Bundle commit of all recent changes on pygmx.
This commit is contained in:
Niels Müller
2
.gitmodules
vendored
2
.gitmodules
vendored
@ -1,3 +1,3 @@
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[submodule "gromacs"]
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path = gromacs
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url = https://github.com/gromacs/gromacs.git
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url = git://git.gromacs.org/gromacs.git
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@ -7,3 +7,4 @@ from . import xtcio
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from . import tngio
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from .tpxio import TPXReader
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from .enxio import EDRFile
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99
pygmx/enxio.pyx
Normal file
99
pygmx/enxio.pyx
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@ -0,0 +1,99 @@
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from cpython.array cimport array
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from array import array
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cimport numpy as np
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import numpy as np
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from utility cimport *
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from mdtypes cimport *
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cdef extern from "gromacs/fileio/enxio.h":
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ctypedef struct gmx_enxnm_t:
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char *name
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char *unit
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ctypedef struct ener_file_t:
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pass
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ctypedef struct t_enxblock:
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pass
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ctypedef struct t_enxframe:
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double t # Timestamp of this frame */
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gmx_int64_t step # MD step */
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gmx_int64_t nsteps # The number of steps between frames */
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double dt # The MD time step */
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int nsum # The number of terms for the sums in ener */
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int nre # Number of energies */
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int e_size # Size (in bytes) of energies */
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int e_alloc # Allocated size (in elements) of ener */
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t_energy *ener # The energies */
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int nblock # Number of following energy blocks */
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t_enxblock *block # The blocks */
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int nblock_alloc # The number of blocks allocated */
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ener_file_t open_enx(const char *fn, const char *mode)
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void close_enx(ener_file_t ef)
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void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms)
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gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
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cdef class EDRFile:
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cdef:
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ener_file_t efile
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gmx_enxnm_t *etypes
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int n_etypes
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t_enxframe *frames
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@property
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def types(self):
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types = []
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for i in range(self.n_etypes):
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types.append(
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)
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def read(self):
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cdef t_enxframe *frame
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cdef np.ndarray[float, ndim=2] energies = np.empty((1,self.n_etypes), np.float32)
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snew(frame, 1)
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while do_enx(self.efile, frame):
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energies = np.resize(energies, (len(energies)+1, self.n_etypes))
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for i in range(frame.nre):
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energies[-1, i] = frame.ener[i].e
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return energies
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def __init__(self, filename):
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filename = cstr(filename)
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self.efile = open_enx(filename, b'r')
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self.etypes = NULL
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do_enxnms(self.efile, &self.n_etypes, &self.etypes)
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print(self.n_etypes)
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#do_enx(self.efile, self.frames)
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def __getitem__(self, item):
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cdef:
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int f = 0
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t_enxframe frame = self.frames[f]
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cdef array values = array('d')
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while frame.nblock > 0:
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if item < frame.nre:
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values.append(frame.ener[item].e)
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i += 1
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frame = self.frames[i]
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print(i, frame.t, frame.nblock)
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return values
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@ -1,12 +1,24 @@
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# from libc.stdio cimport FILE
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from utility cimport *
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#cdef extern from "gromacs/fileio/gmx_system_xdr.h":
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# ctypedef struct XDR:
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# pass
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cdef extern from "gromacs/fileio/gmxfio.h":
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ctypedef struct t_fileio:
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pass
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void gmx_fio_rewind(t_fileio *fio)
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int gmx_fio_seek(t_fileio *fio, gmx_off_t fpos)
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gmx_off_t gmx_fio_ftell(t_fileio *fio)
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# int xtc_seek_frame(t_fileio *fio, int frame, int natoms)
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int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly)
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void gmx_fio_setdebug(t_fileio *fio, gmx_bool bDebug)
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@ -2,6 +2,13 @@
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from utility cimport *
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from math cimport *
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cdef extern from "gromacs/legacyheaders/types/energy.h":
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ctypedef struct t_energy:
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real e
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double eav
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double esum
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cdef extern from "gromacs/legacyheaders/types/inputrec.h":
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ctypedef struct t_simtemp:
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pass
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@ -1,7 +1,7 @@
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# C-API in gromacs/utility
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#cdef extern from "inttypes.h":
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ctypedef int __int64
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ctypedef unsigned long __int64
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cdef extern from "gromacs/utility/basedefinitions.h":
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ctypedef int gmx_bool
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@ -12,3 +12,12 @@ cdef extern from "gromacs/utility/real.h":
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cdef extern from "gromacs/utility/futil.h":
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ctypedef gmx_int64_t gmx_off_t
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cdef extern from "gromacs/utility/smalloc.h":
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void snew(void *ptr, int nelem)
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cdef inline cstr(instr):
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if isinstance(instr, str):
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instr = instr.encode()
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return instr
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113
pygmx/xtcio.pyx
113
pygmx/xtcio.pyx
@ -1,5 +1,8 @@
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# Wrapper for xtcio.h: I/O for xtc files.
