def test_closed(mo_dirpath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
for f in ["mos", "control"]:
shutil.copy2(os.path.join(mo_dirpath, f), f)
s = States.from_file()
assert len(s) == 14
assert s[0].eigenvalue == pytest.approx(-13.968369531218)
assert_MSONable(s)
eiger_out = EigerOutput.from_file(os.path.join(mo_dirpath, "eiger"))
assert eiger_out.compare_states(s) is None
assert not s.is_uhf
assert not s.has_hole
assert s.total_electrons == 10
assert s.irreps[0] == "a1"
assert s.occupations[0] == 2
assert s.spins[0] is None
assert s.eigenvalues[-1] == pytest.approx(2.55164050421)
assert s.irrep_indices[0] == 1
assert str(s)
# test filter
s = States.from_file()
with pytest.raises(ValueError):
s.filter_states(spin="a", irrep="a1")
assert len(s.filter_states(irrep="z")) == 0
filtered = s.filter_states(irrep="a1")
assert filtered[0].irrep == "a1"
# test get_shells
s = States.from_file()
with pytest.raises(ValueError):
s.get_shells(spin="a")
shell = s.get_shells()
assert shell.occupations[0] == 2
assert shell.states[0] == ("a1", 1)
def test_remove_gradient_in_control(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-gradient'),
"control")
c = Control.from_file()
with pytest.raises(ValueError):
c.remove_last_gradient(filename=None)
c.remove_last_gradient(backup_suffix="_backup")
assert os.path.isfile("control_backup")
g = c.gradient
assert len(g.gradients) == 0
with pytest.raises(RuntimeError):
c.remove_last_gradient()
def test_remove_energy_in_control(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-energy'),
"control")
c = Control.from_file()
with pytest.raises(ValueError):
c.remove_last_energy(filename=None)
c.remove_last_energy(backup_suffix="_backup")
assert os.path.isfile("control_backup")
e = c.energy
assert len(e.scf) == 0
with pytest.raises(RuntimeError):
c.remove_last_energy()
def test_mdgo(self, control_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(control_filepath, "control")
options = {
"internal": None,
"redundant": None,
"cartesian": "cartesian off",
"global": None
}
mdgo("optimize", options, backup_file="control_backup")
assert os.path.isfile("control_backup")
with open("control") as f:
s = f.read()
matches = re.findall(r"cartesian off", s, re.MULTILINE)
assert matches == ["cartesian off"]
matches = re.findall(r"\$redundant", s, re.MULTILINE)
assert matches == []
def test_cpc(self, molecule_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir) as tmp_dir:
dp = get_define_template("ridft")
run_define_runner(define_opt=dp, mol_path=molecule_filepath)
run_tm("ridft")
process = subprocess.Popen(["cpc", "cpc_orig"], stdin=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, encoding='utf-8')
process.communicate()
ret_code = process.wait()
if ret_code:
raise RuntimeError("original cpc failed with return code {}".format(ret_code))
cpc("cpc_tmio")
s_orig = set(os.listdir("cpc_orig"))
s_orig.remove("wherefrom")
s_tmio = set(os.listdir("cpc_tmio"))
assert s_orig == s_tmio
def test_gradient(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(
os.path.join(testdir, 'control', 'gradient_test-gradient'),
'gradient')
g = Gradient.from_file()
assert len(g.molecules) == 6
assert g.gradients[0, 1, 0] == pytest.approx(-0.02705094211381)
assert g.energies[-1] == pytest.approx(-76.3449460148)
assert g.norms[1] == pytest.approx(0.013946816251742454)
assert g.max_gradients[-1] == pytest.approx(3.8028925027729e-05)
assert g.n_steps == 6
assert g.last_grad_norm == pytest.approx(5.145114095400708e-05)
assert g.last_grad_max == pytest.approx(3.8028925027729e-05)
assert_MSONable(g)
if has_matplotlib():
assert g.plot(show=False)
def test_eiger_runner(mo_dirpath, delete_tmp_dir):
with mock.patch("subprocess.run") as mock_run:
er = EigerRunner()
with pytest.raises(ValueError):
er.to_file("test")
with pytest.raises(ValueError):
er.get_eiger_output()
