def test_api():
tr = get_rand_traj()
st = get_rand_struct()
for name in st.attr_lst:
assert getattr(tr, name) is not None
for name in tr.attrs_only_traj:
assert getattr(st, name) is None
aa = tr[0] # Structure
bb = tr[0:1] # Trajectory
keys = set.difference(set(aa.attr_lst), set(aa.attrs_only_traj))
assert aa.is_struct
assert bb.is_traj
# remove timeaxis before comparing arrays
for name in bb.attrs_nstep:
attr = getattr(bb, name)
if attr.ndim == 1:
setattr(bb, name, attr[0])
else:
setattr(bb, name, attr[0,...])
assert_dict_with_all_types_equal(aa.__dict__, bb.__dict__, keys=keys)
def test_api():
tr = get_rand_traj()
st = get_rand_struct()
for name in st.attr_lst:
assert getattr(tr, name) is not None
for name in tr.attrs_only_traj:
assert getattr(st, name) is None
aa = tr[0] # Structure
bb = tr[0:1] # Trajectory
keys = set.difference(set(aa.attr_lst), set(aa.attrs_only_traj))
assert aa.is_struct
assert bb.is_traj
# remove timeaxis before comparing arrays
for name in bb.attrs_nstep:
attr = getattr(bb, name)
if attr.ndim == 1:
setattr(bb, name, attr[0])
else:
setattr(bb, name, attr[0, ...])
assert_dict_with_all_types_equal(aa.__dict__, bb.__dict__, keys=keys)
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 assert_equal(d1, d2, keys=None):
if keys is None:
keys = ['x', 'y', 'xx', 'yy', 'zz', 'X', 'Y', 'Z', 'XY']
tools.assert_dict_with_all_types_equal(d1.__dict__, d2.__dict__, keys=keys)
def assert_equal(d1, d2, keys=None):
if keys is None:
keys = ['x','y','xx','yy','zz','X','Y','Z','XY']
tools.assert_dict_with_all_types_equal(d1.__dict__, d2.__dict__,
keys=keys)
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_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_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print(">>> comparing headers")
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref,
dct,
keys=list(ref.keys()),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstephdr, nstep, natoms in [
(fn_lmp, True, True, 101, 16), (fn_lmp, True, False, 101, 16),
(fn_cp2k, False, False, 16, 57)
]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn,
convang=convang,
nstephdr=nstephdr)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py, cc_f)
print(">>> ... coords")
tools.assert_array_equal(co_py, co_f)
print(">>> ... shapes")
assert cc_f.shape == (nstep, 6)
assert co_f.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py[:, 3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstep, natoms in [(fn_lmp, True, 101, 16),
(fn_lmp, True, 101, 16),
(fn_cp2k, False, 16, 57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print(">>> ... coords")
tools.assert_array_equal(co_py_fast, co_py_ref)
print(">>> ... shapes")
assert cc_py_ref.shape == (nstep, 6)
assert co_py_ref.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py_fast[:, 3:] > 50).all()
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
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_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print ">>> comparing headers"
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref, dct, keys=ref.keys(),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstephdr,nstep,natoms in [(fn_lmp,True,True,101,16),
(fn_lmp,True,False,101,16),
(fn_cp2k,False,False,16,57)]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn, convang=convang, nstephdr=nstephdr)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py, cc_f)
print ">>> ... coords"
tools.assert_array_equal(co_py, co_f)
print ">>> ... shapes"
assert cc_f.shape == (nstep,6)
assert co_f.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py[:,3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstep,natoms in [(fn_lmp,True,101,16),
(fn_lmp,True,101,16),
(fn_cp2k,False,16,57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print ">>> ... coords"
tools.assert_array_equal(co_py_fast, co_py_ref)
print ">>> ... shapes"
assert cc_py_ref.shape == (nstep,6)
assert co_py_ref.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py_fast[:,3:] > 50).all()
