src/gromacs/pbcutil/rmpbc.h

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  37 #ifndef GMX_PBCUTIL_RMPBC_H
  38 #define GMX_PBCUTIL_RMPBC_H
  39
  40 #include "gromacs/math/vectypes.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 struct t_atoms;
  47 struct t_idef;
  48 struct t_trxframe;
  49
  50 typedef struct gmx_rmpbc *gmx_rmpbc_t;
  51
  52 gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms);
  53
  54 void gmx_rmpbc_done(gmx_rmpbc_t gpbc);
  55
  56 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[]);
  57 /* Correct coordinates x for atoms within every molecule for the periodic
  58  * boundary conditions such that every molecule is whole.
  59  * natoms is the size x and can be smaller than the number
  60  * of atoms in idef, but should only contain complete molecules.
  61  * When ePBC=-1, the type of pbc is guessed from the box matrix.
  62  */
  63
  64 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[],
  65                     rvec x_s[]);
  66 /* As gmx_rmpbc, but outputs in x_s and does not modify x. */
  67
  68 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, struct t_trxframe *fr);
  69 /* As gmx_rmpbc but operates on a t_trxframe data structure. */
  70
  71 void rm_gropbc(const t_atoms *atoms, rvec x[], const 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