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38 #ifndef GMX_PBCUTIL_MSHIFT_H
39 #define GMX_PBCUTIL_MSHIFT_H
43 #include "gromacs/math/vectypes.h"
44 #include "gromacs/utility/basedefinitions.h"
46 struct InteractionList
;
60 /* Described the connectivity between, potentially, multiple parts of
61 * the ilist that are internally chemically bonded together.
63 enum class BondedParts
65 Single
, /* All atoms are connected through chemical bonds */
66 MultipleDisconnected
, /* There are multiple parts, e.g. monomers, that are all disconnected */
67 MultipleConnected
/* There are multiple parts, e.g. monomers, that are partially or fully connected between each other by interactions other than chemical bonds */
70 int at0
; /* The first atom the graph was constructed for */
71 int at1
; /* The last atom the graph was constructed for */
72 int nnodes
; /* The number of nodes, nnodes=at_end-at_start */
73 int nbound
; /* The number of nodes with edges */
74 int at_start
; /* The first connected atom in this graph */
75 int at_end
; /* The last+1 connected atom in this graph */
76 int* nedge
; /* For each node the number of edges */
77 int** edge
; /* For each node, the actual edges (bidirect.) */
78 gmx_bool bScrewPBC
; /* Screw boundary conditions */
79 ivec
* ishift
; /* Shift for each particle */
81 egCol
* egc
; /* color of each node */
82 BondedParts parts
; /* How chemically bonded parts are connected */
85 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
87 t_graph
* mk_graph(FILE* fplog
, const struct t_idef
* idef
, int at_start
, int at_end
, gmx_bool bShakeOnly
, gmx_bool bSettle
);
88 /* Build a graph from an idef description. The graph can be used
89 * to generate mol-shift indices.
90 * at_start and at_end should coincide will molecule boundaries,
91 * for the whole system this is simply 0 and natoms.
92 * If bShakeOnly, only the connections in the shake list are used.
93 * If bSettle && bShakeOnly the settles are used too.
96 void mk_graph_moltype(const gmx_moltype_t
& moltype
, t_graph
* g
);
97 /* As mk_graph, but takes gmx_moltype_t iso t_idef and does not allocate g */
100 void done_graph(t_graph
* g
);
101 /* Free the memory in g */
103 void p_graph(FILE* log
, const char* title
, t_graph
* g
);
104 /* Print a graph to log */
106 void mk_mshift(FILE* log
, t_graph
* g
, int ePBC
, 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 */