def run(filename, none_attrs=[]):
# filename = 'files/cpmd/md_bo/cpmd.bo.out'
# basename = 'cpmd.bo.out'
# archive = 'files/cpmd/md_bo.tgz'
bar = '='*78
print bar
print "@@testing: %s" %filename
print bar
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdMDOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
attrs3d = ['coords',
'coords_frac',
'forces',
'cell',
'stress',
]
for attr_name in traj.attr_lst:
attr = getattr(traj, attr_name)
if attr_name not in none_attrs:
if hasattr(attr, 'ndim'):
print "%s: ndim: %s, shape: %s" %(attr_name, attr.ndim, attr.shape)
assert attr is not None, "FAILED - None: %s" %attr_name
if attr_name in attrs3d:
assert attr.ndim == 3, "FAILED - not 3d: %s" %attr_name
def run(filename, none_attrs=[]):
# filename = 'files/cpmd/md_bo/cpmd.bo.out'
# basename = 'cpmd.bo.out'
# archive = 'files/cpmd/md_bo.tgz'
bar = '=' * 78
print(bar)
print("@@testing: %s" % filename)
print(bar)
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdMDOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
attrs3d = [
'coords',
'coords_frac',
'forces',
'cell',
'stress',
]
for attr_name in traj.attr_lst:
attr = getattr(traj, attr_name)
if attr_name not in none_attrs:
if hasattr(attr, 'ndim'):
print("%s: ndim: %s, shape: %s" %
(attr_name, attr.ndim, attr.shape))
assert attr is not None, "FAILED - None: %s" % attr_name
if attr_name in attrs3d:
assert attr.ndim == 3, "FAILED - not 3d: %s" % attr_name
def test_cpmd_scf():
filename = "files/cpmd/scf/cpmd.out"
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + ".tgz"
workdir = unpack_compressed(archive)
pp = CpmdSCFOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=[])
def test_cp2k_scf():
attr_lst = parse.Cp2kSCFOutputFile().attr_lst
for base in ['cp2k.scf.out.print_low', 'cp2k.scf.out.print_medium']:
fn = 'files/cp2k/scf/%s' % base
print("testing: %s" % fn)
print(common.backtick("gunzip %s.gz" % fn))
st = io.read_cp2k_scf(fn)
assert_attrs_not_none(st, attr_lst=attr_lst)
def test_cp2k_scf():
attr_lst = parse.Cp2kSCFOutputFile().attr_lst
for base in ['cp2k.scf.out.print_low', 'cp2k.scf.out.print_medium']:
fn = 'files/cp2k/scf/%s' %base
print "testing: %s" %fn
print common.backtick("gunzip %s.gz" %fn)
st = io.read_cp2k_scf(fn)
assert_attrs_not_none(st, attr_lst=attr_lst)
def test_cpmd_scf():
filename = 'files/cpmd/scf/cpmd.out'
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdSCFOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=[])
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' % dr
print("testing: %s" % fn)
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base, dr)))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile() * Ha / Bohr / eV * Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print "testing: %s" %fn
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile()*Ha/Bohr/eV*Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
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_pw_scf_one_atom():
fn = unpack_compressed('files/pw.scf_one_atom.out.gz')
pp = PwSCFOutputFile(fn)
pp.parse()
not_none = [\
'coords',
'symbols',
'stress',
'etot',
'forces',
'nstep_scf',
'cell',
'natoms',
'nkpoints',
]
tools.assert_attrs_not_none(pp, attr_lst=not_none)
assert pp.forces.shape == (1, 3)
assert pp.coords.shape == (1, 3)
assert pp.stress.shape == (3, 3)
assert pp.cell.shape == (3, 3)
def test_pw_scf_one_atom():
fn = unpack_compressed('files/pw.scf_one_atom.out.gz')
pp = PwSCFOutputFile(fn)
pp.parse()
