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) 2011,2014,2015,2016,2018, 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_TOPOLOGY_H
38 #define GMX_TOPOLOGY_TOPOLOGY_H
44 #include "gromacs/math/vectypes.h"
45 #include "gromacs/topology/atoms.h"
46 #include "gromacs/topology/block.h"
47 #include "gromacs/topology/idef.h"
48 #include "gromacs/topology/symtab.h"
49 #include "gromacs/utility/unique_cptr.h"
53 egcTC, egcENER, egcACC, egcFREEZE,
54 egcUser1, egcUser2, egcVCM, egcCompressedX,
58 /* Names corresponding to groups */
59 extern const char *gtypes[egcNR+1];
61 /*! \brief Molecules type data: atoms, interactions and exclusions */
68 /*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
69 gmx_moltype_t &operator=(const gmx_moltype_t &) = delete;
71 /*! \brief Default copy constructor */
72 gmx_moltype_t(const gmx_moltype_t &) = default;
74 char **name; /**< Name of the molecule type */
75 t_atoms atoms; /**< The atoms in this molecule */
76 InteractionLists ilist; /**< Interaction list with local indices */
77 t_block cgs; /**< The charge groups */
78 t_blocka excls; /**< The exclusions */
81 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
84 int type = -1; /**< The molecule type index in mtop.moltype */
85 int nmol = 0; /**< The number of molecules in this block */
86 std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
87 std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
90 /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
91 struct MoleculeBlockIndices
93 int numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
94 int globalAtomStart; /**< Global atom index of the first atom in the block */
95 int globalAtomEnd; /**< Global atom index + 1 of the last atom in the block */
96 int globalResidueStart; /**< Global residue index of the first residue in the block */
97 int residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
98 int moleculeIndexStart; /**< Global molecule indexing starts from this value */
101 typedef struct gmx_groups_t
103 t_grps grps[egcNR]; /* Groups of things */
104 int ngrpname; /* Number of groupnames */
105 char ***grpname; /* Names of the groups */
107 unsigned char *grpnr[egcNR]; /* Group numbers or NULL */
111 * Returns group number of an input group for a given atom.
113 * Returns the group \p type for \p atom in \p group, or 0 if the
114 * entries for all atoms in the group are 0 and the pointer is thus null.
116 * \param[in] group Group to check.
117 * \param[in] type Type of group to check.
118 * \param[in] atom Atom to check if it has an entry.
120 int getGroupType (const gmx_groups_t *group, int type, int atom);
122 /* The global, complete system topology struct, based on molecule types.
123 * This structure should contain no data that is O(natoms) in memory.
125 * TODO: Find a solution for ensuring that the derived data is in sync
126 * with the primary data, possibly by converting to a class.
128 struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
134 //! Name of the topology.
135 char **name = nullptr;
136 //! Force field parameters used.
137 gmx_ffparams_t ffparams;
138 //! Vector of different molecule types.
139 std::vector<gmx_moltype_t> moltype;
140 //! Vector of different molecule blocks.
141 std::vector<gmx_molblock_t> molblock;
142 //! Are there intermolecular interactions?
143 bool bIntermolecularInteractions = false;
145 * List of intermolecular interactions using system wide
146 * atom indices, either NULL or size F_NRE
148 std::unique_ptr<InteractionLists> intermolecular_ilist = nullptr;
149 //! Number of global atoms.
151 //! Parameter for residue numbering.
152 int maxres_renum = 0;
153 //! The maximum residue number in moltype
155 //! Atomtype properties
156 t_atomtypes atomtypes;
157 //! Groups of atoms for different purposes
161 //! Tells whether we have valid molecule indices
162 bool haveMoleculeIndices = false;
163 /*! \brief List of global atom indices of atoms between which
164 * non-bonded interactions must be excluded.
166 std::vector<int> intermolecularExclusionGroup;
168 /* Derived data below */
169 //! Indices for each molblock entry for fast lookup of atom properties
170 std::vector<MoleculeBlockIndices> moleculeBlockIndices;
173 /* The mdrun node-local topology struct, completely written out */
174 typedef struct gmx_localtop_t
176 t_idef idef; /* The interaction function definition */
177 t_atomtypes atomtypes; /* Atomtype properties */
178 t_block cgs; /* The charge groups */
179 t_blocka excls; /* The exclusions */
182 /* The old topology struct, completely written out, used in analysis tools */
183 typedef struct t_topology
185 char **name; /* Name of the topology */
186 t_idef idef; /* The interaction function definition */
187 t_atoms atoms; /* The atoms */
188 t_atomtypes atomtypes; /* Atomtype properties */
189 t_block cgs; /* The charge groups */
190 t_block mols; /* The molecules */
191 gmx_bool bIntermolecularInteractions; /* Inter.mol. int. ? */
192 t_blocka excls; /* The exclusions */
193 t_symtab symtab; /* The symbol table */
196 void init_top(t_topology *top);
197 void done_gmx_groups_t(gmx_groups_t *g);
198 void done_top(t_topology *top);
199 // Frees both t_topology and gmx_mtop_t when the former has been created from
201 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
203 * Properly initialize local topology.
205 * \param[in] top Pointer to topology to initialize.
207 void init_localtop(gmx_localtop_t *top);
209 * Properly clear up local topology,
211 * \param[in] top Pointer to topology to clear up.
213 void done_localtop(gmx_localtop_t *top);
214 void done_and_sfree_localtop(gmx_localtop_t *top);
216 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
217 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
218 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop);
219 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
220 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
222 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
223 gmx_bool bShowNumbers, gmx_bool bShowParameters);
224 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
225 gmx_bool bShowNumbers, gmx_bool bShowParameters);
227 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
228 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
229 int natoms0, int natoms1);
231 //! Deleter for gmx_localtop_t, needed until it has a proper destructor.
232 using ExpandedTopologyPtr = gmx::unique_cptr<gmx_localtop_t, done_and_sfree_localtop>;
234 void copy_moltype(const gmx_moltype_t *src, gmx_moltype_t *dst);