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37 #ifndef GMX_PBCUTIL_MSHIFT_H
38 #define GMX_PBCUTIL_MSHIFT_H
42 #include "gromacs/math/vectypes.h"
43 #include "gromacs/utility/basedefinitions.h"
49 egcolWhite, egcolGrey, egcolBlack, egcolNR
54 /* Described the connectivity between, potentially, multiple parts of
55 * the ilist that are internally chemically bonded together.
57 enum class BondedParts
59 Single, /* All atoms are connected through chemical bonds */
60 MultipleDisconnected, /* There are multiple parts, e.g. monomers, that are all disconnected */
61 MultipleConnected /* There are multiple parts, e.g. monomers, that are partially or fully connected between each other by interactions other than chemical bonds */
64 int at0; /* The first atom the graph was constructed for */
65 int at1; /* The last atom the graph was constructed for */
66 int nnodes; /* The number of nodes, nnodes=at_end-at_start */
67 int nbound; /* The number of nodes with edges */
68 int at_start; /* The first connected atom in this graph */
69 int at_end; /* The last+1 connected atom in this graph */
70 int *nedge; /* For each node the number of edges */
71 int **edge; /* For each node, the actual edges (bidirect.) */
72 gmx_bool bScrewPBC; /* Screw boundary conditions */
73 ivec *ishift; /* Shift for each particle */
75 egCol *egc; /* color of each node */
76 BondedParts parts; /* How chemically bonded parts are connected */
79 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
81 t_graph *mk_graph(FILE *fplog,
82 const struct t_idef *idef, int at_start, int at_end,
83 gmx_bool bShakeOnly, gmx_bool bSettle);
84 /* Build a graph from an idef description. The graph can be used
85 * to generate mol-shift indices.
86 * at_start and at_end should coincide will molecule boundaries,
87 * for the whole system this is simply 0 and natoms.
88 * If bShakeOnly, only the connections in the shake list are used.
89 * If bSettle && bShakeOnly the settles are used too.
92 void mk_graph_ilist(FILE *fplog,
93 const struct t_ilist *ilist, int at_start, int at_end,
94 gmx_bool bShakeOnly, gmx_bool bSettle,
96 /* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
99 void done_graph(t_graph *g);
100 /* Free the memory in g */
102 void p_graph(FILE *log, const char *title, t_graph *g);
103 /* Print a graph to log */
105 void mk_mshift(FILE *log, t_graph *g, int ePBC,
106 const matrix box, const rvec x[]);
107 /* Calculate the mshift codes, based on the connection graph in g. */
109 void shift_x(const t_graph *g, const matrix box, const rvec x[], rvec x_s[]);
110 /* Add the shift vector to x, and store in x_s (may be same array as x) */
112 void shift_self(const t_graph *g, const matrix box, rvec x[]);
113 /* Id. but in place */
115 void unshift_x(const t_graph *g, const matrix box, rvec x[], const rvec x_s[]);
116 /* Subtract the shift vector from x_s, and store in x (may be same array) */
118 void unshift_self(const t_graph *g, const matrix box, rvec x[]);
119 /* Id, but in place */