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Use gromacs 5.1 release (instead of master)

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This commit is contained in:
Niels Müller
2016-03-16 14:54:53 +01:00
parent dbfdc6b7cd
commit 21e6594c07
2 changed files with 23 additions and 18 deletions
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2
pygmx/mdtypes.pxd
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@ -2,7 +2,7 @@
from utility cimport * from utility cimport *
from math cimport * from math cimport *
cdef extern from "gromacs/mdtypes/inputrec.h": cdef extern from "gromacs/legacyheaders/types/inputrec.h":
ctypedef struct t_simtemp: ctypedef struct t_simtemp:
pass pass
ctypedef struct t_lambda: ctypedef struct t_lambda:

39
pygmx/tpxio.pyx
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@ -13,15 +13,13 @@ from topology cimport *
cdef extern from "gromacs/fileio/tpxio.h": cdef extern from "gromacs/fileio/tpxio.h":
void read_tpxheader(const char *fn, t_tpxheader *tpx, bint TopOnlyOK) ctypedef struct t_tpxheader:
int bIr # Non zero if input_rec is present */
cdef struct t_tpxheader: int bBox # Non zero if a box is present */
bint bIr # Non zero if input_rec is present */ int bTop # Non zero if a topology is present */
bint bBox # Non zero if a box is present */ int bX # Non zero if coordinates are present */
bint bTop # Non zero if a topology is present */ int bV # Non zero if velocities are present */
bint bX # Non zero if coordinates are present */ int bF # Non zero if forces are present (no longer
bint bV # Non zero if velocities are present */
bint bF # Non zero if forces are present (no longer
# supported, but retained so old .tpr can be read) */ # supported, but retained so old .tpr can be read) */
int natoms # The total number of atoms */ int natoms # The total number of atoms */
int ngtc # The number of temperature coupling groups */ int ngtc # The number of temperature coupling groups */
@ -29,12 +27,14 @@ cdef extern from "gromacs/fileio/tpxio.h":
int fep_state # Current value of the alchemical state -- int fep_state # Current value of the alchemical state --
void read_tpxheader(const char *fn, t_tpxheader *tpx, bint TopOnlyOK, int *version, int *generation)
int read_tpx(const char *fname, int read_tpx(const char *fname,
t_inputrec *ir, t_inputrec *ir,
double box[3][3], matrix box,
int *natoms, int *natoms,
rvec *x, rvec *x,
rvec *v, rvec *v,
rvec *f,
gmx_mtop_t *mtop) gmx_mtop_t *mtop)
@ -172,20 +172,25 @@ cdef class TPXReader:
def __cinit__(self, filename): def __cinit__(self, filename):
filename = cstr(filename) filename = cstr(filename)
read_tpxheader(<char *>filename, &self.header, True)
self.n_atoms = self.header.natoms
self.n_tcouple_groups = self.header.ngtc
cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.n_atoms, 3), dtype=np.float32) # Arrays for coordinates etc can be NULL, if they shouldn't be read
cdef np.ndarray[real, ndim=2] velocites = np.empty((self.n_atoms, 3), dtype=np.float32) # cdef int version, generation
# read_tpxheader(<char *>filename, &self.header, True, &version, &generation)
# self.n_atoms = self.header.natoms
# self.n_tcouple_groups = self.header.ngtc
# cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.n_atoms, 3), dtype=np.float32)
# cdef np.ndarray[real, ndim=2] velocites = np.empty((self.n_atoms, 3), dtype=np.float32)
# cdef np.ndarray[real, ndim=2] forces = np.empty((self.n_atoms, 3), dtype=np.float32)
return_code = read_tpx( return_code = read_tpx(
<char *>filename, <char *>filename,
&self.input_record, &self.input_record,
self.box, self.box,
&self.n_atoms, &self.n_atoms,
<rvec *>coordinates.data, NULL, NULL, NULL,
<rvec *>velocites.data, # <rvec *>coordinates.data,
# <rvec *>velocites.data,
# <rvec *>forces.data,
&self.topology &self.topology
) )
self.topology_name = self.topology.name[0] self.topology_name = self.topology.name[0]