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41 #include "visibility.h"
48 typedef struct gmx_rmpbc
*gmx_rmpbc_t
;
51 gmx_rmpbc_t
gmx_rmpbc_init(t_idef
*idef
,int ePBC
,int natoms
,
55 void gmx_rmpbc_done(gmx_rmpbc_t gpbc
);
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.
67 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc
,int natoms
,matrix box
,rvec x
[],
69 /* As gmx_rmpbc, but outputs in x_s and does not modify x. */
72 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc
,t_trxframe
*fr
);
73 /* As gmx_rmpbc but operates on a t_trxframe data structure. */
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. */
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