def test_write_mol():
units={'forces': Ha / eV}
nstep = 2
cell2d = np.random.rand(3,3)
cell3d = np.random.rand(nstep,3,3)
# fractional
coords2d_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
# fractional, 2 time steps: (2,2,3) = (nstep, natoms, 3)
coords3d_frac = np.array([coords2d_frac, coords2d_frac[...,None]*0.8])
# cartesian = coords3d_frac + cell2d (fixed cell). For varialbe cell cases
# below, cell3d is used!
coords3d_cart = crys.coord_trans(coords3d_frac,
old=cell2d,
new=np.identity(3),
axis=-1)
coords2d_cart = coords3d_cart[0,...]
symbols = ['H']*2
forces2d = np.random.random(coords2d_frac.shape)
forces3d = np.random.random(coords3d_frac.shape)
# --- AXSF ---------------------------------------------------------------
# fixed cell, forces=0
axsf_fn = pj(testdir, 'foo.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
)
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | egrep -v -e '--|PRIMVEC'" %axsf_fn)))
np.testing.assert_array_almost_equal(arr, np.concatenate((cell2d, cell2d), axis=0))
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
arr2 = np.vstack((coords3d_cart[0,...],coords3d_cart[1,...]))
np.testing.assert_array_almost_equal(arr, arr2)
# fixed cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo3.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols,
forces=forces3d),
)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
t0 = np.concatenate((coords3d_cart[0,...], forces3d[0,...]), axis=-1)
t1 = np.concatenate((coords3d_cart[1,...], forces3d[1,...]), axis=-1)
arr2 = np.vstack((t0,t1))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# variable cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo4.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell3d,
symbols=symbols,
forces=forces3d))
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %axsf_fn)))
arr2 = np.vstack((cell3d[0,...], cell3d[1,...]))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
t0 = np.concatenate((np.dot(coords3d_frac[0,...], cell3d[0,...]),
forces3d[0,...]), axis=-1)
t1 = np.concatenate((np.dot(coords3d_frac[1,...], cell3d[1,...]),
forces3d[1,...]), axis=-1)
arr2 = np.vstack((t0,t1))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# single struct, coords_cart
axsf_fn = pj(testdir, 'foo6.axsf')
io.write_axsf(axsf_fn,
Structure(units=units,coords=coords2d_cart,
cell=cell2d,
symbols=symbols,
forces=forces2d))
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %axsf_fn)))
arr2 = cell2d
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
arr2 = np.concatenate((coords2d_cart, forces2d), axis=1)
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# --- XYZ ----------------------------------------------------------------
# Use cell, coords, etc from above
# input: coords_frac
xyz_fn = pj(testdir, 'foo_frac_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = np.concatenate([coords3d_cart[0,...], coords3d_cart[1,...]], axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords_cart, cell=None
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,coords=coords3d_cart,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = np.concatenate((coords3d_cart[0,...], coords3d_cart[1,...]), axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords2d_frac, cell=cell2d
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Structure(units=units,coords_frac=coords2d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = coords2d_cart
np.testing.assert_array_almost_equal(arr, arr2)
def test_rpdf():
have_vmd = os.system('which vmd > /dev/null 2>&1') == 0
for name in ['rand_3d', 'aln_ibrav0_sc', 'aln_ibrav2_sc']:
print(("name: %s" % name))
dd = 'files/rpdf'
if name == 'rand_3d':
# 2 Trajectory = 2 selections
cell = np.loadtxt(pj(dd, name + '.cell.txt'))
coords_frac = [
load_old(pj(dd, name + '.coords0.txt')),
load_old(pj(dd, name + '.coords1.txt'))
]
trajs = [
crys.Trajectory(coords_frac=cf, cell=cell)
for cf in coords_frac
]
