def test_input_gen():
xtb = XTB()
calc = Calculation(name='tmp',
molecule=test_mol,
method=xtb,
keywords=xtb.keywords.sp)
Config.keep_input_files = True
calc.generate_input()
assert os.path.exists('tmp_xtb.xyz')
calc.clean_up()
# Clean-up should do nothing if keep_input_files = True
assert os.path.exists('tmp_xtb.xyz')
# but should be able to be forced
calc.clean_up(force=True)
assert not os.path.exists('tmp_xtb.xyz')
# Test the keywords parsing
unsupported_func = Functional('PBE', orca='PBE')
calc_kwds = Calculation(name='tmp',
molecule=test_mol,
method=xtb,
keywords=SinglePointKeywords([unsupported_func]))
with pytest.raises(ex.UnsuppportedCalculationInput):
calc_kwds.generate_input()
def test_solvation():
methane = Molecule(name='solvated_methane', smiles='C',
solvent_name='water')
with pytest.raises(UnsuppportedCalculationInput):
# Should raise on unsupported calculation type
method.implicit_solvation_type = 'xxx'
calc = Calculation(name='broken_solvation', molecule=methane,
method=method, keywords=sp_keywords)
calc.run()
method.implicit_solvation_type = 'CPCM'
calc = Calculation(name='methane_cpcm', molecule=methane,
method=method, keywords=sp_keywords)
calc.generate_input()
assert any('cpcm' in line.lower() for line in open('methane_cpcm_orca.inp', 'r'))
os.remove('methane_cpcm_orca.inp')
method.implicit_solvation_type = 'SMD'
calc = Calculation(name='methane_smd', molecule=methane,
method=method, keywords=sp_keywords)
calc.generate_input()
assert any('smd' in line.lower() for line in open('methane_smd_orca.inp', 'r'))
os.remove('methane_smd_orca.inp')
def test_point_charge_calc():
os.chdir(os.path.join(here, 'data'))
# Methane single point using a point charge with a unit positive charge
# located at (10, 10, 10)
calc = Calculation(
name='methane_point_charge',
molecule=test_mol,
method=method,
keywords=sp_keywords,
point_charges=[PointCharge(charge=1.0, x=10.0, y=10.0, z=10.0)])
calc.run()
# Assert that the input file is in the expected configuration
for line in open('methane_point_charge_g09.com', 'r'):
if 'PBE' in line:
assert 'Charge' in line
if len(line.split()) == 4:
if not line.split()[0].isdigit():
continue
x, y, z, charge = line.split()
assert float(x) == 10.0
assert float(y) == 10.0
assert float(z) == 10.0
assert float(charge) == 1.0
assert -40.428 < calc.get_energy() < -40.427
# Gaussian needs x-matrix and nosymm in the input line to run optimisations
# with point charges..
for opt_keyword in ['Opt', 'Opt=Tight', 'Opt=(Tight)']:
calc = Calculation(
name='methane_point_charge_o',
molecule=test_mol,
method=method,
keywords=OptKeywords(['PBE1PBE/Def2SVP', opt_keyword]),
point_charges=[PointCharge(charge=1.0, x=3.0, y=3.0, z=3.0)])
calc.generate_input()
for line in open('methane_point_charge_o_g09.com', 'r').readlines():
if 'PBE' in line:
assert 'charge' in line.lower()
assert 'z-matrix' in line.lower() and 'nosymm' in line.lower()
break
os.remove('methane_point_charge_g09.com')
os.remove('methane_point_charge_o_g09.com')
os.chdir(os.path.join(here))
def test_xtb_calculation():
test_mol = Molecule(name='test_mol',
smiles='O=C(C=C1)[C@@](C2NC3C=C2)([H])[C@@]3([H])C1=O')
calc = Calculation(name='opt', molecule=test_mol, method=method,
keywords=Config.XTB.keywords.opt)
calc.run()
assert os.path.exists('opt_xtb.xyz') is True
assert os.path.exists('opt_xtb.out') is True
assert len(calc.get_final_atoms()) == 22
assert calc.get_energy() == -36.990267613593
assert calc.output.exists()
assert calc.output.file_lines is not None
assert calc.input.filename == 'opt_xtb.xyz'
assert calc.output.filename == 'opt_xtb.out'
with pytest.raises(NotImplementedError):
calc.optimisation_nearly_converged()
with pytest.raises(NotImplementedError):
calc.get_imaginary_freqs()
with pytest.raises(NotImplementedError):
calc.get_normal_mode_displacements(4)
charges = calc.get_atomic_charges()
assert len(charges) == 22
assert all(-1.0 < c < 1.0 for c in charges)
const_opt = Calculation(name='const_opt', molecule=test_mol,
method=method,
distance_constraints={(0, 1): 1.2539792},
cartesian_constraints=[0],
keywords=Config.XTB.keywords.opt)
const_opt.generate_input()
assert os.path.exists('const_opt_xtb.xyz')
assert os.path.exists('xcontrol_const_opt_xtb')
const_opt.clean_up(force=True)
assert not os.path.exists('xcontrol_const_opt_xtb')
# Write an empty output file
open('tmp.out', 'w').close()
const_opt.output.filename = 'tmp.out'
const_opt.output.set_lines()
# cannot get atoms from an empty file
with pytest.raises(AtomsNotFound):
_ = const_opt.get_final_atoms()
def test_opt_single_atom():
h = Molecule(name='H', smiles='[H]')
calc = Calculation(name='opt_h',
molecule=h,
method=method,
keywords=opt_keywords)
calc.generate_input()