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from cpython.array cimport array
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from array import array
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import numpy as np
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cimport numpy as np
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@ -7,6 +10,7 @@ from utility cimport *
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from math cimport *
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from fileio cimport *
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cdef extern from "gromacs/fileio/xtcio.h":
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t_fileio *open_xtc(const char *filename, const char *mode)
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@ -27,69 +31,96 @@ else:
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np_real = np.float
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#cdef array get_xtc_index_by_frames(t_fileio *fio, int length, int natoms):
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# cdef:
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#gmx_bool _bOK
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## int frame = 1
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# cdef array cache = array('L')
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# gmx_fio_rewind(fio)
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# cache.append(gmx_fio_ftell(fio))
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# while xtc_seek_frame(fio, frame*500, natoms) == 0:
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# cache.append(gmx_fio_ftell(fio))
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# #print(frame, cache[-1])
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# frame += 1
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# if frame == length:
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# break
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# return cache
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cdef array get_xtc_index(t_fileio *fio):
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cdef:
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gmx_bool _bOK
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int natoms, step, frame, state = 1
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real time, prec
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matrix box
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rvec *x
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cdef array cache = array('L')
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gmx_fio_rewind(fio)
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cache.append(gmx_fio_ftell(fio))
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read_first_xtc(fio, &natoms, &step, &time, box, &x, &prec, &_bOK)
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cache.append(gmx_fio_ftell(fio))
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while read_next_xtc(fio, natoms, &step, &time, box, x, &prec, &_bOK):
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cache.append(gmx_fio_ftell(fio))
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# the last index is invalid
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return cache[:-1]
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cdef class XTCReader:
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cdef:
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t_fileio *fio
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int natoms, cur_step
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real start_time, timestep, prec, cur_time
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dict _cache
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#rvec *coords
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bint has_cache
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rvec *coords
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array _cache
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def nearest_cache(self, index):
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nearest = 0
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cur_dist = 99999999
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for ind in self._cache:
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dist = abs(ind - index)
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if dist < cur_dist:
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nearest = ind
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cur_dist = dist
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return nearest
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@property
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def cache(self):
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return self._cache
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def seek(self, int frame):
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if self.has_cache:
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gmx_fio_seek(self.fio, self.cache[frame])
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def seek(self, index):
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if index in self._cache:
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gmx_fio_seek(self.fio, self._cache[index])
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else:
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nearest = self.nearest_cache(index)
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gmx_fio_seek(self.fio, self._cache[nearest])
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self.cur_step = index
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self.cur_time = index * self.timestep + self.start_time
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xtc_seek_time(self.fio, self.cur_time, self.natoms, index > nearest)
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self._cache[index] = gmx_fio_ftell(self.fio)
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def make_cache(self):
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self._cache = get_xtc_index(self.fio)
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self.has_cache = True
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def __cinit__(self):
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self.has_cache = False
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def __init__(self, filename):
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def __init__(self, filename, make_cache=True):
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if isinstance(filename, str):
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filename = filename.encode()
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cdef:
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int step
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matrix box
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gmx_bool _bOK
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real time
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cdef rvec *coords # = np.empty((1,3), dtype=np.float32)
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real time, prec
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rvec *x
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self._cache = {}
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self.fio = open_xtc(filename, b'r')
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read_first_xtc(self.fio, &self.natoms, &self.cur_step, &self.start_time, box,
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&coords, &self.prec, &_bOK)
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self._cache[self.cur_step] = gmx_fio_ftell(self.fio)
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read_first_xtc(self.fio, &self.natoms, &step, &time, box, &x, &prec, &_bOK)
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read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box,
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coords, &self.prec, &_bOK)
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if make_cache:
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self.make_cache()
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self._cache[<int>self.cur_step] = gmx_fio_ftell(self.fio)
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self.timestep = time - self.start_time
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def __len__(self):
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return len(self.cache)
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def __getitem__(self, item):
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def __getitem__(self, frame):
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cdef matrix box
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cdef gmx_bool _bOK
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cdef real time
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cdef np.ndarray[real, ndim=2] coords = np.empty((self.natoms, 3), dtype=np_real)
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self.seek(item)
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read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box,
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<rvec *>coords.data, &self.prec, &_bOK)
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return coords
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if frame < len(self):
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self.seek(frame)
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read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box,
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<rvec *>coords.data, &self.prec, &_bOK)
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if _bOK:
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return coords
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else:
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raise
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else:
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raise IndexError('Frame {} is out of range for trajectory of length {}.'.format(frame, len(self)))
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16
setup.py
16
setup.py
@ -26,7 +26,7 @@ elif os.path.exists('gromacs/build/lib'):
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if not library_dirs:
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raise OSError("""
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Gromacs library not found.
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Activate a gromacs module or specify environment variable LD_LIBRARY_PATH.
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Activate a gromacs module or set environment variable LD_LIBRARY_PATH.
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""")
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library_dirs.append('gromacs/src/external/tng_io/build/lib')
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@ -53,14 +53,22 @@ extensions = [
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library_dirs=library_dirs,
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runtime_library_dirs=library_dirs,
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language='c++'),
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Extension('pygmx.tngio',
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sources=['pygmx/tngio.pyx'],
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Extension('pygmx.enxio',
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sources=['pygmx/enxio.pyx'],
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include_dirs=include_dirs,
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libraries=['gromacs'],
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library_dirs=library_dirs,
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runtime_library_dirs=library_dirs,
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language='c++'),
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# Extension('pygmx.tngio',
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# sources=['pygmx/tngio.pyx'],
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# include_dirs=include_dirs,
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# libraries=['gromacs'],
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# library_dirs=library_dirs,
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# runtime_library_dirs=library_dirs,
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#language='c++'
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),
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# ),
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]
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