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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 {
51 /* Some parameters have A and B values for free energy calculations.
52 * The B values are not used for regular simulations of course.
53 * Free Energy for nonbondeds can be computed by changing the atom type.
54 * The harmonic type is used for all harmonic potentials:
55 * bonds, angles and improper dihedrals
63 real rA, krA, rB, krB;
67 real klinA, aA, klinB, aB;
71 real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
73 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
88 real r1e, r2e, r3e, krt;
92 real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
104 real alpha, drcut, khyp;
108 real al_x, al_y, al_z, rOH, rHH, rOD;
112 real a, alpha1, alpha2, rfac;
120 real c6A, c12A, c6B, c12B;
124 real fqq, qi, qj, c6, c12;
128 real qi, qj, c6, c12;
130 /* Proper dihedrals can not have different multiplicity when
131 * doing free energy calculations, because the potential would not
132 * be periodic anymore.
144 /* Settle can not be used for Free energy calculations of water bond geometry.
145 * Use shake (or lincs) instead if you have to change the water bonds.
153 real b0A, cbA, betaA, b0B, cbB, betaB;
157 real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
161 real pos0[DIM], r, k;
166 real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
170 real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
174 real a, b, c, d, e, f;
181 /* NOTE: npair is only set after reading the tpx file */
184 real low, up1, up2, kfac;
185 int type, label, npair;
189 real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
193 int ex, power, label;
208 real buf[MAXFORCEPARAM];
209 } generic; /* Conversion */
212 typedef int t_functype;
214 /* List of listed interactions, see description further down.
216 * TODO: Consider storing the function type as well.
217 * TODO: Consider providing per interaction access.
219 struct InteractionList
221 /* Returns the total number of elements in iatoms */
222 int size() const { return gmx::ssize(iatoms); }
224 /* List of interactions, see explanation further down */
225 std::vector<int> iatoms;
228 /* List of interaction lists, one list for each interaction type
230 * TODO: Consider only including entries in use instead of all F_NRE
232 typedef std::array<InteractionList, F_NRE> InteractionLists;
234 /* Deprecated list of listed interactions.
236 * The nonperturbed/perturbed interactions are now separated (sorted) in the
237 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
238 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
243 /* Returns the total number of elements in iatoms */
244 int size() const { return nr; }
251 /* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
252 * The nr_nonperturbed functionality needs to be ported.
254 * Remove t_ilist and remove templating on list type
255 * in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
259 * The structs InteractionList and t_ilist defines a list of atoms with their interactions.
260 * General field description:
262 * the size (nr elements) of the interactions array (iatoms[]).
264 * specifies which atoms are involved in an interaction of a certain
265 * type. The layout of this array is as follows:
267 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
268 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
269 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
271 * So for interaction type type1 3 atoms are needed, and for type2 and
272 * type3 only 2. The type identifier is used to select the function to
273 * calculate the interaction and its actual parameters. This type
274 * identifier is an index in a params[] and functype[] array.
277 /*! \brief Type for returning a list of InteractionList references
279 * TODO: Remove when the function type is made part of InteractionList
281 struct InteractionListHandle
283 const int functionType; //!< The function type
284 const std::vector<int>& iatoms; //!< Reference to interaction list
287 /*! \brief Returns a list of all non-empty InteractionList entries with any of the interaction flags in \p flags set
289 * \param[in] ilists Set of interaction lists
290 * \param[in] flags Bit mask with one or more IF_... bits set
292 static inline std::vector<InteractionListHandle> extractILists(const InteractionLists& ilists, int flags)
294 std::vector<InteractionListHandle> handles;
295 for (size_t ftype = 0; ftype < ilists.size(); ftype++)
297 if ((interaction_function[ftype].flags & flags) && ilists[ftype].size() > 0)
299 handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
305 /*! \brief Returns the stride for the iatoms array in \p ilistHandle
307 * \param[in] ilistHandle The ilist to return the stride for
309 static inline int ilistStride(const InteractionListHandle& ilistHandle)
311 return 1 + NRAL(ilistHandle.functionType);
314 struct gmx_cmapdata_t
316 std::vector<real> cmap; /* Has length 4*grid_spacing*grid_spacing, */
317 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
322 int grid_spacing = 0; /* Grid spacing */
323 std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
335 typedef struct t_idef
339 t_functype* functype;
342 gmx_cmap_t* cmap_grid;
343 t_iparams * iparams_posres, *iparams_fbposres;
344 int iparams_posres_nalloc, iparams_fbposres_nalloc;
347 /* The number of non-perturbed interactions at the start of each entry in il */
348 int numNonperturbedInteractions[F_NRE];
353 * The struct t_idef defines all the interactions for the complete
354 * simulation. The structure is setup in such a way that the multinode
355 * version of the program can use it as easy as the single node version.
356 * General field description:
358 * defines the number of elements in functype[] and param[].
360 * the node id (if parallel machines)
362 * the number of atomtypes
363 * t_functype *functype
364 * array of length ntypes, defines for every force type what type of
365 * function to use. Every "bond" with the same function but different
366 * force parameters is a different force type. The type identifier in the
367 * forceatoms[] array is an index in this array.
369 * array of length ntypes, defines the parameters for every interaction
370 * type. The type identifier in the actual interaction list
371 * (ilist[ftype].iatoms[]) is an index in this array.
372 * gmx_cmap_t cmap_grid
373 * the grid for the dihedral pair correction maps.
374 * t_iparams *iparams_posres, *iparams_fbposres
375 * defines the parameters for position restraints only.
376 * Position restraints are the only interactions that have different
377 * parameters (reference positions) for different molecules
378 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
380 * The list of interactions for each type. Note that some,
381 * such as LJ and COUL will have 0 entries.
383 * The state of the sorting of il, values are provided above.
391 void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams);
392 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams);
393 void pr_ilist(FILE* fp,
396 const t_functype* functype,
397 const InteractionList& ilist,
398 gmx_bool bShowNumbers,
399 gmx_bool bShowParameters,
400 const t_iparams* iparams);
401 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
404 * Properly initialize idef struct.
406 * \param[in] idef Pointer to idef struct to initialize.
408 void init_idef(t_idef* idef);
411 * Properly clean up idef struct.
413 * \param[in] idef Pointer to idef struct to clean up.
415 void done_idef(t_idef* idef);
417 void copy_ilist(const t_ilist* src, t_ilist* dst);