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37 #ifndef GMX_TOPOLOGY_IDEF_H
38 #define GMX_TOPOLOGY_IDEF_H
40 #include "../legacyheaders/types/simple.h"
47 /* check kernel/toppush.c when you change these numbers */
49 #define MAXFORCEPARAM 12
54 typedef atom_id t_iatom;
56 /* this MUST correspond to the
57 t_interaction_function[F_NRE] in gmxlib/ifunc.c */
139 F_VTEMP_NOLONGERUSED,
149 F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
150 F_NRE /* This number is for the total number of energies */
153 #define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_FBPOSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))
155 /* A macro for checking if ftype is an explicit pair-listed LJ or COULOMB
157 * bonded LJ (usually 1-4), or special listed non-bonded for FEP.
159 #define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
161 typedef union t_iparams
163 /* Some parameters have A and B values for free energy calculations.
164 * The B values are not used for regular simulations of course.
165 * Free Energy for nonbondeds can be computed by changing the atom type.
166 * The harmonic type is used for all harmonic potentials:
167 * bonds, angles and improper dihedrals
173 real rA, krA, rB, krB;
176 real klinA, aA, klinB, aB;
179 real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
181 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
192 real r1e, r2e, r3e, krt;
195 real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
204 real alpha, drcut, khyp;
207 real al_x, al_y, al_z, rOH, rHH, rOD;
210 real a, alpha1, alpha2, rfac;
216 real c6A, c12A, c6B, c12B;
219 real fqq, qi, qj, c6, c12;
222 real qi, qj, c6, c12;
224 /* Proper dihedrals can not have different multiplicity when
225 * doing free energy calculations, because the potential would not
226 * be periodic anymore.
229 real phiA, cpA; int mult; real phiB, cpB;
234 /* Settle can not be used for Free energy calculations of water bond geometry.
235 * Use shake (or lincs) instead if you have to change the water bonds.
241 real b0A, cbA, betaA, b0B, cbB, betaB;
244 real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
247 real pos0[DIM], r, k; int geom;
250 real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
253 real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
256 real a, b, c, d, e, f;
261 /* NOTE: npair is only set after reading the tpx file */
263 real low, up1, up2, kfac; int type, label, npair;
266 real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
269 int ex, power, label; real c, obs, kfac;
272 int table; real kA; real kB;
275 real sar, st, pi, gbr, bmlt;
281 real buf[MAXFORCEPARAM];
282 } generic; /* Conversion */
285 typedef int t_functype;
288 * The nonperturbed/perturbed interactions are now separated (sorted) in the
289 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
290 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
293 typedef struct t_ilist
302 * The struct t_ilist defines a list of atoms with their interactions.
303 * General field description:
305 * the size (nr elements) of the interactions array (iatoms[]).
307 * specifies which atoms are involved in an interaction of a certain
308 * type. The layout of this array is as follows:
310 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
311 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
312 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
314 * So for interaction type type1 3 atoms are needed, and for type2 and
315 * type3 only 2. The type identifier is used to select the function to
316 * calculate the interaction and its actual parameters. This type
317 * identifier is an index in a params[] and functype[] array.
322 real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
323 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
326 typedef struct gmx_cmap_t
328 int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
329 int grid_spacing; /* Grid spacing */
330 gmx_cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
334 typedef struct gmx_ffparams_t
338 t_functype *functype;
340 double reppow; /* The repulsion power for VdW: C12*r^-reppow */
341 real fudgeQQ; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
342 gmx_cmap_t cmap_grid; /* The dihedral correction maps */
346 ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
349 typedef struct t_idef
353 t_functype *functype;
356 gmx_cmap_t cmap_grid;
357 t_iparams *iparams_posres, *iparams_fbposres;
358 int iparams_posres_nalloc, iparams_fbposres_nalloc;
363 int *il_thread_division;
364 int il_thread_division_nalloc;
368 * The struct t_idef defines all the interactions for the complete
369 * simulation. The structure is setup in such a way that the multinode
370 * version of the program can use it as easy as the single node version.
371 * General field description:
373 * defines the number of elements in functype[] and param[].
375 * the node id (if parallel machines)
377 * the number of atomtypes
378 * t_functype *functype
379 * array of length ntypes, defines for every force type what type of
380 * function to use. Every "bond" with the same function but different
381 * force parameters is a different force type. The type identifier in the
382 * forceatoms[] array is an index in this array.
384 * array of length ntypes, defines the parameters for every interaction
385 * type. The type identifier in the actual interaction list
386 * (ilist[ftype].iatoms[]) is an index in this array.
387 * gmx_cmap_t cmap_grid
388 * the grid for the dihedral pair correction maps.
389 * t_iparams *iparams_posres, *iparams_fbposres
390 * defines the parameters for position restraints only.
391 * Position restraints are the only interactions that have different
392 * parameters (reference positions) for different molecules
393 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
395 * The list of interactions for each type. Note that some,
396 * such as LJ and COUL will have 0 entries.
398 * The state of the sorting of il, values are provided above.
400 * The number of threads used to set il_thread_division.
401 * int *il_thread_division
402 * The division of the normal bonded interactions of threads.
403 * il_thread_division[ftype*(nthreads+1)+t] contains an index
404 * into il[ftype].iatoms; thread th operates on t=th to t=th+1.
405 * int il_thread_division_nalloc
406 * The allocated size of il_thread_division,
407 * should be at least F_NRE*(nthreads+1).