for tr in trajs:
assert tr.coords_frac.shape == (20, 10, 3)
assert tr.nstep == 20
assert tr.natoms == 10
else:
# one Structure
struct = parse.CifFile(pj(dd, name + '.cif')).get_struct()
trajs = [struct]
cell = struct.cell
ret = crys.rpdf(trajs, rmax=5.0, dr=0.05, pbc=True)
# rpdf() -- compere w/ ref
results = {
'rad': ret[:, 0],
'hist': ret[:, 1],
'num_int': ret[:, 2],
'rmax_auto': np.array(crys.rmax_smith(cell)),
}
for key, val in results.items():
print((" key: %s" % key))
ref_fn = pj(dd, "result.%s.%s.txt" % (key, name))
print((" reference file: %s" % ref_fn))
ref = np.loadtxt(ref_fn)
if doplot:
plt.figure()
plt.plot(ref, '.-', label='ref')
plt.plot(val, '.-', label='val')
plt.legend()
plt.title(key)
else:
# decimal=3 b/c ref data created w/ older implementation,
# slight numerical noise
np.testing.assert_array_almost_equal(ref, val, decimal=3)
print((" key: %s ... ok" % key))
# API
if name.startswith('aln_'):
sy = np.array(trajs[0].symbols)
ret1 = crys.rpdf(trajs, dr=0.1, amask=[sy == 'Al', sy == 'N'])
ret2 = crys.rpdf(trajs, dr=0.1, amask=['Al', 'N'])
aae(ret1, ret2)
# API:
# [traj, traj]
# [traj]
# traj
traj = crys.Trajectory(coords_frac=rand(100, 20, 3),
cell=np.identity(3) * 20,
symbols=['O'] * 5 + ['H'] * 15)
ret1 = crys.rpdf([traj, traj], rmax=5.0, dr=0.05, pbc=True)
ret2 = crys.rpdf([traj], rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret2)
ret3 = crys.rpdf(traj, rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret3)
# dmask
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask='>=2.0')
msk = ret[:, 0] >= 2.0
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask='{d}>=2.0')
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj,
rmax=5.0,
dr=0.05,
dmask='({d} >= 1.0) & ({d} <= 3.0)')
msk = (ret[:, 0] >= 1.0) & (ret[:, 0] <= 3.0)
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
if have_vmd:
# slicefirst and API
print("vmd_measure_gofr: slicefirst ...")
traj = crys.Trajectory(coords_frac=rand(100, 20, 3),
cell=np.identity(3) * 20,
symbols=['O'] * 5 + ['H'] * 15)
for first, last, step in [(0, -1, 1), (20, 80, 10)]:
ret = []
for sf in [True, False]:
print("first=%i, last=%i, step=%i, slicefirst=%s" %
(first, last, step, sf))
tmp = crys.vmd_measure_gofr(
traj,
dr=0.1,
rmax='auto',
sel=['all', 'all'],
slicefirst=sf,
first=first,
last=last,
step=step,
usepbc=1,
tmpdir=testdir,
verbose=False,
)
ret.append(tmp)
assert np.allclose(ret[0][:, 0], ret[1][:, 0])
assert np.allclose(ret[0][:, 1], ret[1][:, 1])
assert np.allclose(ret[0][:, 2], ret[1][:, 2])
# API call_vmd_measure_gofr()
trajfn = pj(testdir, 'vmd_xsf_call_vmd_measure_gofr')
data = io.write_axsf(trajfn, traj)
ret = crys.call_vmd_measure_gofr(trajfn,
dr=0.1,
rmax=10,
sel=['all', 'all'],
fntype='xsf',
first=0,
last=-1,
step=1,
usepbc=1,
datafn=None,
scriptfn=None,
logfn=None,
tmpdir=testdir,
verbose=False)
# compare results, up to L/2 = rmax_auto = 10 = rmax_smith(cell)
# all-all, hist will differ
rmax = 10
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=['all', 'all'], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=None, rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
##assert np.allclose(vmd[:-1,1], pwt[:,1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
# 2 selections, all ok
sy = np.array(traj.symbols)
vmd = crys.vmd_measure_gofr(traj,
dr=0.1,
sel=['name O', 'name H'],
rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=[sy == 'O', sy == 'H'], rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
assert np.allclose(vmd[:-1, 1], pwt[:, 1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
if doplot:
plt.show()
def test_write_mol():
units = {'forces': Ha / eV}
nstep = 2
cell2d = np.random.rand(3, 3)
cell3d = np.random.rand(nstep, 3, 3)
# fractional
coords2d_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
# fractional, 2 time steps: (2,2,3) = (nstep, natoms, 3)
coords3d_frac = np.array([coords2d_frac, coords2d_frac * 0.8])
