def write(self, val, dir_pth):
""" write data to this file
"""
assert os.path.exists(dir_pth)
pth = self.path(dir_pth)
val_str = self.writer_(val)
autofile.write_file(pth, val_str)
def write(self, args, file_dat):
""" write the data to file
"""
assert self.checker_(file_dat)
file_path = self.path(args)
file_str = self.writer_(file_dat)
autofile.write_file(file_path, file_str)
def test__zmatrix():
""" test the zmatrix read/write functions
"""
ref_zma = ((('C', (None, None, None), (None, None, None)),
('O', (0, None, None), ('r1', None, None)),
('H', (0, 1, None), ('r2', 'a1', None)), ('H', (0, 1, 2),
('r3', 'a2', 'd1')),
('H', (0, 1, 2), ('r4', 'a3', 'd2')), ('H', (1, 0, 2),
('r5', 'a4', 'd3'))), {
'r1': 2.67535,
'r2': 2.06501,
'a1': 1.9116242,
'r3': 2.06501,
'a2': 1.9116242,
'd1': 2.108497362,
'r4': 2.06458,
'a3': 1.9020947,
'd2': 4.195841334,
'r5': 1.83748,
'a4': 1.8690905,
'd3': 5.228936625
})
zma_file_name = autofile.name.zmatrix('test')
zma_file_path = os.path.join(TMP_DIR, zma_file_name)
zma_str = autofile.write.zmatrix(ref_zma)
assert not os.path.isfile(zma_file_path)
autofile.write_file(zma_file_path, zma_str)
assert os.path.isfile(zma_file_path)
zma_str = autofile.read_file(zma_file_path)
zma = autofile.read.zmatrix(zma_str)
assert automol.zmatrix.almost_equal(ref_zma, zma)
def test__trajectory():
""" test the trajectory read/rwrite functions
"""
ref_geo_lst = [(('C', (0.0, 0.0, 0.0)), ('O', (0.0, 0.0, 2.699694868173)),
('O', (0.0, 2.503038629201, -1.011409768236)),
('H', (-1.683942509299, -1.076047850358, -0.583313101501)),
('H', (1.684063451772, -0.943916309940, -0.779079279468)),
('H', (1.56980872050, 0.913848877557, 3.152002706027)),
('H', (-1.57051358834, 3.264399836517, -0.334901043405))),
(('C', (0.0, 0.0, 0.0)), ('O', (0.0, 0.0, 2.70915105770)),
('O', (0.0, 2.55808068205, -0.83913477573)),
('H', (-1.660164085463, -1.04177010816, -0.73213470306)),
('H', (1.711679909369, -0.895873802652, -0.779058492481)),
('H', (0.0238181080852, -1.813377410537, 3.16912929390)),
('H', (-1.36240560905, 3.348313125118, 0.1732746576216)))]
ref_comments = [
'energy: -187.38941054878092', 'energy: -187.3850624381528'
]
traj_file_name = autofile.name.trajectory('test')
traj_file_path = os.path.join(TMP_DIR, traj_file_name)
traj_str = autofile.write.trajectory(ref_geo_lst, ref_comments)
assert not os.path.isfile(traj_file_path)
autofile.write_file(traj_file_path, traj_str)
assert os.path.isfile(traj_file_path)
def test__energy():
""" test the energy read/write functions
"""
ref_ene = -75.00613628303537
ene_file_name = autofile.name.energy('test')
ene_file_path = os.path.join(TMP_DIR, ene_file_name)
ene_str = autofile.write.energy(ref_ene)
assert not os.path.isfile(ene_file_path)
autofile.write_file(ene_file_path, ene_str)
assert os.path.isfile(ene_file_path)
ene_str = autofile.read_file(ene_file_path)
ene = autofile.read.energy(ene_str)
assert numpy.isclose(ref_ene, ene)
def test__lennard_jones_sigma():
""" test the sigma read/write functions
"""
ref_sig = 3.55018590361446
sig_file_name = autofile.name.lennard_jones_sigma('test')
