 numbers)
61 /* We duplicate tables for cache optimization purposes */
62 real *coultab; /* Coul only */
63 real *vdwtab; /* Vdw only */
64 /* The actual neighbor lists, short and long range, see enum above
65 * for definition of neighborlist indices.
67 t_nblist nlist_sr[eNL_NR];
68 t_nblist nlist_lr[eNL_NR];
71 /* macros for the cginfo data in forcerec */
72 /* The maximum cg size in cginfo is 255,
73 * because we only have space for 8 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.
78 #define SET_CGINFO_GID(cgi,gid) (cgi) = (((cgi) & ~65535) | (gid) )
79 #define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
80 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
81 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
82 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
83 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
84 #define SET_CGINFO_SOLOPT(cgi,opt) (cgi) = (((cgi) & ~(15<<18)) | ((opt)<<18))
85 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 15)
86 /* This bit is only used with bBondComm in the domain decomposition */
87 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
88 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
89 #define SET_CGINFO_NATOMS(cgi,opt) (cgi) = (((cgi) & ~(255<<23)) | ((opt)<<23))
90 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>23) & 255)
93 /* Value to be used in mdrun for an infinite cut-off.
94 * Since we need to compare with the cut-off squared,
95 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
97 #define GMX_CUTOFF_INF 1E+18
99 /* enums for the neighborlist type */
100 enum { enbvdwNONE,enbvdwLJ,enbvdwBHAM,enbvdwTAB,enbvdwNR};
101 /* OOR is "one over r" -- standard coul */
102 enum { enbcoulNONE,enbcoulOOR,enbcoulRF,enbcoulTAB,enbcoulGB,enbcoulFEWALD,enbcoulNR};
104 enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
105 egCOUL14, egLJ14, egGB, egNR };
108 int nener; /* The number of energy group pairs */
109 real *ener[egNR]; /* Energy terms for each pair of groups */
113 real term[F_NRE]; /* The energies for all different interaction types */
114 gmx_grppairener_t grpp;
115 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
116 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
118 int fep_state; /*current fep state -- just for printing */
119 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
121 /* The idea is that dvdl terms with linear lambda dependence will be added
122 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
123 * should explicitly determine the energies at foreign lambda points
135 /* ewald table type */
136 typedef struct ewald_tab *ewald_tab_t;
139 /* Domain Decomposition */
149 gmx_detectcpu_t cpu_information;
150 gmx_bool use_acceleration;
152 /* Use special N*N kernels? */
154 /* Private work data */
156 void *AllvsAll_workgb;
159 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
161 real rlist,rlistlong;
163 /* Dielectric constant resp. multiplication factor for charges */
165 real epsilon_r,epsilon_rf,epsfac;
167 /* Constants for reaction fields */
168 real kappa,k_rf,c_rf;
170 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
174 /* Dispersion correction stuff */
176 /* The shift of the shift or user potentials */
178 real enershifttwelve;
179 /* Integrated differces for energy and virial with cut-off functions */
184 /* Constant for long range dispersion correction (average dispersion)
185 * for topology A/B ([0]/[1]) */
187 /* Constant for long range repulsion term. Relative difference of about
188 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
198 /* The normal tables are in the nblists struct(s) below */
199 t_forcetable tab14; /* for 1-4 interactions only */
201 /* PPPM & Shifting stuff */
202 real rcoulomb_switch,rcoulomb;
207 real rvdw_switch,rvdw;
224 /* solvent_opt contains the enum for the most common solvent
225 * in the system, which will be optimized.
226 * It can be set to esolNO to disable all water optimization */
230 cginfo_mb_t *cginfo_mb;
236 /* The neighborlists including tables */
241 /* The wall tables (if used) */
243 t_forcetable **wall_tab;
245 /* This mask array of length nn determines whether or not this bit of the
246 * neighbourlists should be computed. Usually all these are true of course,
247 * but not when shells are used. During minimisation all the forces that
248 * include shells are done, then after minimsation is converged the remaining
249 * forces are computed.
251 /* gmx_bool *bMask; */
253 /* The number of charge groups participating in do_force_lowlevel */
255 /* The number of atoms participating in do_force_lowlevel */
257 /* The number of atoms participating in force and constraints */
258 int natoms_force_constr;
259 /* The allocation size of vectors of size natoms_force */
262 /* Twin Range stuff, f_twin has size natoms_force */
267 /* Forces that should not enter into the virial summation:
268 * PPPM/PME/Ewald/posres
270 gmx_bool bF_NoVirSum;
272 int f_novirsum_nalloc;
273 rvec *f_novirsum_alloc;
274 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
275 * points to the normal force vectors wen pressure is not requested.
279 /* Long-range forces and virial for PPPM/PME/Ewald */
283 /* PME/Ewald stuff */
286 ewald_tab_t ewald_table;
290 rvec vir_diag_posres;
293 /* Non bonded Parameter lists */
294 int ntype; /* Number of atom types */
298 /* Energy group pair flags */
301 /* xmdrun flexible constraints */
304 /* Generalized born implicit solvent */
306 /* Generalized born stuff */
307 real gb_epsilon_solvent;
308 /* Table data for GB */
310 /* VdW radius for each atomtype (dim is thus ntype) */
312 /* Effective radius (derived from effective volume) for each type */
314 /* Implicit solvent - surface tension for each atomtype */
315 real *atype_surftens;
316 /* Implicit solvent - radius for GB calculation */
317 real *atype_gb_radius;
318 /* Implicit solvent - overlap for HCT model */
320 /* Generalized born interaction data */
323 /* Table scale for GB */
325 /* Table range for GB */
327 /* GB neighborlists (the sr list will contain for each atom all other atoms
328 * (for use in the SA calculation) and the lr list will contain
329 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
335 /* Inverse square root of the Born radii for implicit solvent */
337 /* Derivatives of the potential with respect to the Born radii */
339 /* Derivatives of the Born radii with respect to coordinates */
342 int nalloc_dadx; /* Allocated size of dadx */
344 /* If > 0 signals Test Particle Insertion,
345 * the value is the number of atoms of the molecule to insert
346 * Only the energy difference due to the addition of the last molecule
347 * should be calculated.
351 /* Neighbor searching stuff */
358 /* QM-MM neighborlists */
361 /* Limit for printing large forces, negative is don't print */
364 /* coarse load balancing time measurement */
369 /* parameter needed for AdResS simulation */
371 gmx_bool badress_tf_full_box;
372 real adress_const_wf;
373 real adress_ex_width;
374 real adress_hy_width;
378 int n_adress_tf_grps;
379 int * adress_tf_table_index;
380 int *adress_group_explicit;
381 t_forcetable * atf_tabs;
382 real adress_ex_forcecap;
383 gmx_bool adress_do_hybridpairs;
385 /* User determined parameters, copied from the inputrec */
396 #define C6(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))]
397 #define C12(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
398 #define BHAMC(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))]
399 #define BHAMA(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
400 #define BHAMB(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]