src/gromacs/topology/index.h

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  37 #ifndef GMX_TOPOLOGY_INDEX_H
  38 #define GMX_TOPOLOGY_INDEX_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 struct t_atoms;
  49 struct t_blocka;
  50
  51 void check_index(char *gname, int n, int index[],
  52                  char *traj, int natoms);
  53 /* Checks if any index is smaller than zero or larger than natoms,
  54  * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
  55  * and traj (if traj=NULL, "the trajectory" is used).
  56  */
  57
  58 struct t_blocka *init_index(const char *gfile, char ***grpname);
  59 /* Lower level routine than the next */
  60
  61 void rd_index(const char *statfile, int ngrps, int isize[],
  62               int *index[], char *grpnames[]);
  63 /* Assume the group file is generated, so the
  64  * format need not be user-friendly. The format is:
  65  * nr of groups, total nr of atoms
  66  * for each group: name nr of element, elements.
  67  *
  68  * The function opens a file, reads ngrps groups, asks the
  69  * user for group numbers, and puts the resulting sizes in
  70  * isize, the int s in index and the names of
  71  * the groups in grpnames.
  72  *
  73  * It is also assumed, that when ngrps groups are requested
  74  * memory has been allocated for ngrps index arrays, and that
  75  * the dimension of the isize and grpnames arrays are ngrps.
  76  */
  77
  78 void get_index(const t_atoms *atoms, const char *fnm, int ngrps,
  79                int isize[], int *index[], char *grpnames[]);
  80 /* Does the same as rd_index, but if the fnm pointer is NULL it
  81  * will not read from fnm, but it will make default index groups
  82  * for the atoms in *atoms.
  83  */
  84
  85 typedef struct {
  86     int               maxframe;
  87     char            **grpname;
  88     struct t_blocka  *clust;
  89     int              *inv_clust;
  90 } t_cluster_ndx;
  91
  92 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
  93
  94
  95 void write_index(const char *outf, struct t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
  96 /* Writes index blocks to outf (writes an indexfile) */
  97
  98 void add_grp(struct t_blocka *b, char ***gnames, int nra, int a[], const char *name);
  99 /* Ads group a with name name to block b and namelist gnames */
 100
 101 void analyse(const t_atoms *atoms, struct t_blocka *gb, char ***gn,
 102              gmx_bool bASK, gmx_bool bVerb);
 103 /* Makes index groups gb with names gn for atoms in atoms.
 104  * bASK=FALSE gives default groups.
 105  */
 106
 107 /*! \brief Look up a group in a list.
 108  *
 109  * \param[inout] s    The string to look up
 110  * \param[in] ngrps   The number of groups
 111  * \param[in] grpname The names of the groups
 112  * \return the group number or -1 if not found.
 113  */
 114 int find_group(const char *s, int ngrps, char **grpname);
 115
 116
 117 #ifdef __cplusplus
 118 }
 119 #endif
 120
 121 #endif