src/gromacs/pbcutil/mshift.h

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  38 #ifndef GMX_PBCUTIL_MSHIFT_H
  39 #define GMX_PBCUTIL_MSHIFT_H
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45
  46 struct InteractionList;
  47 struct gmx_moltype_t;
  48 struct t_idef;
  49
  50 typedef enum
  51 {
  52     egcolWhite,
  53     egcolGrey,
  54     egcolBlack,
  55     egcolNR
  56 } egCol;
  57
  58 struct t_graph
  59 {
  60     /* Described the connectivity between, potentially, multiple parts of
  61      * the ilist that are internally chemically bonded together.
  62      */
  63     enum class BondedParts
  64     {
  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 */
  68     };
  69
  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                      */
  80     int         negc;
  81     egCol*      egc;   /* color of each node */
  82     BondedParts parts; /* How chemically bonded parts are connected    */
  83 };
  84
  85 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
  86
  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.
  94  */
  95
  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 */
  98
  99
 100 void done_graph(t_graph* g);
 101 /* Free the memory in g */
 102
 103 void p_graph(FILE* log, const char* title, t_graph* g);
 104 /* Print a graph to log */
 105
 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. */
 108
 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) */
 111
 112 void shift_self(const t_graph* g, const matrix box, rvec x[]);
 113 /* Id. but in place */
 114
 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) */
 117
 118 void unshift_self(const t_graph* g, const matrix box, rvec x[]);
 119 /* Id, but in place */
 120
 121 #endif