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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"
45 struct InteractionList;
59 /* Described the connectivity between, potentially, multiple parts of
60 * the ilist that are internally chemically bonded together.
62 enum class BondedParts
64 Single, /* All atoms are connected through chemical bonds */
65 MultipleDisconnected, /* There are multiple parts, e.g. monomers, that are all disconnected */
66 MultipleConnected /* There are multiple parts, e.g. monomers, that are partially or fully connected between each other by interactions other than chemical bonds */
69 int at0; /* The first atom the graph was constructed for */
70 int at1; /* The last atom the graph was constructed for */
71 int nnodes; /* The number of nodes, nnodes=at_end-at_start */
72 int nbound; /* The number of nodes with edges */
73 int at_start; /* The first connected atom in this graph */
74 int at_end; /* The last+1 connected atom in this graph */
75 int* nedge; /* For each node the number of edges */
76 int** edge; /* For each node, the actual edges (bidirect.) */
77 gmx_bool bScrewPBC; /* Screw boundary conditions */
78 ivec* ishift; /* Shift for each particle */
80 egCol* egc; /* color of each node */
81 BondedParts parts; /* How chemically bonded parts are connected */
84 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
86 t_graph* mk_graph(FILE* fplog, const struct t_idef* idef, int at_start, int at_end, gmx_bool bShakeOnly, gmx_bool bSettle);
87 /* Build a graph from an idef description. The graph can be used
88 * to generate mol-shift indices.
89 * at_start and at_end should coincide will molecule boundaries,
90 * for the whole system this is simply 0 and natoms.
91 * If bShakeOnly, only the connections in the shake list are used.
92 * If bSettle && bShakeOnly the settles are used too.
95 void mk_graph_moltype(const gmx_moltype_t& moltype, t_graph* g);
96 /* As mk_graph, but takes gmx_moltype_t 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, const matrix box, const rvec x[]);
106 /* Calculate the mshift codes, based on the connection graph in g. */
108 void shift_x(const t_graph* g, const matrix box, const rvec x[], rvec x_s[]);
109 /* Add the shift vector to x, and store in x_s (may be same array as x) */
111 void shift_self(const t_graph* g, const matrix box, rvec x[]);
112 /* Id. but in place */
114 void unshift_x(const t_graph* g, const matrix box, rvec x[], const rvec x_s[]);
115 /* Subtract the shift vector from x_s, and store in x (may be same array) */
117 void unshift_self(const t_graph* g, const matrix box, rvec x[]);
118 /* Id, but in place */