with open(os.path.join(mo_dirpath, "eiger")) as f:
out = f.read()
m = mock.MagicMock()
m.stdout = out.encode("utf-8")
mock_run.return_value = m
er.run()
assert er.get_eiger_output()
with temp_dir(delete_tmp_dir):
er.to_file("out_test")
assert os.path.isfile("out_test")
def test_adg(self, control_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(control_filepath, "control")
with open("control") as f:
s = f.read()
matches = re.findall(r"\$scfconv 6", s, re.MULTILINE)
assert matches == []
adg("scfconv", "6", backup_file="control_backup")
assert os.path.isfile("control_backup")
with open("control") as f:
s = f.read()
matches = re.findall(r"\$scfconv 6", s, re.MULTILINE)
assert matches == ["$scfconv 6"]
with open("control_backup") as f:
s = f.read()
matches = re.findall(r"\$scfconv 6", s, re.MULTILINE)
assert matches == []
def test_energy_scf(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(
os.path.join(testdir, 'control', 'energy_test-energy'),
'energy')
energy = Energy.from_file()
assert len(energy.scf) == 4
assert energy.n_steps == 4
assert energy.scf[0] == pytest.approx(-10.48350884610)
assert energy.scfkin[2] == pytest.approx(37.86647200156)
assert energy.scfpot[1] == pytest.approx(-59.35016151450)
assert energy.delta_e == pytest.approx(9.99999999577)
assert energy.mp2 is None
assert np.all(energy.scf == energy.total)
assert_MSONable(energy)
if has_matplotlib():
assert energy.plot(show=False)
energy_string = ' SCF SCFKIN SCFPOT\n' \
'1 -10.48350884610 39.86550149370 -50.34901033980\n' \
'2 -20.48350872544 38.86665278906 -59.35016151450\n' \
'\n' \
'3 -30.48350875500 37.86647200156 -68.34998075656\n' \
'4 -40.48350875077 36.86649728669 -77.35000603747\n'
energy = Energy.from_string(energy_string)
assert len(energy.scf) == 4
assert energy.n_steps == 4
assert energy.scf[0] == pytest.approx(-10.48350884610)
assert energy.scfkin[2] == pytest.approx(37.86647200156)
assert energy.scfpot[1] == pytest.approx(-59.35016151450)
assert energy.delta_e == pytest.approx(9.99999999577)
assert energy.mp2 is None
assert np.all(energy.scf == energy.total)
assert_MSONable(energy)
if has_matplotlib():
assert energy.plot(show=False)
def test_cpc(self, control_filepath, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
os.makedirs("orig_dir")
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-subfiles'),
os.path.join("orig_dir", "control"))
shutil.copy2(
os.path.join(testdir, 'control', 'gradient_test-gradient'),
os.path.join("orig_dir", "gradient"))
cpc("test_dir", control_dir="orig_dir")
assert os.path.isfile(os.path.join("test_dir", "control"))
assert os.path.isfile(os.path.join("test_dir", "gradient"))
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-subfiles'),
"control")
cpc("test_dir2")
assert os.path.isfile(os.path.join("test_dir2", "control"))
def test_closed(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-subfiles'),
"control")
with pytest.raises(ValueError):
Shells.from_file("alpha")
s = Shells.from_file("closed")
assert len(s.states) == 3
assert s.states[0] == ("a1", 1)
assert s.occupations[0] == 2
assert "a1" in s.irreps
assert "t2" in s.irreps
assert len(s.irreps) == 2
assert s.total_electrons == 10
original = Control.from_file().sdg("closed shells")
generated = s.to_datagroup()
assert check_equivalent_dg(original, generated)
assert_MSONable(s)
def test_distance_no_val(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.add_distance(0, 1, weights=1.0, value=None)
assert not ms.has_inconsistencies()
with temp_dir(delete_tmp_dir) as tmp_dir:
ms.to_file("coord", fmt="coord")
shutil.copy2(control_filepath, "control")
dr = DefineRunner(parameters=dr_parameters)
assert dr.run_update_internal_coords()
ms_new = MoleculeSystem.from_file("coord")
assert not ms_new.has_inconsistencies()
# check that intdef is present and that the value has been updated
assert len(ms_new.int_def) == 1
