include/rmpbc.h

   1 /*
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  35
  36 #ifndef _rmpbc_h
  37 #define _rmpbc_h
  38
  39 #include "typedefs.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45   typedef struct gmx_rmpbc *gmx_rmpbc_t;
  46
  47   gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
  48                                     matrix box);
  49
  50   void gmx_rmpbc_done(gmx_rmpbc_t gpbc);
  51
  52   void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[]);
  53   /* Correct coordinates x for atoms within every molecule for the periodic
  54    * boundary conditions such that every molecule is whole.
  55    * natoms is the size x and can be smaller than the number
  56    * of atoms in idef, but should only contain complete molecules.
  57    * When ePBC=-1, the type of pbc is guessed from the box matrix.
  58    */
  59
  60   void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],
  61                              rvec x_s[]);
  62   /* As gmx_rmpbc, but outputs in x_s and does not modify x. */
  63
  64   void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr);
  65   /* As gmx_rmpbc but operates on a t_trxframe data structure. */
  66
  67   /*void rm_pbc(t_idef *idef,int ePBC,int natoms,
  68     matrix box,rvec x[],rvec x_s[]);*/
  69   /* Convenience function that still holds a static variable. */
  70
  71   void rm_gropbc(t_atoms *atoms,rvec x[],matrix box);
  72   /* Simple routine for use in analysis tools that just have a pdb or
  73    * similar file.
  74    */
  75
  76 #ifdef __cplusplus
  77 }
  78 #endif
  79
  80 #endif  /* _rmpbc_h */