def run(tgz, skip=[], atol_map={}):
tgz_path = os.path.dirname(tgz)
unpack_path = tgz.replace('.tgz', '')
common.system("tar -C {0} -xzf {1}".format(tgz_path, tgz))
tr1 = io.read_lammps_md_txt("{0}/log.lammps".format(unpack_path))
tr2 = io.read_lammps_md_dcd("{0}/log.lammps".format(unpack_path))
for name in tr1.attr_lst:
if name in skip:
continue
elif name in atol_map:
set_atol(atol_map[name])
else:
set_atol()
x1 = getattr(tr1, name)
x2 = getattr(tr2, name)
print(name)
tools.assert_all_types_almost_equal(x1, x2)
# stress
assert (tr1.stress[:, 0, 1] == tr1.stress[:, 1, 0]).all()
assert (tr1.stress[:, 0, 2] == tr1.stress[:, 2, 0]).all()
assert (tr1.stress[:, 1, 2] == tr1.stress[:, 2, 1]).all()
def run(tgz, skip=[], atol_map={}):
tgz_path = os.path.dirname(tgz)
unpack_path = tgz.replace('.tgz','')
common.system("tar -C {0} -xzf {1}".format(tgz_path,tgz))
tr1 = io.read_lammps_md_txt("{0}/log.lammps".format(unpack_path))
tr2 = io.read_lammps_md_dcd("{0}/log.lammps".format(unpack_path))
for name in tr1.attr_lst:
if name in skip:
continue
elif atol_map.has_key(name):
set_atol(atol_map[name])
else:
set_atol()
x1 = getattr(tr1, name)
x2 = getattr(tr2, name)
print name
tools.assert_all_types_almost_equal(x1, x2)
# stress
assert (tr1.stress[:,0,1] == tr1.stress[:,1,0]).all()
assert (tr1.stress[:,0,2] == tr1.stress[:,2,0]).all()
assert (tr1.stress[:,1,2] == tr1.stress[:,2,1]).all()
def test_mix():
symbols = ['H']*3 + ['Au']*7
natoms = len(symbols)
st1nf = Structure(coords_frac=rand(natoms,3),
symbols=symbols,
cell=rand(3,3))
st2nf = Structure(coords_frac=rand(natoms,3),
symbols=symbols,
cell=rand(3,3))
st1f = Structure(coords_frac=rand(natoms,3),
symbols=symbols,
cell=rand(3,3),
forces=rand(natoms,3))
st2f = Structure(coords_frac=rand(natoms,3),
symbols=symbols,
cell=rand(3,3),
forces=rand(natoms,3))
for st1,st2 in [(st1f, st2f), (st1nf, st2nf)]:
tr = crys.mix(st1, st2, alpha=np.linspace(0,1,20))
assert tr.nstep == 20
assert tr.coords_frac.shape == (20, st1.natoms, 3)
for idx,st in [(0,st1), (-1, st2)]:
tools.assert_dict_with_all_types_almost_equal(st.__dict__,
tr[idx].__dict__,
keys=st1.attr_lst)
for x in [0.5, 0.9]:
tr = crys.mix(st1, st2, alpha=np.array([x]))
assert tr.nstep == 1
tools.assert_all_types_almost_equal(tr[0].coords, (1-x)*st1.coords + x*st2.coords)
tools.assert_all_types_almost_equal(tr[0].cell, (1-x)*st1.cell + x*st2.cell)
if tr.forces is not None:
tools.assert_all_types_almost_equal(tr[0].forces, (1-x)*st1.forces + x*st2.forces)
def test_mix():
symbols = ['H'] * 3 + ['Au'] * 7
natoms = len(symbols)
st1nf = Structure(coords_frac=rand(natoms, 3),
symbols=symbols,
cell=rand(3, 3))
st2nf = Structure(coords_frac=rand(natoms, 3),
symbols=symbols,
cell=rand(3, 3))
st1f = Structure(coords_frac=rand(natoms, 3),
symbols=symbols,
cell=rand(3, 3),
forces=rand(natoms, 3))
st2f = Structure(coords_frac=rand(natoms, 3),
symbols=symbols,
cell=rand(3, 3),
forces=rand(natoms, 3))
for st1, st2 in [(st1f, st2f), (st1nf, st2nf)]:
tr = crys.mix(st1, st2, alpha=np.linspace(0, 1, 20))
assert tr.nstep == 20
assert tr.coords_frac.shape == (20, st1.natoms, 3)
for idx, st in [(0, st1), (-1, st2)]:
tools.assert_dict_with_all_types_almost_equal(st.__dict__,
tr[idx].__dict__,
keys=st1.attr_lst)
for x in [0.5, 0.9]:
tr = crys.mix(st1, st2, alpha=np.array([x]))
assert tr.nstep == 1
tools.assert_all_types_almost_equal(
tr[0].coords, (1 - x) * st1.coords + x * st2.coords)
tools.assert_all_types_almost_equal(
tr[0].cell, (1 - x) * st1.cell + x * st2.cell)
if tr.forces is not None:
tools.assert_all_types_almost_equal(
tr[0].forces, (1 - x) * st1.forces + x * st2.forces)
def test_tools():
x1 = {
'a': 3,
type(1): 'foo',
'b': {
'aa': 1,
'bb': np.array([1, 2]),
'cc': {
'aaa': np.array([1, 2.0]),
'bbb': np.array([2, 4.0])
}
}
}
x2 = copy.deepcopy(x1)
tools.assert_dict_with_all_types_equal(x1, x2)
tools.assert_all_types_equal(x1, x2)
# not equal array
x2['b']['cc']['bbb'] *= 2.0
assert not tools.all_types_equal(x1, x2)