assert ms_new.int_def[0].value == pytest.approx(2.05846, abs=1e-4)
# check that in redundant the coordinate has been taken into account
dg = DataGroups.from_file("coord")
redundant = dg.sdg("redundant", strict=True)
assert re.search(r"\d+\s+f\s+1\.0+\s+stre\s+1\s+2\s+val=\s*2\.05",
redundant)
def test_kdg(self, control_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(control_filepath, "control")
with open("control") as f:
s = f.read()
matches = re.findall(r"\$operating system unix", s,
re.MULTILINE)
assert matches == ["$operating system unix"]
kdg("operating system", backup_file="control_backup")
assert os.path.isfile("control_backup")
with open("control") as f:
s = f.read()
matches = re.findall(r"\$operating system unix", s,
re.MULTILINE)
assert matches == []
with open("control_backup") as f:
s = f.read()
matches = re.findall(r"\$operating system unix", s,
re.MULTILINE)
assert matches == ["$operating system unix"]
def test_cpc(self, testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
c_empty = Control.empty()
c_empty.cpc("test_dir")
assert os.path.isfile(os.path.join("test_dir", "control"))
shutil.copy2(
os.path.join(testdir, 'control', 'control_test-subfiles'),
"control")
shutil.copy2(
os.path.join(testdir, 'control', 'gradient_test-gradient'),
"gradient")
c = Control.from_file("control")
c.cpc("test_dir")
c_test = Control.from_file(os.path.join("test_dir", "control"))
# check that did not overwrite
assert len(c_test.dg_list) == 1
assert os.path.isfile(os.path.join("test_dir", "gradient"))
c.cpc("test_dir", force_overwrite=True)
c_test = Control.from_file(os.path.join("test_dir", "control"))
assert len(c_test.dg_list) > 1
def test_sdgo(self, control_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(control_filepath, "control")
assert sdgo("$optimize", "internal") == " off"
def test_touch_file(self, delete_tmp_dir):
with temp_dir(delete_tmp_dir) as tmp_dir:
touch_file("test_file")
assert os.path.isfile("test_file")
def test_temp_dir(self):
# test that the file is not deleted if delete=False
# manually delete the file after testing
with temp_dir(delete=False) as tmp_dir:
assert tmp_dir == os.getcwd()
shutil.rmtree(tmp_dir)
def test_sdg(self, control_filepath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
shutil.copy2(control_filepath, "control")
assert sdg("operating system") == " unix\n"
def test_uhf(mo_dirpath, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
for f in ["alpha", "beta", "control"]:
shutil.copy2(os.path.join(mo_dirpath, f), f)
s = States.from_file()
assert len(s) == 28
assert s.n_states == 28
assert s[0].eigenvalue == pytest.approx(-14.457427310212)
assert_MSONable(s)
eiger_out = EigerOutput.from_file(os.path.join(mo_dirpath, "eiger"))
eiger_wrong_val = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_val"))
eiger_wrong_length = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_length"))
eiger_wrong_gap = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_gap"))
eiger_wrong_nel = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_nelec"))
eiger_wrong_occ = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_occ"))
eiger_wrong_match = EigerOutput.from_file(
os.path.join(mo_dirpath, "eiger_wrong_match"))
assert eiger_out.compare_states(s) is None
assert "gap" in eiger_wrong_gap.compare_states(s)
assert "states" in eiger_wrong_length.compare_states(s)
assert "eigenvalue" in eiger_wrong_val.compare_states(s)
assert "electrons" in eiger_wrong_nel.compare_states(s)
assert "occupation" in eiger_wrong_occ.compare_states(s)
assert "match" in eiger_wrong_match.compare_states(s)
assert s.is_uhf
assert not s.has_hole
assert s.total_electrons == 9
assert s.irreps[0] == "a1"
assert s.occupations[0] == 1
assert s.spins[0] == "a"
assert s.eigenvalues[-1] == pytest.approx(2.1425788573507)
