include/rmpbc.h

   1 /*
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   9  *                        VERSION 3.2.0
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  35
  36 #ifndef _rmpbc_h
  37 #define _rmpbc_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49   typedef struct gmx_rmpbc *gmx_rmpbc_t;
  50
  51   extern gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
  52                                     matrix box);
  53
  54   extern void gmx_rmpbc_done(gmx_rmpbc_t gpbc);
  55
  56   extern void gmx_rmpbc(gmx_rmpbc_t gpbc,matrix box,rvec x[],rvec x_s[]);
  57   /* Correct coordinates for atoms within every molecule for the periodic
  58    * boundary conditions such that every molecule is whole.
  59    * (note that mdrun only writes whole molecules)
  60    * x are the input coordinates, x_s the shifted coordinates where
  61    * the molecules are whole. x and x_s can be the same array.
  62    * natoms is the size of x and x_s and can be smaller than the number
  63    * of atoms in idef, but should only contain complete molecules.
  64    * When ePBC=-1, the type of pbc is guessed from the box matrix.
  65    */
  66
  67   /*extern 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   extern 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 */