2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
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; }
252 /* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
253 * The nr_nonperturbed functionality needs to be ported.
255 * Remove t_ilist and remove templating on list type
256 * in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
260 * The structs InteractionList and t_ilist defines a list of atoms with their interactions.
261 * General field description:
263 * the size (nr elements) of the interactions array (iatoms[]).
265 * specifies which atoms are involved in an interaction of a certain
266 * type. The layout of this array is as follows:
268 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
269 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
270 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
272 * So for interaction type type1 3 atoms are needed, and for type2 and
273 * type3 only 2. The type identifier is used to select the function to
274 * calculate the interaction and its actual parameters. This type
275 * identifier is an index in a params[] and functype[] array.
278 /*! \brief Type for returning a list of InteractionList references
280 * TODO: Remove when the function type is made part of InteractionList
282 struct InteractionListHandle
284 const int functionType; //!< The function type
285 const std::vector<int>& iatoms; //!< Reference to interaction list
288 /*! \brief Returns a list of all non-empty InteractionList entries with any of the interaction flags in \p flags set
290 * \param[in] ilists Set of interaction lists
291 * \param[in] flags Bit mask with one or more IF_... bits set
293 static inline std::vector<InteractionListHandle> extractILists(const InteractionLists& ilists, int flags)
295 std::vector<InteractionListHandle> handles;
296 for (size_t ftype = 0; ftype < ilists.size(); ftype++)
298 if ((interaction_function[ftype].flags & flags) && ilists[ftype].size() > 0)
300 handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
306 /*! \brief Returns the stride for the iatoms array in \p ilistHandle
308 * \param[in] ilistHandle The ilist to return the stride for
310 static inline int ilistStride(const InteractionListHandle& ilistHandle)
312 return 1 + NRAL(ilistHandle.functionType);
315 struct gmx_cmapdata_t
317 std::vector<real> cmap; /* Has length 4*grid_spacing*grid_spacing, */
318 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
323 int grid_spacing = 0; /* Grid spacing */
324 std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
336 typedef struct t_idef
340 t_functype* functype;
343 gmx_cmap_t* cmap_grid;
344 t_iparams * iparams_posres, *iparams_fbposres;
345 int iparams_posres_nalloc, iparams_fbposres_nalloc;
352 * The struct t_idef defines all the interactions for the complete
353 * simulation. The structure is setup in such a way that the multinode
354 * version of the program can use it as easy as the single node version.
355 * General field description:
357 * defines the number of elements in functype[] and param[].
359 * the node id (if parallel machines)
361 * the number of atomtypes
362 * t_functype *functype
363 * array of length ntypes, defines for every force type what type of
364 * function to use. Every "bond" with the same function but different
365 * force parameters is a different force type. The type identifier in the
366 * forceatoms[] array is an index in this array.
368 * array of length ntypes, defines the parameters for every interaction
369 * type. The type identifier in the actual interaction list
370 * (ilist[ftype].iatoms[]) is an index in this array.
371 * gmx_cmap_t cmap_grid
372 * the grid for the dihedral pair correction maps.
373 * t_iparams *iparams_posres, *iparams_fbposres
374 * defines the parameters for position restraints only.
375 * Position restraints are the only interactions that have different
376 * parameters (reference positions) for different molecules
377 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
379 * The list of interactions for each type. Note that some,
380 * such as LJ and COUL will have 0 entries.
382 * The state of the sorting of il, values are provided above.
385 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams* iparams);
386 void pr_ilist(FILE* fp,
389 const t_functype* functype,
390 const InteractionList& ilist,
391 gmx_bool bShowNumbers,
392 gmx_bool bShowParameters,
393 const t_iparams* iparams);
394 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
397 * Properly initialize idef struct.
399 * \param[in] idef Pointer to idef struct to initialize.
401 void init_idef(t_idef* idef);
404 * Properly clean up idef struct.
406 * \param[in] idef Pointer to idef struct to clean up.
408 void done_idef(t_idef* idef);
410 void copy_ilist(const t_ilist* src, t_ilist* dst);