src/gromacs/topology/index.h

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