include/rmpbc.h

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  38
  39 #ifndef _rmpbc_h
  40 #define _rmpbc_h
  41 #include "visibility.h"
  42 #include "typedefs.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48   typedef struct gmx_rmpbc *gmx_rmpbc_t;
  49
  50 GMX_LIBGMX_EXPORT
  51   gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
  52                                     matrix box);
  53
  54 GMX_LIBGMX_EXPORT
  55   void gmx_rmpbc_done(gmx_rmpbc_t gpbc);
  56
  57 GMX_LIBGMX_EXPORT
  58   void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[]);
  59   /* Correct coordinates x for atoms within every molecule for the periodic
  60    * boundary conditions such that every molecule is whole.
  61    * natoms is the size x and can be smaller than the number
  62    * of atoms in idef, but should only contain complete molecules.
  63    * When ePBC=-1, the type of pbc is guessed from the box matrix.
  64    */
  65
  66 GMX_LIBGMX_EXPORT
  67   void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],
  68                              rvec x_s[]);
  69   /* As gmx_rmpbc, but outputs in x_s and does not modify x. */
  70
  71 GMX_LIBGMX_EXPORT
  72   void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr);
  73   /* As gmx_rmpbc but operates on a t_trxframe data structure. */
  74
  75   /*void rm_pbc(t_idef *idef,int ePBC,int natoms,
  76     matrix box,rvec x[],rvec x_s[]);*/
  77   /* Convenience function that still holds a static variable. */
  78
  79 GMX_LIBGMX_EXPORT
  80   void rm_gropbc(t_atoms *atoms,rvec x[],matrix box);
  81   /* Simple routine for use in analysis tools that just have a pdb or
  82    * similar file.
  83    */
  84
  85 #ifdef __cplusplus
  86 }
  87 #endif
  88
  89 #endif  /* _rmpbc_h */