sig_file_path = os.path.join(TMP_DIR, sig_file_name)
sig_str = autofile.write.lennard_jones_sigma(ref_sig)
assert not os.path.isfile(sig_file_path)
autofile.write_file(sig_file_path, sig_str)
assert os.path.isfile(sig_file_path)
sig_str = autofile.read_file(sig_file_path)
sig = autofile.read.lennard_jones_sigma(sig_str)
assert numpy.isclose(ref_sig, sig)
def test__lennard_jones_epsilon():
""" test the epsilon read/write functions
"""
ref_eps = 247.880866746988
eps_file_name = autofile.name.lennard_jones_epsilon('test')
eps_file_path = os.path.join(TMP_DIR, eps_file_name)
eps_str = autofile.write.lennard_jones_epsilon(ref_eps)
assert not os.path.isfile(eps_file_path)
autofile.write_file(eps_file_path, eps_str)
assert os.path.isfile(eps_file_path)
eps_str = autofile.read_file(eps_file_path)
eps = autofile.read.lennard_jones_epsilon(eps_str)
assert numpy.isclose(ref_eps, eps)
def test__information():
""" test the information read/write functions
"""
ref_inf_obj = autoinf.Info(a=['b', 'c', 'd', 'e'],
x=autoinf.Info(y=1, z=2))
inf_file_name = autofile.name.information('test')
inf_file_path = os.path.join(TMP_DIR, inf_file_name)
inf_str = autofile.write.information(ref_inf_obj)
assert not os.path.isfile(inf_file_path)
autofile.write_file(inf_file_path, inf_str)
assert os.path.isfile(inf_file_path)
inf_str = autofile.read_file(inf_file_path)
inf_obj = autofile.read.information(inf_str)
assert inf_obj == ref_inf_obj
def test__geometry():
""" test the geometry read/write functions
"""
ref_geo = (('C', (-0.70116587131, 0.0146227007587, -0.016166607003)),
('O', (1.7323365056, -0.9538524899, -0.5617192010)),
('H', (-0.9827048283, 0.061897979239, 2.02901783816)),
('H', (-0.8787925682, 1.91673409124, -0.80019507919)),
('H', (-2.12093033745, -1.21447973767, -0.87411360631)),
('H', (2.9512589894, 0.17507745634, 0.22317665541)))
geo_file_name = autofile.name.geometry('test')
geo_file_path = os.path.join(TMP_DIR, geo_file_name)
geo_str = autofile.write.geometry(ref_geo)
assert not os.path.isfile(geo_file_path)
autofile.write_file(geo_file_path, geo_str)
assert os.path.isfile(geo_file_path)
geo_str = autofile.read_file(geo_file_path)
geo = autofile.read.geometry(geo_str)
assert automol.geom.almost_equal(ref_geo, geo)
def test__gradient():
""" test the gradient read/write functions
"""
ref_grad = ((-6.687065494e-05, -2.087360475e-05, -2.900518464e-05),
(2.091815312e-05, -2.162539565e-05, 2.097302071e-05),
(-9.17712798e-06, -2.97043797e-05, -1.378883952e-05),
(2.244858355e-05, 6.0265176e-06, 1.00733398e-06),
(4.676018254e-05, 5.473937899e-05, 1.744549e-05),
(-1.407913705e-05, 1.143748381e-05, 3.3681804e-06))
grad_file_name = autofile.name.gradient('test')
grad_file_path = os.path.join(TMP_DIR, grad_file_name)
grad_str = autofile.write.gradient(ref_grad)
assert not os.path.isfile(grad_file_path)
autofile.write_file(grad_file_path, grad_str)
assert os.path.isfile(grad_file_path)
grad_str = autofile.read_file(grad_file_path)
grad = autofile.read.gradient(grad_str)
assert numpy.allclose(ref_grad, grad)
def test__vmatrix():
