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37 #ifndef GMX_TOPOLOGY_IDEF_H
38 #define GMX_TOPOLOGY_IDEF_H
42 #include "gromacs/math/vectypes.h"
43 #include "gromacs/utility/basedefinitions.h"
44 #include "gromacs/utility/real.h"
46 /* check kernel/toppush.c when you change these numbers */
48 #define MAXFORCEPARAM 12
55 /* this MUST correspond to the
56 t_interaction_function[F_NRE] in gmxlib/ifunc.c */
90 F_NPSOLVATION_NOLONGERUSED,
98 F_BHAM_LR_NOLONGERUSED,
101 F_COUL_LR_NOLONGERUSED,
138 F_VTEMP_NOLONGERUSED,
148 F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
149 F_NRE /* This number is for the total number of energies */
152 #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)))
154 typedef union t_iparams
156 /* Some parameters have A and B values for free energy calculations.
157 * The B values are not used for regular simulations of course.
158 * Free Energy for nonbondeds can be computed by changing the atom type.
159 * The harmonic type is used for all harmonic potentials:
160 * bonds, angles and improper dihedrals
166 real rA, krA, rB, krB;
169 real klinA, aA, klinB, aB;
172 real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
174 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
185 real r1e, r2e, r3e, krt;
188 real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
197 real alpha, drcut, khyp;
200 real al_x, al_y, al_z, rOH, rHH, rOD;
203 real a, alpha1, alpha2, rfac;
209 real c6A, c12A, c6B, c12B;
212 real fqq, qi, qj, c6, c12;
215 real qi, qj, c6, c12;
217 /* Proper dihedrals can not have different multiplicity when
218 * doing free energy calculations, because the potential would not
219 * be periodic anymore.
222 real phiA, cpA; int mult; real phiB, cpB;
227 /* Settle can not be used for Free energy calculations of water bond geometry.
228 * Use shake (or lincs) instead if you have to change the water bonds.
234 real b0A, cbA, betaA, b0B, cbB, betaB;
237 real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
240 real pos0[DIM], r, k; int geom;
243 real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
246 real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
249 real a, b, c, d, e, f;
254 /* NOTE: npair is only set after reading the tpx file */
256 real low, up1, up2, kfac; int type, label, npair;
259 real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
262 int ex, power, label; real c, obs, kfac;
265 int table; real kA; real kB;
271 real buf[MAXFORCEPARAM];
272 } generic; /* Conversion */
275 typedef int t_functype;
278 * The nonperturbed/perturbed interactions are now separated (sorted) in the
279 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
280 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
283 typedef struct t_ilist
292 * The struct t_ilist defines a list of atoms with their interactions.
293 * General field description:
295 * the size (nr elements) of the interactions array (iatoms[]).
297 * specifies which atoms are involved in an interaction of a certain
298 * type. The layout of this array is as follows:
300 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
301 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
302 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
304 * So for interaction type type1 3 atoms are needed, and for type2 and
305 * type3 only 2. The type identifier is used to select the function to
306 * calculate the interaction and its actual parameters. This type
307 * identifier is an index in a params[] and functype[] array.
312 real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
313 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
316 typedef struct gmx_cmap_t
318 int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
319 int grid_spacing; /* Grid spacing */
320 gmx_cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
324 typedef struct gmx_ffparams_t
328 t_functype *functype;
330 double reppow; /* The repulsion power for VdW: C12*r^-reppow */
331 real fudgeQQ; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
332 gmx_cmap_t cmap_grid; /* The dihedral correction maps */
336 ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
339 typedef struct t_idef
343 t_functype *functype;
346 gmx_cmap_t cmap_grid;
347 t_iparams *iparams_posres, *iparams_fbposres;
348 int iparams_posres_nalloc, iparams_fbposres_nalloc;
355 * The struct t_idef defines all the interactions for the complete
356 * simulation. The structure is setup in such a way that the multinode
357 * version of the program can use it as easy as the single node version.
358 * General field description:
360 * defines the number of elements in functype[] and param[].
362 * the node id (if parallel machines)
364 * the number of atomtypes
365 * t_functype *functype
366 * array of length ntypes, defines for every force type what type of
367 * function to use. Every "bond" with the same function but different
368 * force parameters is a different force type. The type identifier in the
369 * forceatoms[] array is an index in this array.
371 * array of length ntypes, defines the parameters for every interaction
372 * type. The type identifier in the actual interaction list
373 * (ilist[ftype].iatoms[]) is an index in this array.
374 * gmx_cmap_t cmap_grid
375 * the grid for the dihedral pair correction maps.
376 * t_iparams *iparams_posres, *iparams_fbposres
377 * defines the parameters for position restraints only.
378 * Position restraints are the only interactions that have different
379 * parameters (reference positions) for different molecules
380 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
382 * The list of interactions for each type. Note that some,
383 * such as LJ and COUL will have 0 entries.
385 * The state of the sorting of il, values are provided above.
388 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
389 void pr_ilist(FILE *fp, int indent, const char *title,
390 const t_functype *functype, const t_ilist *ilist,
391 gmx_bool bShowNumbers,
392 gmx_bool bShowParameters, const t_iparams *iparams);
393 void pr_ffparams(FILE *fp, int indent, const char *title,
394 const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
395 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
396 gmx_bool bShowNumbers, gmx_bool bShowParameters);