not_none = [\
'coords',
'symbols',
'stress',
'etot',
'forces',
'nstep_scf',
'cell',
'natoms',
'nkpoints',
]
tools.assert_attrs_not_none(pp, attr_lst=not_none)
assert pp.forces.shape == (1,3)
assert pp.coords.shape == (1,3)
assert pp.stress.shape == (3,3)
assert pp.cell.shape == (3,3)
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_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_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_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_smooth():
tr = get_rand_traj()
assert len(tr.attrs_nstep) > 0
trs = crys.smooth(tr, hanning(11))
assert len(trs.attrs_nstep) > 0
assert_attrs_not_none(trs, attr_lst=tr.attr_lst)
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs, name)
assert a1.shape == a2.shape
assert np.abs(a1 - a2).sum() > 0.0
assert trs.timestep == tr.timestep
assert trs.nstep == tr.nstep
# reproduce data with kernel [0,1,0]
trs = crys.smooth(tr, hanning(3))
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs, name)
assert np.allclose(a1, a2)
trs1 = crys.smooth(tr, hanning(3), method=1)
trs2 = crys.smooth(tr, hanning(3), method=2)
assert len(trs1.attrs_nstep) > 0
assert len(trs2.attrs_nstep) > 0
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs1, name)
a3 = getattr(trs2, name)
assert np.allclose(a1, a2)
assert np.allclose(a1, a3)
trs1 = crys.smooth(tr, hanning(11), method=1)
trs2 = crys.smooth(tr, hanning(11), method=2)
assert len(trs1.attrs_nstep) > 0
assert len(trs2.attrs_nstep) > 0
for name in trs1.attrs_nstep:
a1 = getattr(trs1, name)
a2 = getattr(trs2, name)
assert np.allclose(a1, a2)
def test_smooth():
tr = get_rand_traj()
assert len(tr.attrs_nstep) > 0
trs = crys.smooth(tr, hanning(11))
assert len(trs.attrs_nstep) > 0
assert_attrs_not_none(trs, attr_lst=tr.attr_lst)
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs, name)
assert a1.shape == a2.shape
assert np.abs(a1 - a2).sum() > 0.0
assert trs.timestep == tr.timestep
assert trs.nstep == tr.nstep
# reproduce data with kernel [0,1,0]
trs = crys.smooth(tr, hanning(3))
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs, name)
assert np.allclose(a1, a2)
trs1 = crys.smooth(tr, hanning(3), method=1)
trs2 = crys.smooth(tr, hanning(3), method=2)
assert len(trs1.attrs_nstep) > 0
assert len(trs2.attrs_nstep) > 0
for name in tr.attrs_nstep:
a1 = getattr(tr, name)
a2 = getattr(trs1, name)
a3 = getattr(trs2, name)
assert np.allclose(a1, a2)
assert np.allclose(a1, a3)
trs1 = crys.smooth(tr, hanning(11), method=1)
trs2 = crys.smooth(tr, hanning(11), method=2)
assert len(trs1.attrs_nstep) > 0
assert len(trs2.attrs_nstep) > 0
for name in trs1.attrs_nstep:
a1 = getattr(trs1, name)
a2 = getattr(trs2, name)
assert np.allclose(a1, a2)
def test_cp2k_cell_opt():
attr_lst = parse.Cp2kRelaxOutputFile().attr_lst
attr_lst.pop(attr_lst.index('econst'))
# There is no PROJECT-frc-1.xyz file, but the input file has
# &force_eval
# &print
# &forces
# &end forces
# &end print
# &end force_eval
# therefore we can parse forces from the outfile.
none_attrs = ['ekin',
'temperature',
'timestep',
'velocity',
]
for dr in ['files/cp2k/cell_opt/cell_opt']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print "testing: %s" %fn
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_relax(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst, none_attrs=none_attrs)
def test_cp2k_cell_opt():
attr_lst = parse.Cp2kRelaxOutputFile().attr_lst
attr_lst.pop(attr_lst.index('econst'))
