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Implement Gromacs internal Whole Procedure

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Niels Müller
2019-10-25 09:55:20 +02:00
parent b71961979f
commit 92addd3148
3 changed files with 55 additions and 8 deletions
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25
pygmx/tpxio.pyx
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@ -2,9 +2,11 @@
# Cython wrapper around tpxio.cpp
from libc cimport stdio
from libc.string cimport memcpy
import numpy as np
#cimport numpy as np
import cython
cimport numpy as np
from utility cimport *
from math cimport *
@ -254,9 +256,20 @@ cdef class TPXReader:
@cython.binding(True)
def make_xtcframe_whole(coords, box, <TPXReader>reader):
cdef t_atoms = gmx_mtop_global_atoms(reader.topology)
def make_xtcframe_whole(coords, box, TPXReader reader):
cdef int natoms = reader.topology.natoms
cdef gmx_localtop_t *top = gmx_mtop_generate_local_top(&reader.topology, True)
cdef gmx_rmpbc_t gpbc = gmx_rmpbc_init(&top.idef, -1, natoms)
cdef np.ndarray[real, ndim=2] b = np.asarray(box, dtype=np.float32)
cdef np.ndarray[real, ndim=2] x = np.asarray(coords, dtype=np.float32)
rm_gropbc(const t_atoms *atoms, <rvec *>x.data, <matrix> b)
return x
cdef np.ndarray[real, ndim=2] x = np.array(coords, dtype=np.float32).copy()
gmx_rmpbc(gpbc, natoms, <rvec *>b.data, <rvec *>x.data)
# free up memory - in fact, we should free memory of 'top' too
# however, it shares memory with 'reader.topology', so we can not free it correctly
gmx_rmpbc_done(gpbc)
return x