include/mshift.h

   1 /*
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  35
  36 #ifndef _mshift_h
  37 #define _mshift_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44
  45
  46 extern t_graph *mk_graph(FILE *fplog,
  47                          t_idef *idef,int at_start,int at_end,
  48                          bool bShakeOnly,bool bSettle);
  49 /* Build a graph from an idef description. The graph can be used
  50  * to generate mol-shift indices.
  51  * If bShakeOnly, only the connections in the shake list are used.
  52  * If bSettle && bShakeOnly the settles are used too.
  53  */
  54
  55 extern void mk_graph_ilist(FILE *fplog,
  56                            t_ilist *ilist,int at_start,int at_end,
  57                            bool bShakeOnly,bool bSettle,
  58                            t_graph *g);
  59 /* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
  60
  61
  62 extern void done_graph(t_graph *g);
  63 /* Free the memory in g */
  64
  65 extern void p_graph(FILE *log,const char *title,t_graph *g);
  66 /* Print a graph to log */
  67
  68 extern void mk_mshift(FILE *log,t_graph *g,int ePBC,matrix box,rvec x[]);
  69 /* Calculate the mshift codes, based on the connection graph in g. */
  70
  71 extern void shift_x(t_graph *g,matrix box,rvec x[],rvec x_s[]);
  72 /* Add the shift vector to x, and store in x_s (may be same array as x) */
  73
  74 extern void shift_self(t_graph *g,matrix box,rvec x[]);
  75 /* Id. but in place */
  76
  77 extern void unshift_x(t_graph *g,matrix box,rvec x[],rvec x_s[]);
  78 /* Subtract the shift vector from x_s, and store in x (may be same array) */
  79
  80 extern void unshift_self(t_graph *g,matrix box,rvec x[]);
  81 /* Id, but in place */
  82
  83 #endif  /* _mshift_h */