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37 #ifndef GMX_TOPOLOGY_IDEF_H
38 #define GMX_TOPOLOGY_IDEF_H
45 #include "gromacs/math/vectypes.h"
46 #include "gromacs/topology/ifunc.h"
47 #include "gromacs/utility/basedefinitions.h"
48 #include "gromacs/utility/real.h"
50 typedef union t_iparams
52 /* Some parameters have A and B values for free energy calculations.
53 * The B values are not used for regular simulations of course.
54 * Free Energy for nonbondeds can be computed by changing the atom type.
55 * The harmonic type is used for all harmonic potentials:
56 * bonds, angles and improper dihedrals
62 real rA, krA, rB, krB;
65 real klinA, aA, klinB, aB;
68 real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
70 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
81 real r1e, r2e, r3e, krt;
84 real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
93 real alpha, drcut, khyp;
96 real al_x, al_y, al_z, rOH, rHH, rOD;
99 real a, alpha1, alpha2, rfac;
105 real c6A, c12A, c6B, c12B;
108 real fqq, qi, qj, c6, c12;
111 real qi, qj, c6, c12;
113 /* Proper dihedrals can not have different multiplicity when
114 * doing free energy calculations, because the potential would not
115 * be periodic anymore.
118 real phiA, cpA; int mult; real phiB, cpB;
123 /* Settle can not be used for Free energy calculations of water bond geometry.
124 * Use shake (or lincs) instead if you have to change the water bonds.
130 real b0A, cbA, betaA, b0B, cbB, betaB;
133 real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
136 real pos0[DIM], r, k; int geom;
139 real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
142 real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
145 real a, b, c, d, e, f;
150 /* NOTE: npair is only set after reading the tpx file */
152 real low, up1, up2, kfac; int type, label, npair;
155 real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
158 int ex, power, label; real c, obs, kfac;
161 int table; real kA; real kB;
167 real buf[MAXFORCEPARAM];
168 } generic; /* Conversion */
171 typedef int t_functype;
173 /* List of listed interactions, see description further down.
175 * TODO: Consider storing the function type as well.
176 * TODO: Consider providing per interaction access.
178 struct InteractionList
180 /* Returns the total number of elements in iatoms */
183 return iatoms.size();
186 /* List of interactions, see explanation further down */
187 std::vector<int> iatoms;
190 /* List of interaction lists, one list for each interaction type
192 * TODO: Consider only including entries in use instead of all F_NRE
194 typedef std::array<InteractionList, F_NRE> InteractionLists;
196 /* Deprecated list of listed interactions.
198 * The nonperturbed/perturbed interactions are now separated (sorted) in the
199 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
200 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
205 /* Returns the total number of elements in iatoms */
217 /* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
218 * The nr_nonperturbed functionality needs to be ported.
220 * Remove t_ilist and remove templating on list type
221 * in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
225 * The structs InteractionList and t_ilist defines a list of atoms with their interactions.
226 * General field description:
228 * the size (nr elements) of the interactions array (iatoms[]).
230 * specifies which atoms are involved in an interaction of a certain
231 * type. The layout of this array is as follows:
233 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
234 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
235 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
237 * So for interaction type type1 3 atoms are needed, and for type2 and
238 * type3 only 2. The type identifier is used to select the function to
239 * calculate the interaction and its actual parameters. This type
240 * identifier is an index in a params[] and functype[] array.
245 real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
246 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
249 typedef struct gmx_cmap_t
251 int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
252 int grid_spacing; /* Grid spacing */
253 gmx_cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
257 typedef struct gmx_ffparams_t
261 t_functype *functype;
263 double reppow; /* The repulsion power for VdW: C12*r^-reppow */
264 real fudgeQQ; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
265 gmx_cmap_t cmap_grid; /* The dihedral correction maps */
269 ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
272 typedef struct t_idef
276 t_functype *functype;
279 gmx_cmap_t cmap_grid;
280 t_iparams *iparams_posres, *iparams_fbposres;
281 int iparams_posres_nalloc, iparams_fbposres_nalloc;
288 * The struct t_idef defines all the interactions for the complete
289 * simulation. The structure is setup in such a way that the multinode
290 * version of the program can use it as easy as the single node version.
291 * General field description:
293 * defines the number of elements in functype[] and param[].
295 * the node id (if parallel machines)
297 * the number of atomtypes
298 * t_functype *functype
299 * array of length ntypes, defines for every force type what type of
300 * function to use. Every "bond" with the same function but different
301 * force parameters is a different force type. The type identifier in the
302 * forceatoms[] array is an index in this array.
304 * array of length ntypes, defines the parameters for every interaction
305 * type. The type identifier in the actual interaction list
306 * (ilist[ftype].iatoms[]) is an index in this array.
307 * gmx_cmap_t cmap_grid
308 * the grid for the dihedral pair correction maps.
309 * t_iparams *iparams_posres, *iparams_fbposres
310 * defines the parameters for position restraints only.
311 * Position restraints are the only interactions that have different
312 * parameters (reference positions) for different molecules
313 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
315 * The list of interactions for each type. Note that some,
316 * such as LJ and COUL will have 0 entries.
318 * The state of the sorting of il, values are provided above.
321 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
322 void pr_ilist(FILE *fp, int indent, const char *title,
323 const t_functype *functype, const InteractionList &ilist,
324 gmx_bool bShowNumbers,
325 gmx_bool bShowParameters, const t_iparams *iparams);
326 void pr_ffparams(FILE *fp, int indent, const char *title,
327 const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
328 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
329 gmx_bool bShowNumbers, gmx_bool bShowParameters);