def test_run(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
inp = InputParams({"dft": {"rmult": [5, 7], "hgrids": 0.55}})
base = Job(posinp=pos,
inputparams=inp,
name="N2",
run_dir="tests/rmult_convergence_N2")
rmc = RmultConvergence(base, [8, 11], [-1, -1],
n_jobs=4,
precision_per_atom=0.01 * EV_TO_HA)
assert not rmc.is_completed
rmc.run(nmpi=6, nomp=3)
assert rmc.is_completed
# The correct minimum rmult is found
assert rmc.converged.param == [6., 9.]
# The output energies are correct
expected_energies = [-19.871104, -19.871032, -19.870892, -19.869907]
energies = [job.logfile.energy for job in rmc.queue]
np.testing.assert_array_almost_equal(energies, expected_energies)
# Print the summary of the workflow
rmc.summary()
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
rmc.run()
def test_run(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
inp = InputParams({"dft": {"rmult": [5, 7]}})
base = Job(inputparams=inp,
posinp=pos,
name="N2",
run_dir="tests/hgrids_convergence_N2")
hgc = HgridsConvergence(base,
0.36,
0.02,
n_jobs=8,
precision_per_atom=0.01 * EV_TO_HA)
assert not hgc.is_completed
hgc.run(nmpi=6, nomp=3)
assert hgc.is_completed
# The correct maximum hgrids is found
assert hgc.converged.param == [0.38] * 3
# The output energies are correct
expected_energies = [-19.888197, -19.887715, -19.887196, 0, 0, 0, 0, 0]
energies = [
job.logfile.energy if job.is_completed else 0 for job in hgc.queue
]
np.testing.assert_array_almost_equal(energies, expected_energies)
# Print the summary of the workflow
hgc.summary()
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
hgc.run()
def test___eq__(self):
atom1 = Atom('N', [0.0, 0.0, 0.0])
atom2 = Atom('N', [0.0, 0.0, 1.1])
pos1 = Posinp([atom1, atom2], 'angstroem', 'free')
pos2 = Posinp([atom2, atom1], 'angstroem', 'free')
assert pos1 == pos2 # The order of the atoms in the list do not count
assert pos1 != 1 # No error if other object is not a posinp
def test_run(self):
frag1 = Posinp([Atom('N', [0.0, 0.0, 0.0])], units="angstroem",
boundary_conditions="free")
frag2 = frag1
distances = np.arange(0.95, 1.25, 0.05)
dc = Dissociation(frag1, frag2, distances, name="N2",
run_dir="tests/dissociation_N2")
assert not dc.is_completed
dc.run(nmpi=6, nomp=3)
assert dc.is_completed
# The first job has the correct posinp
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0.95, 0])]
expected_pos = Posinp(
atoms, units="angstroem", boundary_conditions="free")
assert expected_pos == dc.queue[0].posinp
# The correct minimum distance is found
assert dc.minimum.distance == 1.1
# The output energies are correct
expected_energies = [
-19.805444659275025, -19.85497382791818, -19.878933352041976,
-19.884549270710195, -19.87716483741823, -19.86087438302968,
-19.838574516454962
]
np.testing.assert_array_almost_equal(dc.energies, expected_energies)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
dc.run()
def test_to_barycenter(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
expected_atoms = [Atom('N', [0, 0, -0.55]), Atom('N', [0, 0, 0.55])]
expected_pos = Posinp(expected_atoms,
units="angstroem",
boundary_conditions="free")
assert pos.to_barycenter() == expected_pos
def test_init_raises_ValueError(self):
frag1 = Posinp([Atom('N', [0.0, 0.0, 0.0])],
units="angstroem", boundary_conditions="free")
frag2 = Posinp([Atom('N', [0.0, 0.0, 0.0])], cell=[8, 8, 8],
units="angstroem", boundary_conditions="periodic")
distances = np.arange(0.95, 1.25, 0.05)
with pytest.raises(ValueError):
Dissociation(frag1, frag2, distances)
def dry_gwf(self):
new_pos = Posinp([Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])],
units="angstroem", boundary_conditions="free")
base_job = Job(posinp=new_pos, name="N2", run_dir="tests/geopt_N2/dry")
gwf = Geopt(base_job, maxrise=0.5)
yield gwf
with gwf.queue[0] as job:
job.clean()
os.rmdir(job.run_dir)
def test_init(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
base = Job(posinp=pos, name="N2", run_dir="tests/rmult_convergence_N2")