""" test the vmatrix read/write functions
"""
ref_vma = (('C', (None, None, None), (None, None, None)),
('O', (0, None, None), ('r1', None, None)),
('H', (0, 1, None), ('r2', 'a1', None)), ('H', (0, 1, 2),
('r3', 'a2', 'd1')),
('H', (0, 1, 2), ('r4', 'a3', 'd2')), ('H', (1, 0, 2),
('r5', 'a4', 'd3')))
vma_file_name = autofile.name.vmatrix('test')
vma_file_path = os.path.join(TMP_DIR, vma_file_name)
vma_str = autofile.write.vmatrix(ref_vma)
assert not os.path.isfile(vma_file_path)
autofile.write_file(vma_file_path, vma_str)
assert os.path.isfile(vma_file_path)
vma_str = autofile.read_file(vma_file_path)
vma = autofile.read.vmatrix(vma_str)
assert vma == ref_vma
def test__hessian():
""" test the hessian read/write functions
"""
ref_hess = ((0.70455411073336, -0.08287472697212, 0.0, -0.0798647434566,
0.05385932364624, 0.0, -0.62468936727659, 0.02901540332588,
0.0), (-0.08287472697212, 0.73374800936533, 0.0,
-0.06694564915575, -0.63928635896955, 0.0,
0.14982037612785, -0.09446165039567, 0.0),
(0.0, 0.0, 0.00019470176975, 0.0, 0.0, -9.734161519e-05, 0.0,
0.0,
-9.736015438e-05), (-0.0798647434566, -0.06694564915575, 0.0,
0.08499297871932, -0.02022391947876, 0.0,
-0.00512823526272, 0.0871695686345, 0.0),
(0.05385932364624, -0.63928635896955, 0.0, -0.02022391947876,
0.65384367318451, 0.0, -0.03363540416748, -0.01455731421496,
0.0), (0.0, 0.0, -9.734161519e-05, 0.0, 0.0, 4.370597581e-05,
0.0, 0.0, 5.363563938e-05),
(-0.62468936727659, 0.14982037612785, 0.0, -0.00512823526272,
-0.03363540416748, 0.0, 0.6298176025393, -0.11618497196038,
0.0), (0.02901540332588, -0.09446165039567, 0.0,
0.0871695686345, -0.01455731421496, 0.0,
-0.11618497196038, 0.10901896461063,
0.0), (0.0, 0.0, -9.736015438e-05, 0.0, 0.0,
5.363563938e-05, 0.0, 0.0, 4.3724515e-05))
hess_file_name = autofile.name.hessian('test')
hess_file_path = os.path.join(TMP_DIR, hess_file_name)
hess_str = autofile.write.hessian(ref_hess)
assert not os.path.isfile(hess_file_path)
autofile.write_file(hess_file_path, hess_str)
assert os.path.isfile(hess_file_path)
hess_str = autofile.read_file(hess_file_path)
hess = autofile.read.hessian(hess_str)
assert numpy.allclose(ref_hess, hess)
def test__file():
""" test the file read/write functions
"""
inp_str = '<input file contents>'
out_str = '<output file contents>'
scr_str = '<shell script contents>'
inp_file_name = autofile.name.input_file('test')
out_file_name = autofile.name.output_file('test')
scr_file_name = autofile.name.run_script('test')
inp_file_path = os.path.join(TMP_DIR, inp_file_name)
out_file_path = os.path.join(TMP_DIR, out_file_name)
scr_file_path = os.path.join(TMP_DIR, scr_file_name)
assert not os.path.isfile(inp_file_path)
assert not os.path.isfile(out_file_path)
assert not os.path.isfile(scr_file_path)
autofile.write_file(inp_file_path, inp_str)
autofile.write_file(out_file_path, out_str)
autofile.write_file(scr_file_path, scr_str)
def write(self, val, prefix, args=()):
""" write the data to file
"""
file_path = self.path(prefix, args)
val_str = self.writer_(val)
autofile.write_file(file_path, val_str)
