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41 #include "visibility.h"
49 t_graph *mk_graph(FILE *fplog,
50 t_idef *idef,int at_start,int at_end,
51 gmx_bool bShakeOnly,gmx_bool bSettle);
52 /* Build a graph from an idef description. The graph can be used
53 * to generate mol-shift indices.
54 * at_start and at_end should coincide will molecule boundaries,
55 * for the whole system this is simply 0 and natoms.
56 * If bShakeOnly, only the connections in the shake list are used.
57 * If bSettle && bShakeOnly the settles are used too.
61 void mk_graph_ilist(FILE *fplog,
62 t_ilist *ilist,int at_start,int at_end,
63 gmx_bool bShakeOnly,gmx_bool bSettle,
65 /* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
69 void done_graph(t_graph *g);
70 /* Free the memory in g */
73 void p_graph(FILE *log,const char *title,t_graph *g);
74 /* Print a graph to log */
77 void mk_mshift(FILE *log,t_graph *g,int ePBC,matrix box,rvec x[]);
78 /* Calculate the mshift codes, based on the connection graph in g. */
81 void shift_x(t_graph *g,matrix box,rvec x[],rvec x_s[]);
82 /* Add the shift vector to x, and store in x_s (may be same array as x) */
85 void shift_self(t_graph *g,matrix box,rvec x[]);
86 /* Id. but in place */
89 void unshift_x(t_graph *g,matrix box,rvec x[],rvec x_s[]);
90 /* Subtract the shift vector from x_s, and store in x (may be same array) */
93 void unshift_self(t_graph *g,matrix box,rvec x[]);
94 /* Id, but in place */
100 #endif /* _mshift_h */