IPKM/python-pygmx
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Switched to Headers fo the Gromacs-2016 branch.

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This commit is contained in:
Niels Müller
2016-09-27 12:22:58 +02:00
parent f4e2501142
commit ad482006b0
6 changed files with 36 additions and 10 deletions
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11
pygmx/xtcio.pyx
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@ -21,11 +21,11 @@ cdef extern from "gromacs/fileio/xtcio.h":
void close_xtc(t_fileio *fio)
int read_first_xtc(t_fileio *fio,
int *natoms, int *step, real *time,
int *natoms, gmx_int64_t *step, real *time,
matrix box, rvec **x, real *prec, gmx_bool *_bOK)
int read_next_xtc(t_fileio *fio,
int natoms, int *step, real *time,
int natoms, gmx_int64_t *step, real *time,
matrix box, rvec *x, real *prec, gmx_bool *_bOK)
@ -53,7 +53,8 @@ else:
cdef array get_xtc_index(t_fileio *fio):
cdef:
gmx_bool _bOK
int natoms, step, frame, state = 1
int natoms, frame, state = 1
gmx_int64_t step
real time, prec
matrix box
rvec *x
@ -156,7 +157,7 @@ cdef class XTCReader:
self.filename = filename.decode()
cdef:
int step
gmx_int64_t step
matrix box
gmx_bool _bOK
real time, prec
@ -193,7 +194,7 @@ cdef class XTCReader:
cdef np.ndarray[real, ndim=2] coords = np.empty((self.natoms, 3), dtype=np_real)
if frame < len(self):
self.seek(frame)
read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box,
read_next_xtc(self.fio, self.natoms, <gmx_int64_t *>self.cur_step, &time, box,
<rvec *>coords.data, &self.prec, &_bOK)
if _bOK:
frame = XTCFrame()