# Can't do an optimisation of a hydrogen atom..
assert os.path.exists('opt_h_nwchem.nw')
input_lines = open('opt_h_nwchem.nw', 'r').readlines()
assert 'opt' not in [keyword.lower() for keyword in input_lines[0].split()]
os.remove('opt_h_nwchem.nw')
def test_exec_not_avail_method():
orca = ORCA()
orca.path = '/a/non/existent/path'
assert not orca.available
calc = Calculation(name='tmp',
molecule=test_mol,
method=orca,
keywords=orca.keywords.sp)
calc.generate_input()
with pytest.raises(ex.MethodUnavailable):
calc.execute_calculation()
with pytest.raises(ex.MethodUnavailable):
calc.run()
def test_xtb_calculation():
os.chdir(os.path.join(here, 'data'))
XTB.available = True
test_mol = Molecule(name='test_mol',
smiles='O=C(C=C1)[C@@](C2NC3C=C2)([H])[C@@]3([H])C1=O')
calc = Calculation(name='opt', molecule=test_mol, method=method,
keywords=Config.XTB.keywords.opt)
calc.run()
assert os.path.exists('opt_xtb.xyz') is True
assert os.path.exists('opt_xtb.out') is True
assert len(calc.get_final_atoms()) == 22
assert calc.get_energy() == -36.990267613593
assert calc.output.exists()
assert calc.output.file_lines is not None
assert calc.input.filename == 'opt_xtb.xyz'
assert calc.output.filename == 'opt_xtb.out'
with pytest.raises(NotImplementedError):
calc.optimisation_nearly_converged()
with pytest.raises(NotImplementedError):
calc.get_imaginary_freqs()
with pytest.raises(NotImplementedError):
calc.get_normal_mode_displacements(4)
charges = calc.get_atomic_charges()
assert len(charges) == 22
assert all(-1.0 < c < 1.0 for c in charges)
const_opt = Calculation(name='const_opt', molecule=test_mol,
method=method,
distance_constraints={(0, 1): 1.2539792},
cartesian_constraints=[0],
keywords=Config.XTB.keywords.opt)
const_opt.generate_input()
assert os.path.exists('xcontrol_const_opt_xtb')
os.remove('const_opt_xtb.xyz')
os.remove('xcontrol_const_opt_xtb')
os.remove('opt_xtb.xyz')
os.chdir(here)
def test_keyword_setting():
orca = ORCA()
orca.keywords.sp.functional = 'B3LYP'
# Setter should generate a Functional from the keyword string
assert isinstance(orca.keywords.sp.functional, Functional)
calc = Calculation(name='tmp',
molecule=test_mol.copy(),
method=orca,
keywords=orca.keywords.sp)
calc.generate_input()
assert calc.input.exists()
# B3LYP should now be in the in input
inp_lines = open(calc.input.filename, 'r').readlines()
assert any('B3LYP' in line for line in inp_lines)
# With a keyword without ORCA defined then raise an exception
with pytest.raises(UnsuppportedCalculationInput):
orca.keywords.sp.functional = Functional(name='B3LYP', g09='B3LYP')
calc = Calculation(name='tmp',
molecule=test_mol.copy(),
method=orca,
keywords=orca.keywords.sp)
calc.generate_input()
# Without a default wavefunction method defined in the single point method
# we can't set keywords.wf
with pytest.raises(ValueError):
orca.keywords.sp.wf_method = 'HF'
# but if we have a WF method in the keywords we should be able to set it
orca.keywords.sp = SinglePointKeywords(
[WFMethod('MP2'), BasisSet('def2-TZVP')])
orca.keywords.sp.wf_method = 'HF'
assert orca.keywords.sp.wf_method == 'HF'
def test_single_atom_opt():
mol = Molecule(smiles='[H]')
mol.name = 'molecule'
calc = Calculation(name='H',
molecule=mol,
method=method,
keywords=opt_keywords, n_cores=2)
calc.generate_input()
assert os.path.exists('H_g09.com')
input_file_lines = open('H_g09.com', 'r').readlines()
n_cores_set = False
for line in input_file_lines:
if 'PBE' in line:
assert 'Opt' not in line
if '%nprocshared=2' in line:
n_cores_set = True
assert n_cores_set
