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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
99 enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
100 egCOUL14, egLJ14, egGB, egNR };
103 int nener; /* The number of energy group pairs */
104 real *ener[egNR]; /* Energy terms for each pair of groups */
108 real term[F_NRE]; /* The energies for all different interaction types */
109 gmx_grppairener_t grpp;
110 double dvdl_lin; /* Contributions to dvdl with linear lam-dependence */
111 double dvdl_nonlin; /* Idem, but non-linear dependence */
113 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
115 /* The idea is that dvdl terms with linear lambda dependence will be added
116 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
117 * should explicitly determine the energies at foreign lambda points
129 /* ewald table type */
130 typedef struct ewald_tab *ewald_tab_t;
133 /* Domain Decomposition */
143 gmx_bool UseOptimizedKernels;
145 /* Use special N*N kernels? */
147 /* Private work data */
149 void *AllvsAll_workgb;
152 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
154 real rlist,rlistlong;
156 /* Dielectric constant resp. multiplication factor for charges */
158 real epsilon_r,epsilon_rf,epsfac;
160 /* Constants for reaction fields */
161 real kappa,k_rf,c_rf;
163 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
167 /* Dispersion correction stuff */
169 /* The shift of the shift or user potentials */
171 real enershifttwelve;
172 /* Integrated differces for energy and virial with cut-off functions */
177 /* Constant for long range dispersion correction (average dispersion)
178 * for topology A/B ([0]/[1]) */
180 /* Constant for long range repulsion term. Relative difference of about
181 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
191 /* The normal tables are in the nblists struct(s) below */
192 t_forcetable tab14; /* for 1-4 interactions only */
194 /* PPPM & Shifting stuff */
195 real rcoulomb_switch,rcoulomb;
200 real rvdw_switch,rvdw;
215 /* solvent_opt contains the enum for the most common solvent
216 * in the system, which will be optimized.
217 * It can be set to esolNO to disable all water optimization */
221 cginfo_mb_t *cginfo_mb;
227 /* The neighborlists including tables */
232 /* The wall tables (if used) */
234 t_forcetable **wall_tab;
236 /* This mask array of length nn determines whether or not this bit of the
237 * neighbourlists should be computed. Usually all these are true of course,
238 * but not when shells are used. During minimisation all the forces that
239 * include shells are done, then after minimsation is converged the remaining
240 * forces are computed.
242 /* gmx_bool *bMask; */
244 /* The number of charge groups participating in do_force_lowlevel */
246 /* The number of atoms participating in do_force_lowlevel */
248 /* The number of atoms participating in force and constraints */
249 int natoms_force_constr;
250 /* The allocation size of vectors of size natoms_force */
253 /* Twin Range stuff, f_twin has size natoms_force */
258 /* Forces that should not enter into the virial summation:
259 * PPPM/PME/Ewald/posres
261 gmx_bool bF_NoVirSum;
263 int f_novirsum_nalloc;
264 rvec *f_novirsum_alloc;
265 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
266 * points to the normal force vectors wen pressure is not requested.
270 /* Long-range forces and virial for PPPM/PME/Ewald */
274 /* PME/Ewald stuff */
277 ewald_tab_t ewald_table;
281 rvec vir_diag_posres;
284 /* Non bonded Parameter lists */
285 int ntype; /* Number of atom types */
289 /* Energy group pair flags */
292 /* xmdrun flexible constraints */
295 /* Generalized born implicit solvent */
297 /* Generalized born stuff */
298 real gb_epsilon_solvent;
299 /* Table data for GB */
301 /* VdW radius for each atomtype (dim is thus ntype) */
303 /* Effective radius (derived from effective volume) for each type */
305 /* Implicit solvent - surface tension for each atomtype */
306 real *atype_surftens;
307 /* Implicit solvent - radius for GB calculation */
308 real *atype_gb_radius;
309 /* Implicit solvent - overlap for HCT model */
311 /* Generalized born interaction data */
314 /* Table scale for GB */
316 /* Table range for GB */
318 /* GB neighborlists (the sr list will contain for each atom all other atoms
319 * (for use in the SA calculation) and the lr list will contain
320 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
326 /* Inverse square root of the Born radii for implicit solvent */
328 /* Derivatives of the potential with respect to the Born radii */
330 /* Derivatives of the Born radii with respect to coordinates */
333 int nalloc_dadx; /* Allocated size of dadx */
335 /* If > 0 signals Test Particle Insertion,
336 * the value is the number of atoms of the molecule to insert
337 * Only the energy difference due to the addition of the last molecule
338 * should be calculated.
342 /* Neighbor searching stuff */
349 /* QM-MM neighborlists */
352 /* Limit for printing large forces, negative is don't print */
355 /* coarse load balancing time measurement */
360 /* parameter needed for AdResS simulation */
362 gmx_bool badress_tf_full_box;
363 real adress_const_wf;
364 real adress_ex_width;
365 real adress_hy_width;
369 int n_adress_tf_grps;
370 int * adress_tf_table_index;
371 int *adress_group_explicit;
372 t_forcetable * atf_tabs;
373 real adress_ex_forcecap;
374 gmx_bool adress_do_hybridpairs;
376 /* User determined parameters, copied from the inputrec */
387 #define C6(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))]
388 #define C12(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
389 #define BHAMC(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))]
390 #define BHAMA(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
391 #define BHAMB(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]