def test_rms():
natoms = 5
nstep = 10
arr1 = np.random.rand(nstep, 3, natoms)
arr2 = np.random.rand(natoms, nstep, 3)
arr3 = np.random.rand(natoms, 3, nstep)
# Test if rms() works.
r3_rms_all1 = crys.rms(arr3, nitems='all')
r3_rms_natoms1 = crys.rms(arr3, nitems=natoms)
r3_rms_all2 = np.sqrt((arr3**2.0).sum() / float(3*natoms*nstep))
r3_rms_natoms2 = np.sqrt((arr3**2.0).sum() / float(natoms))
np.testing.assert_almost_equal(r3_rms_all1, r3_rms_all2)
np.testing.assert_almost_equal(r3_rms_natoms1, r3_rms_natoms2)
# Test if rms3d() operates correctly along each axis.
r1_3d = crys.rms3d(arr1, axis=0, nitems='all')
r2_3d = crys.rms3d(arr2, axis=1, nitems='all')
r3_3d = crys.rms3d(arr3, axis=2, nitems='all')
r1_loop = np.empty((nstep,), dtype=float)
r2_loop = np.empty((nstep,), dtype=float)
r3_loop = np.empty((nstep,), dtype=float)
for k in range(nstep):
r1_loop[k] = crys.rms(arr1[k,...], nitems='all')
r2_loop[k] = crys.rms(arr2[:,k,:], nitems='all')
r3_loop[k] = crys.rms(arr3[...,k], nitems='all')
np.testing.assert_array_almost_equal(r1_3d,r1_loop)
np.testing.assert_array_almost_equal(r2_3d,r2_loop)
np.testing.assert_array_almost_equal(r3_3d,r3_loop)
# Test if rmsd() works.
#
# NOTE: Subtle numpy issue here:
# It is very important NOT to use
# R -= R[...,0][...,None]
# or
# for k in range(R.shape[-1]):
# R[...,k] -= R[...,0][...,None]
# because R itself is changed in the loop! You have to copy the reference
# R[...,0] first and then broadcast it for subtracting. What also works is
# this:
# R = R - R[...,0][...,None]
# HOWEVER, THIS DOES NOT:
# for k in range(R.shape[-1]):
# R[...,k] = R[...,k] - R[...,0][...,None]
traj = crys.Trajectory(coords=np.random.rand(nstep, natoms, 3))
assert traj.timeaxis == 0
assert traj.nstep == nstep
from_rmsd = crys.rmsd(traj, ref_idx=0)
from_loop = np.empty((nstep,), dtype=float)
from_rms3d = crys.rms3d(traj.coords - traj.coords[0,...][None,...],
nitems=natoms, axis=0)
R = traj.coords.copy()
ref = R[0,...].copy()
for k in range(nstep):
R[k,...] -= ref
from_loop[k] = np.sqrt((R[k,...]**2.0).sum() / natoms)
np.testing.assert_array_almost_equal(from_rmsd, from_loop)
np.testing.assert_array_almost_equal(from_rmsd, from_rms3d)
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_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_rms():
natoms = 5
nstep = 10
arr1 = np.random.rand(nstep, 3, natoms)
arr2 = np.random.rand(natoms, nstep, 3)
arr3 = np.random.rand(natoms, 3, nstep)
# Test if rms() works.
r3_rms_all1 = crys.rms(arr3, nitems='all')
r3_rms_natoms1 = crys.rms(arr3, nitems=natoms)
r3_rms_all2 = np.sqrt((arr3**2.0).sum() / float(3 * natoms * nstep))
r3_rms_natoms2 = np.sqrt((arr3**2.0).sum() / float(natoms))
np.testing.assert_almost_equal(r3_rms_all1, r3_rms_all2)
np.testing.assert_almost_equal(r3_rms_natoms1, r3_rms_natoms2)
# Test if rms3d() operates correctly along each axis.
r1_3d = crys.rms3d(arr1, axis=0, nitems='all')
r2_3d = crys.rms3d(arr2, axis=1, nitems='all')
r3_3d = crys.rms3d(arr3, axis=2, nitems='all')
r1_loop = np.empty((nstep, ), dtype=float)
r2_loop = np.empty((nstep, ), dtype=float)
r3_loop = np.empty((nstep, ), dtype=float)
for k in range(nstep):
r1_loop[k] = crys.rms(arr1[k, ...], nitems='all')
r2_loop[k] = crys.rms(arr2[:, k, :], nitems='all')
r3_loop[k] = crys.rms(arr3[..., k], nitems='all')
np.testing.assert_array_almost_equal(r1_3d, r1_loop)
np.testing.assert_array_almost_equal(r2_3d, r2_loop)
np.testing.assert_array_almost_equal(r3_3d, r3_loop)
# Test if rmsd() works.
#
# NOTE: Subtle numpy issue here:
# It is very important NOT to use
# R -= R[...,0][...,None]
# or
# for k in range(R.shape[-1]):
# R[...,k] -= R[...,0][...,None]
# because R itself is changed in the loop! You have to copy the reference
# R[...,0] first and then broadcast it for subtracting. What also works is
# this:
# R = R - R[...,0][...,None]
# HOWEVER, THIS DOES NOT:
# for k in range(R.shape[-1]):
# R[...,k] = R[...,k] - R[...,0][...,None]
traj = crys.Trajectory(coords=np.random.rand(nstep, natoms, 3))
assert traj.timeaxis == 0
assert traj.nstep == nstep
from_rmsd = crys.rmsd(traj, ref_idx=0)
from_loop = np.empty((nstep, ), dtype=float)
from_rms3d = crys.rms3d(traj.coords - traj.coords[0, ...][None, ...],
nitems=natoms,
axis=0)
R = traj.coords.copy()
ref = R[0, ...].copy()
for k in range(nstep):
R[k, ...] -= ref
from_loop[k] = np.sqrt((R[k, ...]**2.0).sum() / natoms)
np.testing.assert_array_almost_equal(from_rmsd, from_loop)
np.testing.assert_array_almost_equal(from_rmsd, from_rms3d)