# cartesian = coords3d_frac + cell2d (fixed cell). For varialbe cell cases
# below, cell3d is used!
coords3d_cart = crys.coord_trans(coords3d_frac,
old=cell2d,
new=np.identity(3),
axis=-1)
coords2d_cart = coords3d_cart[0, ...]
symbols = ['H'] * 2
forces2d = np.random.random(coords2d_frac.shape)
forces3d = np.random.random(coords3d_frac.shape)
# --- AXSF ---------------------------------------------------------------
# fixed cell, forces=0
axsf_fn = pj(testdir, 'foo.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
)
arr = np.loadtxt(
StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -vE -e '--|PRIMVEC'" %
axsf_fn)))
np.testing.assert_array_almost_equal(
arr, np.concatenate((cell2d, cell2d), axis=0))
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
arr2 = np.vstack((coords3d_cart[0, ...], coords3d_cart[1, ...]))
np.testing.assert_array_almost_equal(arr, arr2)
# fixed cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo3.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols,
forces=forces3d),
)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
t0 = np.concatenate((coords3d_cart[0, ...], forces3d[0, ...]), axis=-1)
t1 = np.concatenate((coords3d_cart[1, ...], forces3d[1, ...]), axis=-1)
arr2 = np.vstack((t0, t1))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# variable cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo4.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell3d,
symbols=symbols,
forces=forces3d))
arr = np.loadtxt(
StringIO(
common.backtick(
"grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %
axsf_fn)))
arr2 = np.vstack((cell3d[0, ...], cell3d[1, ...]))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
t0 = np.concatenate(
(np.dot(coords3d_frac[0, ...], cell3d[0, ...]), forces3d[0, ...]),
axis=-1)
t1 = np.concatenate(
(np.dot(coords3d_frac[1, ...], cell3d[1, ...]), forces3d[1, ...]),
axis=-1)
arr2 = np.vstack((t0, t1))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# single struct, coords_cart
axsf_fn = pj(testdir, 'foo6.axsf')
io.write_axsf(
axsf_fn,
Structure(units=units,
coords=coords2d_cart,
cell=cell2d,
symbols=symbols,
forces=forces2d))
arr = np.loadtxt(
StringIO(
common.backtick(
"grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %
axsf_fn)))
arr2 = cell2d
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
arr2 = np.concatenate((coords2d_cart, forces2d), axis=1)
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# --- XYZ ----------------------------------------------------------------
# Use cell, coords, etc from above
# input: coords_frac
xyz_fn = pj(testdir, 'foo_frac_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = np.concatenate([coords3d_cart[0, ...], coords3d_cart[1, ...]],
axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords_cart, cell=None
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units, coords=coords3d_cart,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = np.concatenate((coords3d_cart[0, ...], coords3d_cart[1, ...]),
axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords2d_frac, cell=cell2d
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Structure(units=units,
coords_frac=coords2d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = coords2d_cart
np.testing.assert_array_almost_equal(arr, arr2)
def test_rpdf():
have_vmd = os.system("which vmd > /dev/null 2>&1") == 0
for name in ["rand_3d", "aln_ibrav0_sc", "aln_ibrav2_sc"]:
print ("name: %s" % name)
dd = "files/rpdf"
if name == "rand_3d":
# 2 Trajectory = 2 selections
cell = np.loadtxt(pj(dd, name + ".cell.txt"))
coords_frac = [load_old(pj(dd, name + ".coords0.txt")), load_old(pj(dd, name + ".coords1.txt"))]
