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37 #ifndef GMX_TOPOLOGY_TOPOLOGY_H
38 #define GMX_TOPOLOGY_TOPOLOGY_H
40 #include "../math/vectypes.h"
51 egcTC, egcENER, egcACC, egcFREEZE,
52 egcUser1, egcUser2, egcVCM, egcCompressedX,
57 typedef struct gmx_moltype_t
59 char **name; /* Name of the molecule type */
60 t_atoms atoms; /* The atoms */
62 t_block cgs; /* The charge groups */
63 t_blocka excls; /* The exclusions */
66 typedef struct gmx_molblock_t
68 int type; /* The molcule type index in mtop.moltype */
69 int nmol; /* The number of molecules in this block */
70 int natoms_mol; /* The number of atoms in one molecule */
71 int nposres_xA; /* The number of posres coords for top A */
72 rvec *posres_xA; /* The posres coords for top A */
73 int nposres_xB; /* The number of posres coords for top B */
74 rvec *posres_xB; /* The posres coords for top B */
77 typedef struct gmx_groups_t
79 t_grps grps[egcNR]; /* Groups of things */
80 int ngrpname; /* Number of groupnames */
81 char ***grpname; /* Names of the groups */
83 unsigned char *grpnr[egcNR]; /* Group numbers or NULL */
86 /* This macro gives the group number of group type egc for atom i.
87 * This macro is useful, since the grpnr pointers are NULL
88 * for group types that have all entries 0.
90 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
92 /* The global, complete system topology struct, based on molecule types.
93 This structure should contain no data that is O(natoms) in memory. */
94 typedef struct gmx_mtop_t
96 char **name; /* Name of the topology */
97 gmx_ffparams_t ffparams;
99 gmx_moltype_t *moltype;
101 gmx_molblock_t *molblock;
103 int maxres_renum; /* Parameter for residue numbering */
104 int maxresnr; /* The maximum residue number in moltype */
105 t_atomtypes atomtypes; /* Atomtype properties */
106 t_block mols; /* The molecules */
108 t_symtab symtab; /* The symbol table */
111 /* The mdrun node-local topology struct, completely written out */
112 typedef struct gmx_localtop_t
114 t_idef idef; /* The interaction function definition */
115 t_atomtypes atomtypes; /* Atomtype properties */
116 t_block cgs; /* The charge groups */
117 t_blocka excls; /* The exclusions */
120 /* The old topology struct, completely written out, used in analysis tools */
121 typedef struct t_topology
123 char **name; /* Name of the topology */
124 t_idef idef; /* The interaction function definition */
125 t_atoms atoms; /* The atoms */
126 t_atomtypes atomtypes; /* Atomtype properties */
127 t_block cgs; /* The charge groups */
128 t_block mols; /* The molecules */
129 t_blocka excls; /* The exclusions */
130 t_symtab symtab; /* The symbol table */
133 void init_mtop(gmx_mtop_t *mtop);
134 void init_top(t_topology *top);
135 void done_moltype(gmx_moltype_t *molt);
136 void done_molblock(gmx_molblock_t *molb);
137 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
138 void done_top(t_topology *top);
140 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
141 /* generate a t_atoms struct for the system from gmx_mtop_t */