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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 gmx_bool use_cpu_acceleration;
202 /* Interaction for calculated in kernels. In many cases this is similar to
203 * the electrostatics settings in the inputrecord, but the difference is that
204 * these variables always specify the actual interaction in the kernel - if
205 * we are tabulating reaction-field the inputrec will say reaction-field, but
206 * the kernel interaction will say cubic-spline-table. To be safe we also
207 * have a kernel-specific setting for the modifiers - if the interaction is
208 * tabulated we already included the inputrec modification there, so the kernel
209 * modification setting will say 'none' in that case.
211 int nbkernel_elec_interaction;
212 int nbkernel_vdw_interaction;
213 int nbkernel_elec_modifier;
214 int nbkernel_vdw_modifier;
216 /* Use special N*N kernels? */
218 /* Private work data */
220 void *AllvsAll_workgb;
223 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
225 real rlist, rlistlong;
227 /* Dielectric constant resp. multiplication factor for charges */
229 real epsilon_r, epsilon_rf, epsfac;
231 /* Constants for reaction fields */
232 real kappa, k_rf, c_rf;
234 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
239 /* Dispersion correction stuff */
242 /* The shift of the shift or user potentials */
244 real enershifttwelve;
245 /* Integrated differces for energy and virial with cut-off functions */
250 /* Constant for long range dispersion correction (average dispersion)
251 * for topology A/B ([0]/[1]) */
253 /* Constant for long range repulsion term. Relative difference of about
254 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
264 /* The normal tables are in the nblists struct(s) below */
265 t_forcetable tab14; /* for 1-4 interactions only */
267 /* PPPM & Shifting stuff */
268 int coulomb_modifier;
269 real rcoulomb_switch, rcoulomb;
275 real rvdw_switch, rvdw;
292 /* solvent_opt contains the enum for the most common solvent
293 * in the system, which will be optimized.
294 * It can be set to esolNO to disable all water optimization */
298 gmx_bool bExcl_IntraCGAll_InterCGNone;
299 cginfo_mb_t *cginfo_mb;
305 /* The neighborlists including tables */
310 int cutoff_scheme; /* group- or Verlet-style cutoff */
311 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
312 nonbonded_verlet_t *nbv;
314 /* The wall tables (if used) */
316 t_forcetable **wall_tab;
318 /* The number of charge groups participating in do_force_lowlevel */
320 /* The number of atoms participating in do_force_lowlevel */
322 /* The number of atoms participating in force and constraints */
323 int natoms_force_constr;
324 /* The allocation size of vectors of size natoms_force */
327 /* Twin Range stuff, f_twin has size natoms_force */
332 /* Forces that should not enter into the virial summation:
333 * PPPM/PME/Ewald/posres
335 gmx_bool bF_NoVirSum;
337 int f_novirsum_nalloc;
338 rvec *f_novirsum_alloc;
339 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
340 * points to the normal force vectors wen pressure is not requested.
344 /* Long-range forces and virial for PPPM/PME/Ewald */
348 /* PME/Ewald stuff */
351 ewald_tab_t ewald_table;
355 rvec vir_diag_posres;
358 /* Non bonded Parameter lists */
359 int ntype; /* Number of atom types */
363 /* Energy group pair flags */
366 /* Shell molecular dynamics flexible constraints */
369 /* Generalized born implicit solvent */
371 /* Generalized born stuff */
372 real gb_epsilon_solvent;
373 /* Table data for GB */
375 /* VdW radius for each atomtype (dim is thus ntype) */
377 /* Effective radius (derived from effective volume) for each type */
379 /* Implicit solvent - surface tension for each atomtype */
380 real *atype_surftens;
381 /* Implicit solvent - radius for GB calculation */
382 real *atype_gb_radius;
383 /* Implicit solvent - overlap for HCT model */
385 /* Generalized born interaction data */
388 /* Table scale for GB */
390 /* Table range for GB */
392 /* GB neighborlists (the sr list will contain for each atom all other atoms
393 * (for use in the SA calculation) and the lr list will contain
394 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
400 /* Inverse square root of the Born radii for implicit solvent */
402 /* Derivatives of the potential with respect to the Born radii */
404 /* Derivatives of the Born radii with respect to coordinates */
407 int nalloc_dadx; /* Allocated size of dadx */
409 /* If > 0 signals Test Particle Insertion,
410 * the value is the number of atoms of the molecule to insert
411 * Only the energy difference due to the addition of the last molecule
412 * should be calculated.
416 /* Neighbor searching stuff */
423 /* QM-MM neighborlists */
426 /* Limit for printing large forces, negative is don't print */
429 /* coarse load balancing time measurement */
434 /* parameter needed for AdResS simulation */
436 gmx_bool badress_tf_full_box;
437 real adress_const_wf;
438 real adress_ex_width;
439 real adress_hy_width;
443 int n_adress_tf_grps;
444 int * adress_tf_table_index;
445 int *adress_group_explicit;
446 t_forcetable * atf_tabs;
447 real adress_ex_forcecap;
448 gmx_bool adress_do_hybridpairs;
450 /* User determined parameters, copied from the inputrec */
460 /* Thread local force and energy data */
461 /* FIXME move to bonded_thread_data_t */
467 /* Exclusion load distribution over the threads */
471 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
472 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
473 * in the code, but beware if you are using these macros externally.
475 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
476 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
477 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
478 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
479 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]