rmc = RmultConvergence(base, [6, 8], [0.5, 0.5],
n_jobs=3,
precision_per_atom=0.01 * EV_TO_HA)
rmults = [job.param for job in rmc.queue]
expected = [[6.0, 8.0], [5.5, 7.5], [5.0, 7.0]]
np.testing.assert_array_almost_equal(rmults, expected)
def test_run_warns_UserWarning_too_low_energy(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
inp = InputParams({"dft": {"rmult": [5, 7], "hgrids": 0.55}})
base = Job(posinp=pos,
inputparams=inp,
name="N2",
run_dir="tests/rmult_convergence_N2")
rmc = RmultConvergence(base, [9, 12], [-1, -1],
n_jobs=2,
precision_per_atom=0.01 * EV_TO_HA)
with pytest.warns(UserWarning):
rmc.run(nmpi=6, nomp=3)
def test_init(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
base = Job(posinp=pos,
name="N2",
run_dir="tests/hgrids_convergence_N2")
hgc = HgridsConvergence(base,
0.36,
0.02,
n_jobs=8,
precision_per_atom=0.01 * EV_TO_HA)
hgrids = [job.param for job in hgc.queue]
expected = [[0.36 + i * 0.02] * 3 for i in range(8)]
np.testing.assert_array_almost_equal(hgrids, expected)
def test_set_posinp_key(self):
inp = InputParams()
inp["posinp"] = {
"units": "angstroem",
"positions": [{
'N': [0.0, 0.0, 0.0]
}, {
'N': [0.0, 0.0, 1.1]
}]
}
assert inp.posinp == Posinp(
[Atom('N', [0, 0, 0]),
Atom('N', [0, 0, 1.1])],
units="angstroem",
boundary_conditions="free")
def test_run(self):
atoms = [Atom('N', [3.571946174, 3.571946174, 3.620526682]),
Atom('N', [3.571946174, 3.571946174, 4.71401439])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
gs = Job(posinp=pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs)
ir = InfraredSpectrum(ph)
assert not ir.is_completed
ir.run()
assert ir.is_completed
# Test the only physically relevant infrared intensity
i = np.argmax(ir.energies)
np.testing.assert_almost_equal(ir.intensities[i], 1.100446469749e-06)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
ir.run()
def place_first_nitrogen(posinp):
distances_to_middle = np.linalg.norm(posinp.positions -
np.array(posinp.cell) / 2,
axis=1)
idx = np.argmin(distances_to_middle)
posinp.atoms[idx] = Atom("N", posinp.atoms[idx].position)
return posinp, idx
def test_positions(self):
expected = [7.327412521, 0.0, 3.461304757]
pos1 = Posinp([Atom('C', expected)],
units="angstroem",
boundary_conditions="free")
pos2 = pos1.translate_atom(0, [-7.327412521, 0.0, -3.461304757])
assert np.allclose(pos1.positions, expected)
assert np.allclose(pos2.positions, [0, 0, 0])
def test_run(self):
new_pos = Posinp([Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])],
units="angstroem", boundary_conditions="free")
base_job = Job(posinp=new_pos, name="N2", run_dir="tests/geopt_N2")
gwf = Geopt(base_job, maxrise=0.5)
assert not gwf.is_completed
gwf.run(nomp=3, nmpi=6)
assert gwf.is_completed
expected_pos = Posinp(
[Atom('N', [-3.5879386957696453e-22, -2.564986669721281e-21,
0.0032486860088205526]),
Atom('N', [2.5251356228246713e-22, 2.423609962870671e-21,
1.0967513378330371])],
"angstroem", "free", cell=None)
assert gwf.final_posinp == expected_pos
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
gwf.run()
def place_second_nitrogen(initpos, theta, r, first_idx):
posinp = deepcopy(initpos)
point = np.array(posinp.cell) / 2 + np.array(
[r * np.cos(theta), 0, r * np.sin(theta)])
distances_to_point = np.linalg.norm(posinp.positions - point, axis=1)
weigths = np.exp(-(distances_to_point**2) / 2)
weigths[first_idx] = 0
weigths = weigths / np.sum(weigths)
second_idx = int(np.random.choice(len(posinp), 1, p=weigths))
posinp.atoms[second_idx] = Atom("N", posinp.atoms[second_idx].position)
return posinp, second_idx
def test_run(self):
atoms = [Atom('N', [3.571946174, 3.571946174, 3.620526682]),
Atom('N', [3.571946174, 3.571946174, 4.71401439])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
gs = Job(posinp=pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs)
ir = InfraredSpectrum(ph)
vpt = VibPolTensor(ir)
assert not vpt.is_completed
vpt.run()
assert vpt.is_completed
# Test the mean vibrational polarizability
np.testing.assert_almost_equal(vpt.mean_polarizability,
