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