def test_concatenate():
st = get_rand_struct()
nstep = 5
# cat Structure
tr_cat = crys.concatenate([st]*nstep)
keys = tr_cat.attr_lst
assert tr_cat.nstep == nstep
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__,
keys=keys)
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
print "test_concatenate: shape[0] == nstep:", attr_name
assert getattr(tr_cat, attr_name).shape[0] == nstep
print "test_concatenate: shape[0] == nstep:", attr_name, "...ok"
# cat Trajectory
tr = get_rand_traj()
tr_cat = crys.concatenate([tr]*3)
assert tr_cat.nstep == 3*tr.nstep
none_attrs = ['timestep', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in [tr_cat[0:tr.nstep],
tr_cat[tr.nstep:2*tr.nstep],
tr_cat[2*tr.nstep:3*tr.nstep]]:
assert_dict_with_all_types_equal(x.__dict__, tr.__dict__,
keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 3*tr.nstep
# cat mixed, Structure is minimal API
st = get_rand_struct()
tr = crys.concatenate([st]*5)
tr_cat = crys.concatenate([st]*5 + [tr])
assert tr_cat.nstep == 10
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__,
keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 10
def test_concatenate():
st = get_rand_struct()
nstep = 5
# cat Structure
tr_cat = crys.concatenate([st] * nstep)
keys = tr_cat.attr_lst
assert tr_cat.nstep == nstep
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__, keys=keys)
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
print("test_concatenate: shape[0] == nstep:", attr_name)
assert getattr(tr_cat, attr_name).shape[0] == nstep
print("test_concatenate: shape[0] == nstep:", attr_name, "...ok")
# cat Trajectory
tr = get_rand_traj()
tr_cat = crys.concatenate([tr] * 3)
assert tr_cat.nstep == 3 * tr.nstep
none_attrs = ['timestep', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in [
tr_cat[0:tr.nstep], tr_cat[tr.nstep:2 * tr.nstep],
tr_cat[2 * tr.nstep:3 * tr.nstep]
]:
assert_dict_with_all_types_equal(x.__dict__, tr.__dict__, keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 3 * tr.nstep
# cat mixed, Structure is minimal API
st = get_rand_struct()
tr = crys.concatenate([st] * 5)
tr_cat = crys.concatenate([st] * 5 + [tr])
assert tr_cat.nstep == 10
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__, keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 10
def test_scf_cell():
filename = 'files/pw.vc_relax_coords_fixed.out'
common.system('gunzip %s.gz' %filename)
pp = parse.PwSCFOutputFile(filename, use_alat=False)
cell_2d_red = pp.get_cell()
assert np.allclose(cell_2d_red, cell_2d_red_ref, atol=1e-15, rtol=0)
pp = parse.PwSCFOutputFile(filename, use_alat=True)
assert np.allclose(pp.get_cell(),
cell_2d_red*pp.get_alat(),
atol=1e-15,
rtol=0)
st = io.read_pw_scf(filename)
tr = io.read_pw_md(filename)
# tr is from a vc-relax w/ fixed fractional coords, check that
assert np.allclose(np.zeros((tr.nstep,tr.natoms,3)),
tr.coords_frac - tr.coords_frac[0,...].copy(),
rtol=0, atol=1e-15)
# check if scf parser gets the same coords_frac as the trajectory parser
# Note: this and the next test have the same max error of
# 4.33868466709e-08 (b/c of limited accuracy in printed numbers in
# pwscf output)
assert np.allclose(st.coords_frac,tr.coords_frac[0,...], atol=1e-7, rtol=0)
# same test, plus test of concatenate() works
trcat = crys.concatenate((st,tr))
assert np.allclose(np.zeros((trcat.nstep,trcat.natoms,3)),
trcat.coords_frac - trcat.coords_frac[0,...].copy(),
rtol=0, atol=1e-7)
def test_scf_cell():
filename = 'files/pw.vc_relax_coords_fixed.out'
common.system('gunzip %s.gz' % filename)
pp = parse.PwSCFOutputFile(filename, use_alat=False)
cell_2d_red = pp.get_cell()
assert np.allclose(cell_2d_red, cell_2d_red_ref, atol=1e-15, rtol=0)
pp = parse.PwSCFOutputFile(filename, use_alat=True)
assert np.allclose(pp.get_cell(),
cell_2d_red * pp.get_alat(),
atol=1e-15,
rtol=0)
st = io.read_pw_scf(filename)
tr = io.read_pw_md(filename)
# tr is from a vc-relax w/ fixed fractional coords, check that
assert np.allclose(np.zeros((tr.nstep, tr.natoms, 3)),
tr.coords_frac - tr.coords_frac[0, ...].copy(),
rtol=0,
atol=1e-15)
# check if scf parser gets the same coords_frac as the trajectory parser
# Note: this and the next test have the same max error of
# 4.33868466709e-08 (b/c of limited accuracy in printed numbers in
# pwscf output)
assert np.allclose(st.coords_frac,
tr.coords_frac[0, ...],
atol=1e-7,
rtol=0)
# same test, plus test of concatenate() works
trcat = crys.concatenate((st, tr))
assert np.allclose(np.zeros((trcat.nstep, trcat.natoms, 3)),
trcat.coords_frac - trcat.coords_frac[0, ...].copy(),
rtol=0,
atol=1e-7)
{st}
only in Trajectory:
{onlytr}
only in Structure:
{onlyst}
Attributes which are None w.r.t. the Trajectory API after the following
operation, starting with a fully populated struct or traj (all attrs not None):
""".format(st=st.attr_lst, tr=tr.attr_lst, onlytr=list(onlytr),
onlyst=list(onlyst))
items = [\
('tr', tr),
('tr.copy', tr.copy()),
('tr[0:5]', tr[0:5]),
('st', st),
('st.copy', st.copy()),
('tr[0]', tr[0]),
('mean(tr)', crys.mean(tr)),
('concatenate([st,st])', crys.concatenate([st,st])),
('concatenate([st,tr])', crys.concatenate([st,tr])),
('concatenate([tr,tr])', crys.concatenate([tr,tr])),
]
for name,obj in items:
none_attrs = set.difference(set(tr.attr_lst),
crys.populated_attrs([obj]))
typ = 'traj' if obj.is_traj else 'struct'
print "{:25} {:7} {}".format(name, typ, list(none_attrs))
{st}
only in Trajectory:
{onlytr}
only in Structure:
{onlyst}
Attributes which are None w.r.t. the Trajectory API after the following
operation, starting with a fully populated struct or traj (all attrs not None):
""".format(st=st.attr_lst, tr=tr.attr_lst, onlytr=list(onlytr),
onlyst=list(onlyst)))
items = [\
('tr', tr),
('tr.copy', tr.copy()),
('tr[0:5]', tr[0:5]),
('st', st),
('st.copy', st.copy()),
('tr[0]', tr[0]),
('mean(tr)', crys.mean(tr)),
('concatenate([st,st])', crys.concatenate([st,st])),
('concatenate([st,tr])', crys.concatenate([st,tr])),
('concatenate([tr,tr])', crys.concatenate([tr,tr])),
]
for name,obj in items:
none_attrs = set.difference(set(tr.attr_lst),
crys.populated_attrs([obj]))
typ = 'traj' if obj.is_traj else 'struct'
print("{:25} {:7} {}".format(name, typ, list(none_attrs)))