1.092296473682357e-08)
# Changing the value of e_cut changes the value of the mean
# vibrational polarizability
vpt.e_cut = 0
np.testing.assert_almost_equal(vpt.mean_polarizability,
0.0007775548377767935)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
vpt.run()
class TestPosinp:
# Posinp with surface boundary conditions
surface_filename = os.path.join(tests_fol, "surface.xyz")
pos = Posinp.from_file(surface_filename)
# Posinp with free boundary conditions
free_filename = os.path.join(tests_fol, "free.xyz")
free_pos = Posinp.from_file(free_filename)
# Posinp read from a string
string = """\
4 atomic
free
C 0.6661284109 0.000000000 1.153768252
C 3.330642055 0.000000000 1.153768252
C 4.662898877 0.000000000 3.461304757
C 7.327412521 0.000000000 3.461304757"""
str_pos = Posinp.from_string(string)
# Posinp read from an N2 calculation of bad quality
log_pos = Logfile.from_file(logname).posinp
# Posinp read from an InputParams instance with surface BC
surf_inp = InputParams({
'posinp': {
'units': 'angstroem',
'cell': [8.0, '.inf', 8.0],
'positions': [{
'C': [0.0, 0.0, 0.0]
}]
}
})
surf_pos = surf_inp.posinp
# Posinp read from an InputParams instance with periodic BC
per_inp = InputParams({
'posinp': {
'units': 'angstroem',
'cell': [8.0, 1.0, 8.0],
'positions': [{
'C': [0.0, 0.0, 0.0]
}]
}
})
per_pos = per_inp.posinp
@pytest.mark.parametrize("value, expected", [
(len(pos), 4),
(pos.units, "reduced"),
(len(pos), 4),
(pos.boundary_conditions, "surface"),
(pos.cell, [8.07007483423, 'inf', 4.65925987792]),
(pos[0], Atom('C', [0.08333333333, 0.5, 0.25])),
])
def test_from_file(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(log_pos), 2),
(log_pos.units, "angstroem"),
(len(log_pos), 2),
(log_pos.boundary_conditions, "free"),
(log_pos.cell, None),
(log_pos[0],
Atom('N', [
2.9763078243490115e-23, 6.872205952043537e-23, 0.01071619987487793
])),
])
def test_from_Logfile(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(surf_pos), 1),
(surf_pos.units, "angstroem"),
(len(surf_pos), 1),
(surf_pos.boundary_conditions, "surface"),
(surf_pos.cell, [8, "inf", 8]),
(surf_pos[0], Atom('C', [0, 0, 0])),
])
def test_from_surface_InputParams(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(per_pos), 1),
(per_pos.units, "angstroem"),
(len(per_pos), 1),
(per_pos.boundary_conditions, "periodic"),
(per_pos.cell, [8, 1.0, 8]),
(per_pos[0], Atom('C', [0, 0, 0])),
])
def test_from_periodic_InputParams(self, value, expected):
assert value == expected
def test_from_string(self):
assert self.str_pos == self.free_pos
def test_repr(self):
atoms = [Atom('C', [0, 0, 0]), Atom('N', [0, 0, 1])]
new_pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
msg = "Posinp([Atom('C', [0.0, 0.0, 0.0]), Atom('N', [0.0, 0.0, "\
"1.0])], 'angstroem', 'free', cell=None)"
assert repr(new_pos) == msg
def test_write(self):
fname = os.path.join(tests_fol, "test.xyz")
self.pos.write(fname)
assert self.pos == Posinp.from_file(fname)
os.remove(fname)
def test_free_boundary_conditions_has_no_cell(self):
assert self.free_pos.cell is None
def test_translate_atom(self):
new_pos = self.pos.translate_atom(0, [0.5, 0, 0])
assert new_pos != self.pos
assert new_pos[0] == Atom("C", [0.58333333333, 0.5, 0.25])
@pytest.mark.parametrize("fname", [
"free_reduced.xyz",
"missing_atom.xyz",
"additional_atom.xyz",
])
def test_init_raises_ValueError(self, fname):
with pytest.raises(ValueError):
Posinp.from_file(os.path.join(tests_fol, fname))
@pytest.mark.parametrize("to_evaluate", [
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic')",
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic', cell=[1, 1])",
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic', cell=[1,'inf',1])",
])
def test_init_raises_ValueError2(self, to_evaluate):
with pytest.raises(ValueError):
eval(to_evaluate)
def test_positions(self):
expected = [7.327412521, 0.0, 3.461304757]
pos1 = Posinp([Atom('C', expected)],
units="angstroem",
boundary_conditions="free")
