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37 #ifndef GMX_LEGACYHEADERS_TOPOLOGY_H
38 #define GMX_LEGACYHEADERS_TOPOLOGY_H
42 #include "../../topology/atoms.h"
43 #include "../../topology/block.h"
44 #include "../../topology/symtab.h"
51 egcTC, egcENER, egcACC, egcFREEZE,
52 egcUser1, egcUser2, egcVCM, egcCompressedX,
58 char **name; /* Name of the molecule type */
59 t_atoms atoms; /* The atoms */
61 t_block cgs; /* The charge groups */
62 t_blocka excls; /* The exclusions */
66 int type; /* The molcule type index in mtop.moltype */
67 int nmol; /* The number of molecules in this block */
68 int natoms_mol; /* The number of atoms in one molecule */
69 int nposres_xA; /* The number of posres coords for top A */
70 rvec *posres_xA; /* The posres coords for top A */
71 int nposres_xB; /* The number of posres coords for top B */
72 rvec *posres_xB; /* The posres coords for top B */
76 t_grps grps[egcNR]; /* Groups of things */
77 int ngrpname; /* Number of groupnames */
78 char ***grpname; /* Names of the groups */
80 unsigned char *grpnr[egcNR]; /* Group numbers or NULL */
83 /* This macro gives the group number of group type egc for atom i.
84 * This macro is useful, since the grpnr pointers are NULL
85 * for group types that have all entries 0.
87 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
89 /* The global, complete system topology struct, based on molecule types.
90 This structure should contain no data that is O(natoms) in memory. */
92 char **name; /* Name of the topology */
93 gmx_ffparams_t ffparams;
95 gmx_moltype_t *moltype;
97 gmx_molblock_t *molblock;
99 int maxres_renum; /* Parameter for residue numbering */
100 int maxresnr; /* The maximum residue number in moltype */
101 t_atomtypes atomtypes; /* Atomtype properties */
102 t_block mols; /* The molecules */
104 t_symtab symtab; /* The symbol table */
107 /* The mdrun node-local topology struct, completely written out */
109 t_idef idef; /* The interaction function definition */
110 t_atomtypes atomtypes; /* Atomtype properties */
111 t_block cgs; /* The charge groups */
112 t_blocka excls; /* The exclusions */
115 /* The old topology struct, completely written out, used in analysis tools */
117 char **name; /* Name of the topology */
118 t_idef idef; /* The interaction function definition */
119 t_atoms atoms; /* The atoms */
120 t_atomtypes atomtypes; /* Atomtype properties */
121 t_block cgs; /* The charge groups */
122 t_block mols; /* The molecules */
123 t_blocka excls; /* The exclusions */
124 t_symtab symtab; /* The symbol table */