# There is no PROJECT-frc-1.xyz file, but the input file has
# &force_eval
# &print
# &forces
# &end forces
# &end print
# &end force_eval
# therefore we can parse forces from the outfile.
none_attrs = [
'ekin',
'temperature',
'timestep',
'velocity',
]
for dr in ['files/cp2k/cell_opt/cell_opt']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' % dr
print("testing: %s" % fn)
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base, dr)))
tr = io.read_cp2k_relax(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst, none_attrs=none_attrs)
def test_traj():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
stress = rand(nstep,3,3)
forces = rand(nstep,natoms,3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep,natoms,3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep,natoms,3)
symbols = ['H']*natoms
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print "test if getters work:", name
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" %name
assert eval('traj.get_%s()'%name) is not None, "getter returns None: %s" %name
print "test if getters work:", name, "... ok"
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2)/3.0, traj.pressure)
assert traj.coords.shape == (nstep,natoms,3)
assert traj.cell.shape == (nstep,3,3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep,)
assert traj.ekin.shape == (nstep,)
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3,3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac,
cell=cell2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cell[ii,...] == cell2d).all()
assert (traj.cryst_const[ii,:] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii,:] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={'length': 2, 'forces': 3, 'stress': 4})
aaae(2*coords, traj.coords)
aaae(3*forces, traj.forces)
aaae(4*stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" %attr_name
assert getattr(struct,attr_name) is None, msg
else:
msg = "tr[0] %s is None" %attr_name
assert getattr(struct,attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10,80,2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" %(cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj,name)
if val is not None and not (isinstance(val, types.IntType) or \
isinstance(val, types.FloatType)):
val2 = getattr(traj2,name)
print "test copy:", name, type(val), type(val2)
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__,
keys=traj.attr_lst)
def test_traj():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
stress = rand(nstep, 3, 3)
forces = rand(nstep, natoms, 3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep, natoms, 3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,
axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep, natoms, 3)
symbols = ['H'] * natoms
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(
coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print("test if getters work:", name)
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" % name
assert eval('traj.get_%s()' %
name) is not None, "getter returns None: %s" % name
print("test if getters work:", name, "... ok")
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2) / 3.0, traj.pressure)
assert traj.coords.shape == (nstep, natoms, 3)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep, )
assert traj.ekin.shape == (nstep, )
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3, 3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cell[ii, ...] == cell2d).all()
assert (traj.cryst_const[ii, :] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii, :] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={
'length': 2,
'forces': 3,
'stress': 4
})
aaae(2 * coords, traj.coords)
aaae(3 * forces, traj.forces)
aaae(4 * stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" % attr_name
assert getattr(struct, attr_name) is None, msg
else:
msg = "tr[0] %s is None" % attr_name
assert getattr(struct, attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10, 80, 2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" % (cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj, name)
if val is not None and not (isinstance(val, int) or \
isinstance(val, float)):
val2 = getattr(traj2, name)
print("test copy:", name, type(val), type(val2))
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__,
traj2.__dict__,
keys=traj.attr_lst)
def test_pw_scf_out():
# ref data for Structure, all lengths in Ang, energy in eV
natoms = 2
symbols = ['Si', 'Si']
cell = np.array([[-2.71536701, 0. , 2.71536701],
[ 0. , 2.71536701, 2.71536701],
[-2.71536701, 2.71536701, 0. ]])
forces = np.array([[ 2.57110316, 5.14220632, 7.71330948],
[-2.57110316, -5.14220632, -7.71330948]]) # eV / Ang
nspecies = {'Si': 2}
mass = np.array([ 28.0855, 28.0855]) # amu
cryst_const = np.array([ 3.84010885, 3.84010885, 3.84010885, 60. ,
60. , 60. ])
symbols_unique = ['Si']
etot = -258.58148870118305 # eV
typat = [1, 1]
volume = 40.041985843396688 # Ang**3
stress = np.array([[ 9.825, 0. , 0. ],
[ 0. , 9.825, 0. ],
[ 0. , 0. , 9.825]]) # GPa
coords_frac = np.array([[ 0. , 0. , 0. ],
[ 0.25, 0.25, 0.25]])
pressure = 9.825 # GPa
coords = np.array([[ 0. , 0. , 0. ],
[-1.35768351, 1.35768351, 1.35768351]])
order = {'Si': 1}
alat = 10.2626 # Bohr
filename = 'files/pw.scf.out'
common.system('gunzip %s.gz' %filename)