trajs = [crys.Trajectory(coords_frac=cf, cell=cell) for cf in coords_frac]
for tr in trajs:
assert tr.coords_frac.shape == (20, 10, 3)
assert tr.nstep == 20
assert tr.natoms == 10
else:
# one Structure
struct = parse.CifFile(pj(dd, name + ".cif")).get_struct()
trajs = [struct]
cell = struct.cell
ret = crys.rpdf(trajs, rmax=5.0, dr=0.05, pbc=True)
# rpdf() -- compere w/ ref
results = {
"rad": ret[:, 0],
"hist": ret[:, 1],
"num_int": ret[:, 2],
"rmax_auto": np.array(crys.rmax_smith(cell)),
}
for key, val in results.iteritems():
print (" key: %s" % key)
ref_fn = pj(dd, "result.%s.%s.txt" % (key, name))
print (" reference file: %s" % ref_fn)
ref = np.loadtxt(ref_fn)
if doplot:
plt.figure()
plt.plot(ref, ".-", label="ref")
plt.plot(val, ".-", label="val")
plt.legend()
plt.title(key)
else:
# decimal=3 b/c ref data created w/ older implementation,
# slight numerical noise
np.testing.assert_array_almost_equal(ref, val, decimal=3)
print (" key: %s ... ok" % key)
# API
if name.startswith("aln_"):
sy = np.array(trajs[0].symbols)
ret1 = crys.rpdf(trajs, dr=0.1, amask=[sy == "Al", sy == "N"])
ret2 = crys.rpdf(trajs, dr=0.1, amask=["Al", "N"])
aae(ret1, ret2)
# API:
# [traj, traj]
# [traj]
# traj
traj = crys.Trajectory(coords_frac=rand(100, 20, 3), cell=np.identity(3) * 20, symbols=["O"] * 5 + ["H"] * 15)
ret1 = crys.rpdf([traj, traj], rmax=5.0, dr=0.05, pbc=True)
ret2 = crys.rpdf([traj], rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret2)
ret3 = crys.rpdf(traj, rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret3)
# dmask
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask=">=2.0")
msk = ret[:, 0] >= 2.0
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask="{d}>=2.0")
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask="({d} >= 1.0) & ({d} <= 3.0)")
msk = (ret[:, 0] >= 1.0) & (ret[:, 0] <= 3.0)
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
if have_vmd:
# slicefirst and API
print "vmd_measure_gofr: slicefirst ..."
traj = crys.Trajectory(coords_frac=rand(100, 20, 3), cell=np.identity(3) * 20, symbols=["O"] * 5 + ["H"] * 15)
for first, last, step in [(0, -1, 1), (20, 80, 10)]:
ret = []
for sf in [True, False]:
print "first=%i, last=%i, step=%i, slicefirst=%s" % (first, last, step, sf)
tmp = crys.vmd_measure_gofr(
traj,
dr=0.1,
rmax="auto",
sel=["all", "all"],
slicefirst=sf,
first=first,
last=last,
step=step,
usepbc=1,
tmpdir=testdir,
verbose=False,
)
ret.append(tmp)
assert np.allclose(ret[0][:, 0], ret[1][:, 0])
assert np.allclose(ret[0][:, 1], ret[1][:, 1])
assert np.allclose(ret[0][:, 2], ret[1][:, 2])
# API call_vmd_measure_gofr()
trajfn = pj(testdir, "vmd_xsf_call_vmd_measure_gofr")
data = io.write_axsf(trajfn, traj)
ret = crys.call_vmd_measure_gofr(
trajfn,
dr=0.1,
rmax=10,
sel=["all", "all"],
fntype="xsf",
first=0,
last=-1,
step=1,
usepbc=1,
datafn=None,
scriptfn=None,
logfn=None,
tmpdir=testdir,
verbose=False,
)
# compare results, up to L/2 = rmax_auto = 10 = rmax_smith(cell)
# all-all, hist will differ
rmax = 10
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=["all", "all"], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=None, rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
##assert np.allclose(vmd[:-1,1], pwt[:,1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
# 2 selections, all ok
sy = np.array(traj.symbols)
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=["name O", "name H"], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=[sy == "O", sy == "H"], rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
assert np.allclose(vmd[:-1, 1], pwt[:, 1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
if doplot:
plt.show()