# almost equal array and float
x2 = copy.deepcopy(x1)
x2['b']['cc']['bbb'] += 1e-5
x2['b']['aa'] += 1e-5
tools.assert_all_types_almost_equal(x1, x2)
# sub-dict different (keys don't match)
x2 = copy.deepcopy(x1)
x2['b']['cc']['fff'] = 'extra'
assert not tools.all_types_equal(x1, x2)
# test only some keys of a dict
tools.assert_dict_with_all_types_equal({
'a': 1,
'b': 1
}, {
'a': 1,
'b': 3
},
keys=['a'])
# simple stuff
tools.assert_all_types_equal(1, 1)
tools.assert_all_types_equal(1.0, 1.0)
tools.assert_all_types_equal(1.0, 1)
tools.assert_all_types_equal(1, 1.0)
tools.assert_all_types_equal([1], [1])
tools.assert_all_types_equal([1], [1.0])
tools.assert_all_types_equal('a', 'a')
tools.assert_all_types_almost_equal(1.0, 1.0 + 1e-5)
tools.assert_all_types_almost_equal(np.array([1.0]),
np.array([1.0 + 1e-5]))
assert not tools.all_types_equal(1, 2)
assert not tools.all_types_equal(1.0, 1.1)
assert not tools.all_types_equal([1], [1, 2])
assert not tools.all_types_equal('a', 'b')
# different types not allowed if strict=True
assert not tools.all_types_equal(1.0, 1, strict=True)
# test keys=[...], i.e. ignore some keys in both dicts
x2 = copy.deepcopy(x1)
x2['c'] = 1.0
assert tools.dict_with_all_types_equal(x1, x2, keys=['a', 'b', type(1)])
# fail on same array content but different dimensions
a = np.random.rand(1, 2, 3)
b = a[None, ...]
# this is True and IMHO a numpy bug b/c the dimensions are
# different
assert (a == b).all()
# must catch that here
assert not tools.array_equal(a, b)
a = np.random.rand(1, 2, 3)
b = (a + 1e-8)[None, ...]
assert not (a == b).all() # make sure they are numerically differrent
assert np.allclose(a, b) # True but should be False
assert not tools.array_almost_equal(a, b) # ok
flt = 1.0
np_flt = np.array([1.0 + 1e-9])[0]
assert not tools.all_types_equal(flt, np_flt)
assert not tools.all_types_equal(np_flt, flt)
assert tools.all_types_almost_equal(flt, np_flt)
assert tools.all_types_almost_equal(np_flt, flt)
def test_tools():
x1 = {'a': 3,
type(1): 'foo',
'b': {'aa': 1,
'bb': np.array([1,2]),
'cc': {'aaa': np.array([1,2.0]),
'bbb': np.array([2,4.0])}}}
x2 = copy.deepcopy(x1)
tools.assert_dict_with_all_types_equal(x1, x2)
tools.assert_all_types_equal(x1, x2)
# not equal array
x2['b']['cc']['bbb'] *= 2.0
assert not tools.all_types_equal(x1, x2)
# almost equal array and float
x2 = copy.deepcopy(x1)
x2['b']['cc']['bbb'] += 1e-5
x2['b']['aa'] += 1e-5
tools.assert_all_types_almost_equal(x1, x2)
# sub-dict different (keys don't match)
x2 = copy.deepcopy(x1)
x2['b']['cc']['fff'] = 'extra'
assert not tools.all_types_equal(x1, x2)
# test only some keys of a dict
tools.assert_dict_with_all_types_equal({'a':1,'b':1}, {'a':1, 'b':3},
keys=['a'])
# simple stuff
tools.assert_all_types_equal(1, 1)
tools.assert_all_types_equal(1.0, 1.0)
tools.assert_all_types_equal(1.0, 1)
tools.assert_all_types_equal(1, 1.0)
tools.assert_all_types_equal([1], [1])
tools.assert_all_types_equal([1], [1.0])
tools.assert_all_types_equal('a', 'a')
tools.assert_all_types_almost_equal(1.0, 1.0+1e-5)
tools.assert_all_types_almost_equal(np.array([1.0]), np.array([1.0+1e-5]))
assert not tools.all_types_equal(1, 2)
assert not tools.all_types_equal(1.0, 1.1)
assert not tools.all_types_equal([1], [1,2])
assert not tools.all_types_equal('a', 'b')
# different types not allowed if strict=True
assert not tools.all_types_equal(1.0, 1, strict=True)
# test keys=[...], i.e. ignore some keys in both dicts
x2 = copy.deepcopy(x1)
x2['c'] = 1.0
assert tools.dict_with_all_types_equal(x1, x2, keys=['a','b',type(1)])
# fail on same array content but different dimensions
a = np.random.rand(1,2,3)
b = a[None,...]
# this is True and IMHO a numpy bug b/c the dimensions are
# different
assert (a==b).all()
# must catch that here
assert not tools.array_equal(a,b)
a = np.random.rand(1,2,3)
b = (a + 1e-8)[None,...]
assert not (a==b).all() # make sure they are numerically differrent
assert np.allclose(a,b) # True but should be False
assert not tools.array_almost_equal(a,b) # ok