# use_alat=False. Provide high-precision alat from outside (e.g.
# from pw.in instead of parsing and using low-precision value from pw.out).
# Here we use the same alat for the tests.
pp1 = PwSCFOutputFile(filename=filename,
use_alat=False, # alat=1.0
units={'length': alat*Bohr/Ang})
struct1 = pp1.get_struct() # pp1.parse() called here
assert_attrs_not_none(struct1)
assert_attrs_not_none(pp1)
assert pp1.scf_converged is True
assert alat == pp1.get_alat(True)
assert 1.0 == pp1.get_alat(False)
aaae(cryst_const, struct1.cryst_const)
aaae(cell, struct1.cell)
aaae(coords, struct1.coords)
aaae(coords_frac, struct1.coords_frac)
aaae(forces, struct1.forces)
aaae(stress, struct1.stress)
assert np.allclose(volume, struct1.volume)
assert np.allclose(etot, struct1.etot)
assert np.allclose(pressure, struct1.pressure)
# use_alat=True, alat = 10.2626 Bohr
pp2 = PwSCFOutputFile(filename=filename, use_alat=True)
struct2 = pp2.get_struct() # pp.parse() called here
assert_attrs_not_none(struct2)
assert_attrs_not_none(pp2)
assert np.allclose(alat, pp2.alat)
assert pp2.scf_converged is True
assert alat == pp2.get_alat(True) # Bohr
assert 1.0 == pp2.get_alat(False)
# Skip coords adn cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 10.2626
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
attr_lst = struct1.attr_lst
adae(struct1.__dict__, struct2.__dict__, keys=attr_lst)
pp3 = PwSCFOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
common.system('gzip %s' %filename)
def test_pw_scf_out():
# ref data for Structure, all lengths in Ang, energy in eV
natoms = 2
symbols = ['Si', 'Si']
cell = np.array([[-2.71536701, 0.,
2.71536701], [0., 2.71536701, 2.71536701],
[-2.71536701, 2.71536701, 0.]])
forces = np.array([[2.57110316, 5.14220632, 7.71330948],
[-2.57110316, -5.14220632, -7.71330948]]) # eV / Ang
nspecies = {'Si': 2}
mass = np.array([28.0855, 28.0855]) # amu
cryst_const = np.array([3.84010885, 3.84010885, 3.84010885, 60., 60., 60.])
symbols_unique = ['Si']
etot = -258.58148870118305 # eV
typat = [1, 1]
volume = 40.041985843396688 # Ang**3
stress = np.array([[9.825, 0., 0.], [0., 9.825, 0.], [0., 0.,
9.825]]) # GPa
coords_frac = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
pressure = 9.825 # GPa
coords = np.array([[0., 0., 0.], [-1.35768351, 1.35768351, 1.35768351]])
order = {'Si': 1}
alat = 10.2626 # Bohr
filename = 'files/pw.scf.out'
common.system('gunzip %s.gz' % filename)
# use_alat=False. Provide high-precision alat from outside (e.g.
# from pw.in instead of parsing and using low-precision value from pw.out).
# Here we use the same alat for the tests.
pp1 = PwSCFOutputFile(
filename=filename,
use_alat=False, # alat=1.0
units={'length': alat * Bohr / Ang})
struct1 = pp1.get_struct() # pp1.parse() called here
assert_attrs_not_none(struct1)
assert_attrs_not_none(pp1)
assert pp1.scf_converged is True
assert alat == pp1.get_alat(True)
assert 1.0 == pp1.get_alat(False)
aaae(cryst_const, struct1.cryst_const)
aaae(cell, struct1.cell)
aaae(coords, struct1.coords)
aaae(coords_frac, struct1.coords_frac)
aaae(forces, struct1.forces)
aaae(stress, struct1.stress)
assert np.allclose(volume, struct1.volume)
assert np.allclose(etot, struct1.etot)
assert np.allclose(pressure, struct1.pressure)
# use_alat=True, alat = 10.2626 Bohr
pp2 = PwSCFOutputFile(filename=filename, use_alat=True)
struct2 = pp2.get_struct() # pp.parse() called here
assert_attrs_not_none(struct2)
assert_attrs_not_none(pp2)
assert np.allclose(alat, pp2.alat)
assert pp2.scf_converged is True
assert alat == pp2.get_alat(True) # Bohr
assert 1.0 == pp2.get_alat(False)
# Skip coords adn cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 10.2626
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
attr_lst = struct1.attr_lst
adae(struct1.__dict__, struct2.__dict__, keys=attr_lst)
pp3 = PwSCFOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
common.system('gzip %s' % filename)
