def test_pw_md_out():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
alat = 5.9098 # Bohr
pp1 = PwMDOutputFile(filename=filename, use_alat=True)
pp1.parse()
none_attrs = [\
'coords_frac',
]
assert_attrs_not_none(pp1, none_attrs=none_attrs)
assert np.allclose(pp1.timestep, 150.0) # tryd
traj1 = pp1.get_traj()
assert_attrs_not_none(traj1)
pp2 = PwMDOutputFile(filename=filename,
use_alat=False,
units={'length': alat*Bohr/Ang})
pp2.parse()
assert np.allclose(pp2.timestep, 150.0) # tryd
assert_attrs_not_none(pp2, none_attrs=none_attrs)
# Skip coords and cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 5.9098
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
traj2 = pp2.get_traj()
adae(traj1.__dict__, traj2.__dict__, keys=traj1.attr_lst)
pp3 = PwMDOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
def test_pw_vc_relax_out():
filename = 'files/pw.vc_relax.out'
common.system('gunzip %s.gz' %filename)
pp = PwMDOutputFile(filename=filename)
pp.parse()
common.system('gzip %s' %filename)
none_attrs = ['coords',
'ekin',
'temperature',
'timestep',
]
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
none_attrs = [\
'ekin',
'temperature',
'timestep',
'velocity',
'time',
]
assert_attrs_not_none(traj, none_attrs=none_attrs)
def test_save_object():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
dumpfile = os.path.join(testdir, 'pw.md.pk')
c = PwMDOutputFile(filename=filename)
print ">>> parsing ..."
c.parse()
print ">>> ... done"
print ">>> saving %s ..." %dumpfile
c.dump(dumpfile)
print ">>> ... done"
print ">>> loading ..."
c2 = PwMDOutputFile()
c2.load(dumpfile)
print ">>> ... done"
print ">>> checking equalness of attrs in loaded object ..."
known_fails = {'fd': 'closed/uninitialized file',
'cont': 'container object'}
arr_t = type(np.array([1]))
dict_t = type({})
for attr in c.__dict__.iterkeys():
c_val = getattr(c, attr)
c2_val = getattr(c2, attr)
dotest = True
for name, string in known_fails.iteritems():
if name == attr:
print "known fail: %s: %s: %s" %(name, string, attr)
dotest = False
if dotest:
print "testing:", attr, type(c_val), type(c2_val)
type_c = type(c_val)
type_c2 = type(c2_val)
assert type_c is type_c2, "attr: %s: types differ: %s, %s" \
%(attr, str(type_c), str(type_c2))
if type(c_val) is arr_t:
assert (c_val == c2_val).all(), "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
elif type(c_val) is dict_t:
ade(c_val, c2_val)
else:
assert c_val == c2_val, "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
def test_pw_vc_relax_out():
filename = 'files/pw.vc_relax_cell_unit.out'
common.system('gunzip %s.gz' % filename)
pp = PwMDOutputFile(filename=filename)
pp.parse()
common.system('gzip %s' % filename)
none_attrs = [
'coords',
'ekin',
'temperature',
'timestep',
]
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
none_attrs = [\
'ekin',
'temperature',
'timestep',
'velocity',
'time',
]
assert_attrs_not_none(traj, none_attrs=none_attrs)
assert pp.cell_unit == 'alat'
assert pp.cell.shape == (6, 3, 3)
for idx in range(1, pp.cell.shape[0]):
assert crys.rms(pp.cell[idx, ...] - pp.cell[0, ...]) > 0.0
# Test _get_block_header_unit, which is used in get_cell_unit().
dct = \
{'FOO': None,
'FOO alat': 'alat',
'FOO (alat)': 'alat',
'FOO {alat}': 'alat',
'FOO (alat=1.23)': 'alat',
'FOO (alat= 1.23)': 'alat',
}
for txt, val in dct.items():
fn = pj(testdir, 'test_block_header_unit.txt')
common.file_write(fn, txt)
pp.filename = fn
assert pp._get_block_header_unit('FOO') == val
def test_save_object():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
dumpfile = os.path.join(testdir, 'pw.md.pk')
c = PwMDOutputFile(filename=filename)
print(">>> parsing ...")
c.parse()
print(">>> ... done")
print(">>> saving %s ..." %dumpfile)
c.dump(dumpfile)
print(">>> ... done")
print(">>> loading ...")
c2 = io.read_pickle(dumpfile)
print(">>> ... done")
print(">>> checking equalness of attrs in loaded object ...")