assert s.irrep_indices[0] == 1
assert str(s)
s.pop(0)
assert len(s) == 27
s[0] = s[1]
assert s[0] == s[1]
s.insert(0, s[-1])
assert s[0] == s[-1]
# test filter
s = States.from_file()
assert len(s.filter_states(irrep="z")) == 0
filtered = s.filter_states(spin="b", irrep="a1")
assert filtered[0].spin == "b"
assert filtered[0].irrep == "a1"
# test get_shells
s = States.from_file()
with pytest.raises(ValueError):
s.get_shells(spin=None)
shell = s.get_shells(spin="a")
assert shell.occupations[0] == 1
assert shell.states[0] == ("a1", 1)
def test_sdg_subfiles(testdir, delete_tmp_dir):
with temp_dir(delete_tmp_dir):
for fname in ['control', 'coord', 'energy', 'mos', 'basis']:
shutil.copy2(
os.path.join(testdir, 'control',
'{}_test-subfiles'.format(fname)), fname)
cc = DataGroups.from_file("control")
energy_dg = cc.sdg(data_group='energy',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert energy_dg == ' SCF ' \
'SCFKIN SCFPOT\n' \
' 1 -40.48328750375' \
' 39.86406749278 -80.34735499653\n'
udef_bonds_dg = cc.sdg(data_group='user-defined bonds',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert udef_bonds_dg == '\n'
udef_bonds_dg = cc.sdg(data_group='user-defined bonds',
show_from_subfile=False,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert udef_bonds_dg == ' file=coord\n'
redundant_dg = cc.sdg(data_group='redundant',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert redundant_dg.startswith('\n number_of_atoms'
' 5\n'
' degrees_of_freedom'
' 9\n'
' internal_coordinates'
' 9\n'
' frozen_coordinates'
' 0\n'
' 1 k 1.0000000000000 stre'
' 1 2'
' val= 2.06326\n')
assert redundant_dg.endswith(' 7\n 8'
' 0.699953222 8 0\n'
' 8\n 9'
' 0.699953222 9 0\n'
' 9\n')
basis_dg = cc.sdg(data_group='basis',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert basis_dg.startswith('\n*\nc SVP\n*\n')
assert basis_dg.endswith(' 1 p\n'
' 0.80000000000 1.0000000000\n*\n')
mos_dg = cc.sdg(data_group='scfmo',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert mos_dg.startswith(' scfconv=6 format(4d20.14)\n'
' 1 a1 '
'eigenvalue=-.98973943603420D+01'
' nsaos=6\n')
assert mos_dg.endswith('-.11000018463806D+01-.60830569311504D+00'
'0.13711445998604D+010.13421520432673D+01\n'
'0.53804368223874D+00-.91129252301913D+00'
'0.11101532709297D+01\n')
scfintunit_dg = cc.sdg(data_group='scfintunit',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert scfintunit_dg == '\n unit=30 size=35' \
' file=twoint1\n' \
' unit=31 size=35' \
' file=twoint2\n'
with pytest.raises(RuntimeError,
match='Multiple "file=FILENAME" directives.'):
cc.sdg(data_group='scfintunit',
show_from_subfile=True,
raise_if_multiple_subfiles=True,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
with pytest.raises(RuntimeError,
match=r'Both a reference to a file '
r'\("file=FILENAME"\) and regular data '
r'blocks are in the data group.'):
cc.sdg(data_group='user-defined',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=True)
with pytest.raises(RuntimeError,
match='File "gradient" for data group "grad" '
'is missing.'):
cc.sdg(data_group='grad',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=True,
raise_if_regular_and_subfile=False)
grad_db = cc.sdg(data_group='grad',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert grad_db == ' file=gradient\n'
# create a gradient empty file and check that the behavior is the same
# as when the file is missing
touch_file("gradient")
with pytest.raises(RuntimeError,
match='File "gradient" for data group "grad" '
'is missing.'):
cc.sdg(data_group='grad',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=True,
raise_if_regular_and_subfile=False)
grad_db = cc.sdg(data_group='grad',
show_from_subfile=True,
raise_if_multiple_subfiles=False,
raise_if_missing_subfile=False,
raise_if_regular_and_subfile=False)
assert grad_db == ' file=gradient\n'