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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 t_ilist ilist[F_NRE]; /**< 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 char **name; /* Name of the topology */
135 gmx_ffparams_t ffparams;
136 std::vector<gmx_moltype_t> moltype;
137 std::vector<gmx_molblock_t> molblock;
138 gmx_bool bIntermolecularInteractions; /* Are there intermolecular
140 t_ilist *intermolecular_ilist; /* List of intermolecular interactions
141 * using system wide atom indices,
142 * either NULL or size F_NRE */
144 int maxres_renum; /* Parameter for residue numbering */
145 int maxresnr; /* The maximum residue number in moltype */
146 t_atomtypes atomtypes; /* Atomtype properties */
147 gmx_groups_t groups; /* Groups of atoms for different purposes */
148 t_symtab symtab; /* The symbol table */
149 bool haveMoleculeIndices; /* Tells whether we have valid molecule indices */
152 std::vector<MoleculeBlockIndices> moleculeBlockIndices; /* Indices for each molblock entry for fast lookup of atom properties */
155 /* The mdrun node-local topology struct, completely written out */
156 typedef struct gmx_localtop_t
158 t_idef idef; /* The interaction function definition */
159 t_atomtypes atomtypes; /* Atomtype properties */
160 t_block cgs; /* The charge groups */
161 t_blocka excls; /* The exclusions */
164 /* The old topology struct, completely written out, used in analysis tools */
165 typedef struct t_topology
167 char **name; /* Name of the topology */
168 t_idef idef; /* The interaction function definition */
169 t_atoms atoms; /* The atoms */
170 t_atomtypes atomtypes; /* Atomtype properties */
171 t_block cgs; /* The charge groups */
172 t_block mols; /* The molecules */
173 gmx_bool bIntermolecularInteractions; /* Inter.mol. int. ? */
174 t_blocka excls; /* The exclusions */
175 t_symtab symtab; /* The symbol table */
178 void init_mtop(gmx_mtop_t *mtop);
179 void init_top(t_topology *top);
180 void done_gmx_groups_t(gmx_groups_t *g);
181 void done_top(t_topology *top);
182 // Frees both t_topology and gmx_mtop_t when the former has been created from
184 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
185 void done_localtop(gmx_localtop_t *top);
186 void done_and_sfree_localtop(gmx_localtop_t *top);
188 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
189 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
190 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop);
191 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
192 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
194 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
195 gmx_bool bShowNumbers, gmx_bool bShowParameters);
196 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
197 gmx_bool bShowNumbers, gmx_bool bShowParameters);
199 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
200 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
201 int natoms0, int natoms1);
203 //! Deleter for gmx_localtop_t, needed until it has a proper destructor.
204 using ExpandedTopologyPtr = gmx::unique_cptr<gmx_localtop_t, done_and_sfree_localtop>;