known_fails = {'fd': 'closed/uninitialized file',
'cont': 'container object'}
arr_t = type(np.array([1]))
dict_t = type({})
for attr in c.__dict__.keys():
c_val = getattr(c, attr)
c2_val = getattr(c2, attr)
dotest = True
for name, string in known_fails.items():
if name == attr:
print("known fail: %s: %s: %s" %(name, string, attr))
dotest = False
if dotest:
print("testing:", attr, type(c_val), type(c2_val))
type_c = type(c_val)
type_c2 = type(c2_val)
assert type_c is type_c2, "attr: %s: types differ: %s, %s" \
%(attr, str(type_c), str(type_c2))
if type(c_val) is arr_t:
assert (c_val == c2_val).all(), "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
elif type(c_val) is dict_t:
ade(c_val, c2_val)
else:
assert c_val == c2_val, "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
def test_pw_vc_relax_out():
filename = 'files/pw.vc_relax_cell_unit.out'
common.system('gunzip %s.gz' %filename)
pp = PwMDOutputFile(filename=filename)
pp.parse()
common.system('gzip %s' %filename)
none_attrs = ['coords',
'ekin',
'temperature',
'timestep',
]
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
none_attrs = [\
'ekin',
'temperature',
'timestep',
'velocity',
'time',
]
assert_attrs_not_none(traj, none_attrs=none_attrs)
assert pp.cell_unit == 'alat'
assert pp.cell.shape == (6,3,3)
for idx in range(1, pp.cell.shape[0]):
assert crys.rms(pp.cell[idx,...] - pp.cell[0,...]) > 0.0
# Test _get_block_header_unit, which is used in get_cell_unit().
dct = \
{'FOO': None,
'FOO alat': 'alat',
'FOO (alat)': 'alat',
'FOO {alat}': 'alat',
'FOO (alat=1.23)': 'alat',
'FOO (alat= 1.23)': 'alat',
}
for txt,val in dct.iteritems():
fn = pj(testdir, 'test_block_header_unit.txt')
common.file_write(fn, txt)
pp.filename = fn
assert pp._get_block_header_unit('FOO') == val
def test_pw_more_forces():
fac = Ry / eV / Bohr * Ang
# MD: london=.true.
filename = 'files/pw.md_london.out'
common.system('gunzip %s.gz' %filename)
natoms = 141
nstep = 10
# traj case
pp = PwMDOutputFile(filename=filename)
tr = pp.get_traj()
assert tr.natoms == natoms
assert tr.forces.shape == (nstep,natoms,3)
assert tr.coords.shape == (nstep,natoms,3)
assert pp._forces_raw.shape == (nstep+1,2*natoms,3)
assert np.allclose(tr.forces, pp._forces_raw[1:,:natoms,:] * fac)
# scf case, return only 1st step
pp = PwSCFOutputFile(filename=filename)
st = pp.get_struct()
assert st.natoms == natoms
assert st.forces.shape == (natoms,3)
assert st.coords.shape == (natoms,3)
assert pp._forces_raw.shape == (nstep+1,2*natoms,3)
assert np.allclose(st.forces, pp._forces_raw[0,:natoms,:] * fac)
common.system('gzip %s' %filename)
# SCF: verbosity='high' + london=.true.
filename = 'files/pw.scf_verbose_london.out'
common.system('gunzip %s.gz' %filename)
natoms = 4
nstep = 1
pp = PwSCFOutputFile(filename=filename)
st = pp.get_struct()
assert st.natoms == natoms
assert st.forces.shape == (natoms,3)
assert st.coords.shape == (natoms,3)
assert pp._forces_raw.shape == (nstep, 8*natoms,3)
assert np.allclose(st.forces, pp._forces_raw[0,:natoms,:] * fac)
common.system('gzip %s' %filename)
# MD: verbosity='high' + natoms=1
filename = 'files/pw.md_one_atom.out'
common.system('gunzip %s.gz' %filename)
natoms = 1
nstep = 4
# traj case
pp = PwMDOutputFile(filename=filename)
tr = pp.get_traj()
assert tr.natoms == natoms
assert tr.forces.shape == (nstep,natoms,3)
assert tr.coords.shape == (nstep,natoms,3)
assert pp._forces_raw.shape == (nstep+1,7*natoms,3)
assert np.allclose(tr.forces, pp._forces_raw[1:,:natoms,:] * fac)
# scf case, return only 1st step
pp = PwSCFOutputFile(filename=filename)
st = pp.get_struct()
assert st.natoms == natoms
assert st.forces.shape == (natoms,3)
assert st.coords.shape == (natoms,3)
assert pp._forces_raw.shape == (nstep+1,7*natoms,3)
assert np.allclose(st.forces, pp._forces_raw[0,:natoms,:] * fac)
common.system('gzip %s' %filename)
def test_return_3d_if_no_cell_unit():
filename = tools.unpack_compressed('files/pw.vc_relax_no_cell_unit.out.gz',
prefix=__file__)
pp = PwMDOutputFile(filename=filename)
pp.parse()
assert np.allclose(pp.cell, _cell*pp.get_alat())
def test_pw_md_out():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
alat = 5.9098 # Bohr
pp1 = PwMDOutputFile(filename=filename, use_alat=True)
pp1.parse()
none_attrs = [\
'coords_frac',
]
assert_attrs_not_none(pp1, none_attrs=none_attrs)
assert np.allclose(pp1.timestep, 150.0) # tryd
traj1 = pp1.get_traj()
assert_attrs_not_none(traj1)
pp2 = PwMDOutputFile(filename=filename,
use_alat=False,
units={'length': alat * Bohr / Ang})
pp2.parse()
assert np.allclose(pp2.timestep, 150.0) # tryd
assert_attrs_not_none(pp2, none_attrs=none_attrs)
# Skip coords and cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 5.9098
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
traj2 = pp2.get_traj()
adae(traj1.__dict__, traj2.__dict__, keys=traj1.attr_lst)
pp3 = PwMDOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
