def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
"""Read ``dynmat.x`` output.
`freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
alawys Gamma, i.e. [0,0,0].
Output format is the same as in :func:`read_dyn`.
Parameters
----------
path : str
path where output files are
natoms : int
filename : str
Text output from dynmat.x, where the frequencies are printed, relative
to `path`.
axsf : str
AXSF file (``filxsf`` in input) with mode vectors as forces.
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint, which is Gamma, i.e. [0,0,0]
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d real array (nmodes, natoms, 3)
Real parts (???) if the eigenvectors of the dynamical matrix for the
q-point.
Notes
-----
We assume the output to be generated with ``dynmat.x < dynmat.in >
dynmat.out``.
"""
assert natoms is not None, ("natoms is None")
nmodes = 3*natoms
out_fn = pj(path, filename)
axsf_fn = pj(path, axsf)
cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
qpoints = np.zeros((3,))
vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
awk '{{print $2}}'".format(nmodes, out_fn)
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints,freqs,vecs
def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
"""Read ``dynmat.x`` output.
`freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
alawys Gamma, i.e. [0,0,0].
Output format is the same as in :func:`read_dyn`.
Parameters
----------
path : str
path where output files are
natoms : int
filename : str
Text output from dynmat.x, where the frequencies are printed, relative
to `path`.
axsf : str
AXSF file (``filxsf`` in input) with mode vectors as forces.
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint, which is Gamma, i.e. [0,0,0]
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d real array (nmodes, natoms, 3)
Real parts (???) if the eigenvectors of the dynamical matrix for the
q-point.
Notes
-----
We assume the output to be generated with ``dynmat.x < dynmat.in >
dynmat.out``.
"""
assert natoms is not None, ("natoms is None")
nmodes = 3*natoms
out_fn = pj(path, filename)
axsf_fn = pj(path, axsf)
cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
qpoints = np.zeros((3,))
vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
awk '{{print $2}}'".format(nmodes, out_fn)
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints,freqs,vecs
def test_write_lammps():
st = crys.Structure(coords_frac=rand(20, 3),
cell=rand(3, 3),
symbols=['Al'] * 10 + ['N'] * 10)
# align cell to lammps standard [[x,0,0],...]
st.coords = None
st.cell = None
st.set_all()
st_fn = common.pj(testdir, 'lmp.struct')
io.write_lammps(st_fn, st)
symbols = common.file_read(st_fn + '.symbols').split()
assert st.symbols == symbols
cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" % st_fn
arr = parse.arr2d_from_txt(common.backtick(cmd))
assert arr.shape == (20, 5)
assert np.allclose(st.coords, arr[:, 2:])
def test_write_lammps():
st = crys.Structure(coords_frac=rand(20,3),
cell=rand(3,3),
symbols=['Al']*10+['N']*10)
# align cell to lammps standard [[x,0,0],...]
st.coords = None
st.cell = None
st.set_all()
st_fn = common.pj(testdir, 'lmp.struct')
io.write_lammps(st_fn, st)
symbols = common.file_read(st_fn + '.symbols').split()
assert st.symbols == symbols
cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" %st_fn
arr = parse.arr2d_from_txt(common.backtick(cmd))
assert arr.shape == (20,5)
assert np.allclose(st.coords, arr[:,2:])
def test_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print(">>> comparing headers")
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref,
dct,
keys=list(ref.keys()),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstephdr, nstep, natoms in [
(fn_lmp, True, True, 101, 16), (fn_lmp, True, False, 101, 16),
(fn_cp2k, False, False, 16, 57)
]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn,
convang=convang,
nstephdr=nstephdr)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py, cc_f)
print(">>> ... coords")
tools.assert_array_equal(co_py, co_f)
print(">>> ... shapes")
assert cc_f.shape == (nstep, 6)
assert co_f.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py[:, 3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstep, natoms in [(fn_lmp, True, 101, 16),
(fn_lmp, True, 101, 16),
(fn_cp2k, False, 16, 57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print(">>> ... coords")
tools.assert_array_equal(co_py_fast, co_py_ref)
print(">>> ... shapes")
assert cc_py_ref.shape == (nstep, 6)
assert co_py_ref.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py_fast[:, 3:] > 50).all()
def test_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print ">>> comparing headers"
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref, dct, keys=ref.keys(),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstephdr,nstep,natoms in [(fn_lmp,True,True,101,16),
(fn_lmp,True,False,101,16),
(fn_cp2k,False,False,16,57)]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn, convang=convang, nstephdr=nstephdr)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py, cc_f)
print ">>> ... coords"
tools.assert_array_equal(co_py, co_f)
print ">>> ... shapes"
assert cc_f.shape == (nstep,6)
assert co_f.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py[:,3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstep,natoms in [(fn_lmp,True,101,16),
(fn_lmp,True,101,16),
(fn_cp2k,False,16,57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print ">>> ... coords"
tools.assert_array_equal(co_py_fast, co_py_ref)
print ">>> ... shapes"
assert cc_py_ref.shape == (nstep,6)
assert co_py_ref.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py_fast[:,3:] > 50).all()