src/gromacs/pbcutil/mshift.h

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  37 #ifndef GMX_PBCUTIL_MSHIFT_H
  38 #define GMX_PBCUTIL_MSHIFT_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 struct t_idef;
  50 struct t_ilist;
  51
  52 typedef enum {
  53     egcolWhite, egcolGrey, egcolBlack, egcolNR
  54 } egCol;
  55
  56 typedef struct t_graph {
  57     int          at0;       /* The first atom the graph was constructed for */
  58     int          at1;       /* The last atom the graph was constructed for  */
  59     int          nnodes;    /* The number of nodes, nnodes=at_end-at_start  */
  60     int          nbound;    /* The number of nodes with edges               */
  61     int          at_start;  /* The first connected atom in this graph       */
  62     int          at_end;    /* The last+1 connected atom in this graph      */
  63     int         *nedge;     /* For each node the number of edges            */
  64     int        **edge;      /* For each node, the actual edges (bidirect.)  */
  65     gmx_bool     bScrewPBC; /* Screw boundary conditions                    */
  66     ivec        *ishift;    /* Shift for each particle                      */
  67     int          negc;
  68     egCol       *egc;       /* color of each node */
  69 } t_graph;
  70
  71 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
  72
  73 t_graph *mk_graph(FILE *fplog,
  74                   const struct t_idef *idef, int at_start, int at_end,
  75                   gmx_bool bShakeOnly, gmx_bool bSettle);
  76 /* Build a graph from an idef description. The graph can be used
  77  * to generate mol-shift indices.
  78  * at_start and at_end should coincide will molecule boundaries,
  79  * for the whole system this is simply 0 and natoms.
  80  * If bShakeOnly, only the connections in the shake list are used.
  81  * If bSettle && bShakeOnly the settles are used too.
  82  */
  83
  84 void mk_graph_ilist(FILE *fplog,
  85                     const struct t_ilist *ilist, int at_start, int at_end,
  86                     gmx_bool bShakeOnly, gmx_bool bSettle,
  87                     t_graph *g);
  88 /* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
  89
  90
  91 void done_graph(t_graph *g);
  92 /* Free the memory in g */
  93
  94 void p_graph(FILE *log, const char *title, t_graph *g);
  95 /* Print a graph to log */
  96
  97 void mk_mshift(FILE *log, t_graph *g, int ePBC,
  98                const matrix box, const rvec x[]);
  99 /* Calculate the mshift codes, based on the connection graph in g. */
 100
 101 void shift_x(const t_graph *g, const matrix box, const rvec x[], rvec x_s[]);
 102 /* Add the shift vector to x, and store in x_s (may be same array as x) */
 103
 104 void shift_self(const t_graph *g, const matrix box, rvec x[]);
 105 /* Id. but in place */
 106
 107 void unshift_x(const t_graph *g, const matrix box, rvec x[], const rvec x_s[]);
 108 /* Subtract the shift vector from x_s, and store in x (may be same array) */
 109
 110 void unshift_self(const t_graph *g, const matrix box, rvec x[]);
 111 /* Id, but in place */
 112
 113 #ifdef __cplusplus
 114 }
 115 #endif
 116
 117 #endif