pos2 = pos1.translate_atom(0, [-7.327412521, 0.0, -3.461304757])
assert np.allclose(pos1.positions, expected)
assert np.allclose(pos2.positions, [0, 0, 0])
def test___eq__(self):
atom1 = Atom('N', [0.0, 0.0, 0.0])
atom2 = Atom('N', [0.0, 0.0, 1.1])
pos1 = Posinp([atom1, atom2], 'angstroem', 'free')
pos2 = Posinp([atom2, atom1], 'angstroem', 'free')
assert pos1 == pos2 # The order of the atoms in the list do not count
assert pos1 != 1 # No error if other object is not a posinp
def test_with_surface_boundary_conditions(self):
# Two Posinp instances with surface BC are the same even if they
# have a different cell size along y-axis
pos_with_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, ".inf", 40])
pos_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, 40, 40])
assert pos_with_inf == pos_wo_inf
# They are obviously different if the cell size along the other
# directions are not the same
pos2_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[20, "inf", 40])
assert pos_with_inf != pos2_wo_inf
# They still have the same BC
assert \
pos2_wo_inf.boundary_conditions == pos_with_inf.boundary_conditions
# You can only have a cell with ".inf" in 2nd positiion to
# initialize a calculation with surface BC without using a
# Posinp instance
inp_with_inf = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", 40],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
assert pos_with_inf == inp_with_inf.posinp
def test_to_centroid(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
expected_atoms = [Atom('N', [0, 0, -0.55]), Atom('N', [0, 0, 0.55])]
expected_pos = Posinp(expected_atoms,
units="angstroem",
boundary_conditions="free")
assert pos.to_centroid() == expected_pos
def test_to_barycenter(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
expected_atoms = [Atom('N', [0, 0, -0.55]), Atom('N', [0, 0, 0.55])]
expected_pos = Posinp(expected_atoms,
units="angstroem",
boundary_conditions="free")
assert pos.to_barycenter() == expected_pos
def test_translate_atom(self):
new_pos = self.pos.translate_atom(0, [0.5, 0, 0])
assert new_pos != self.pos
assert new_pos[0] == Atom("C", [0.58333333333, 0.5, 0.25])
from __future__ import absolute_import
import os
import pytest
import numpy as np
from mybigdft import Atom, Posinp, Job, InputParams
from mybigdft.workflows import (
PolTensor, Phonons, RamanSpectrum, Geopt, Dissociation, InfraredSpectrum,
VibPolTensor,
)
from mybigdft.workflows.workflow import Workflow
pos = Posinp(
[Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.095])], 'angstroem', 'free')
class TestWorkflow:
def test_init(self):
wf = Workflow()
assert wf.queue == []
def test_run(self):
wf = Workflow()
wf.run()
assert wf.completed
assert wf.is_completed
class TestPolTensor:
# Polarizibility tensor workflow which is not run
def test_with_surface_boundary_conditions(self):
# Two Posinp instances with surface BC are the same even if they
# have a different cell size along y-axis
pos_with_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, ".inf", 40])
pos_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, 40, 40])
assert pos_with_inf == pos_wo_inf
# They are obviously different if the cell size along the other
# directions are not the same
pos2_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[20, "inf", 40])
assert pos_with_inf != pos2_wo_inf
# They still have the same BC
assert \
pos2_wo_inf.boundary_conditions == pos_with_inf.boundary_conditions
# You can only have a cell with ".inf" in 2nd positiion to
# initialize a calculation with surface BC without using a
# Posinp instance
inp_with_inf = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", 40],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
assert pos_with_inf == inp_with_inf.posinp
def test_repr(self):
atoms = [Atom('C', [0, 0, 0]), Atom('N', [0, 0, 1])]
new_pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
msg = "Posinp([Atom('C', [0.0, 0.0, 0.0]), Atom('N', [0.0, 0.0, "\
"1.0])], 'angstroem', 'free', cell=None)"
assert repr(new_pos) == msg