def test_pw_scf_no_forces_stress():
fn = unpack_compressed('files/pw.scf_no_forces_stress.out.gz')
pp = PwSCFOutputFile(fn)
assert pp.get_forces() is None
assert pp.get_stress() is None
st = io.read_pw_scf(fn)
assert st.stress is None
assert st.forces is None
def test_pw_scf_no_forces_stress():
fn = unpack_compressed('files/pw.scf_no_forces_stress.out.gz')
pp = PwSCFOutputFile(fn)
assert pp.get_forces() is None
assert pp.get_stress() is None
st = io.read_pw_scf(fn)
assert st.stress is None
assert st.forces is None
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_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_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)
