def test_reaction_warnings(): test_reac = Reactant(name='test', smiles='C') test_reac.energy = -1 test_prod = Product(name='test', smiles='C') test_prod.energy = -1.03187251 tsguess = TSguess(atoms=test_reac.atoms, reactant=ReactantComplex(test_reac), product=ProductComplex()) tsguess.bond_rearrangement = BondRearrangement() ts = TransitionState(tsguess) ts.energy = -0.98 ts.imaginary_frequencies = [-100] reaction = Reaction(test_reac, test_prod) reaction.ts = None # Should be some warning with no TS assert len( plotting.get_reaction_profile_warnings(reactions=[reaction])) > 10 # Should be no warnings with a TS that exists and has an energy and one # imaginary freq reaction.ts = ts warnings = plotting.get_reaction_profile_warnings(reactions=[reaction]) assert 'None' in warnings
def test_plot_reaction_profile(): r = Reactant(name='reactant', smiles='C') p = Product(name='product', smiles='C') tsguess = TSguess(atoms=r.atoms, reactant=ReactantComplex(r), product=ProductComplex(p)) tsguess.bond_rearrangement = BondRearrangement() ts = TransitionState(tsguess) reaction = Reaction(r, p) reaction.ts = ts plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test') assert os.path.exists('test_reaction_profile.png') os.remove('test_reaction_profile.png') with pytest.raises(AssertionError): plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test', free_energy=True, enthalpy=True) return None
def test_multistep_reaction(): Config.num_conformers = 1 # Spoof installs Config.lcode = 'xtb' Config.XTB.path = here Config.hcode = 'orca' Config.ORCA.path = here # Don't run the calculation without a working XTB install if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'): return Config.XTB.path = shutil.which('xtb') Config.ORCA.implicit_solvation_type = 'cpcm' Config.make_ts_template = False Config.num_complex_sphere_points = 2 Config.num_complex_random_rotations = 1 # SN2 forwards then backwards example forwards = Reaction('CCl.[F-]>>CF.[Cl-]', name='sn2_forwards', solvent_name='water') backwards = Reaction('CF.[Cl-]>>CCl.[F-]', name='sn2_backwards', solvent_name='water') reaction = MultiStepReaction(forwards, backwards) reaction.calculate_reaction_profile() assert reaction.reactions is not None
def test_calculate_reaction_profile_energies(): test_reac = Reactant(name='test', smiles='C') test_reac.energy = -1 test_prod = Product(name='test', smiles='C') test_prod.energy = -1.03187251 tsguess = TSguess(atoms=test_reac.atoms, reactant=ReactantComplex(test_reac), product=ProductComplex()) tsguess.bond_rearrangement = BondRearrangement() ts = TransitionState(tsguess) ts.energy = -0.96812749 reaction = Reaction(test_reac, test_prod) reaction.ts = ts energies = plotting.calculate_reaction_profile_energies(reactions=[reaction], units=KcalMol) # Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively assert energies[0] == 0 assert 19 < energies[1] < 21 assert -21 < energies[2] < -19 # Copying the reaction should give relative energies [0, 20, -20, 0, -40] energies = plotting.calculate_reaction_profile_energies(reactions=[reaction, deepcopy(reaction)], units=KcalMol) # Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively assert energies[0] == 0 assert -0.1 < energies[3] < 0.1 assert -41 < energies[4] < -39
def test_find_tss(): Config.num_conformers = 1 # Spoof ORCA install Config.ORCA.path = here # Don't run the calculation without a working XTB install if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'): return if os.path.exists('/dev/shm'): Config.ll_tmp_dir = '/dev/shm' Config.XTB.path = shutil.which('xtb') Config.ORCA.implicit_solvation_type = cpcm Config.make_ts_template = False Config.num_complex_sphere_points = 2 Config.num_complex_random_rotations = 1 # SN2 example flouride = Reactant(name='F-', smiles='[F-]') methyl_chloride = Reactant(name='CH3Cl', smiles='ClC') chloride = Product(name='Cl-', smiles='[Cl-]') methyl_flouride = Product(name='CH3F', smiles='CF') reaction = Reaction(flouride, methyl_chloride, chloride, methyl_flouride, name='sn2', solvent_name='water') # Will work in data/locate_ts/transition_states reaction.locate_transition_state() assert reaction.ts is not None os.chdir('transition_states') assert reaction.ts.is_true_ts() os.chdir('..') reaction.ts.save_ts_template(folder_path=os.getcwd()) assert os.path.exists('template0.txt') # There should now be a saved template templates = get_ts_templates(folder_path=os.getcwd()) assert len(templates) == 1 template = templates[0] assert template.solvent.name == 'water' assert template.mult == 1 assert template.charge == -1 assert template.graph.number_of_nodes() == 6 # Reset the configuration Config.ll_tmp_dir = None
def test_isomorphic_reactant_product(): r_water = Reactant(name='h2o', smiles='O') r_methane = Reactant(name='methane', smiles='C') p_water = Product(name='h2o', smiles='O') p_methane = Product(name='methane', smiles='C') # Reaction where the reactant and product complexes are isomorphic # should return no TS reaction = Reaction(r_water, r_methane, p_water, p_methane) reaction.locate_transition_state() assert reaction.ts is None
def test_plot_reaction_profile(): r = Reactant(name='reactant', smiles='C') p = Product(name='product', smiles='C') tsguess = TSguess(atoms=r.atoms, reactant=ReactantComplex(r), product=ProductComplex(p)) tsguess.bond_rearrangement = BondRearrangement() ts = TransitionState(tsguess) reaction = Reaction(r, p) reaction.ts = ts plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test_reaction') assert os.path.exists('test_reaction_reaction_profile.png') os.remove('test_reaction_reaction_profile.png')
def test_plot_reaction_profile(): # only tests the file is created with the right name os.chdir(os.path.join(here, 'data')) r = Reactant(name='reactant', smiles='C') p = Product(name='product', smiles='C') tsguess = TSguess(atoms=r.atoms, reactant=ReactantComplex(r), product=ProductComplex(p)) tsguess.bond_rearrangement = BondRearrangement() ts = TransitionState(tsguess) reaction = Reaction(r, p) reaction.ts = ts plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test_reaction') assert os.path.exists('test_reaction_reaction_profile.png') os.remove('test_reaction_reaction_profile.png') os.chdir(here)
def test_bonds(): h1 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.0) h2 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.7) h3 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=1.7) hydrogen = Reactant(name='H2', atoms=[h1, h2], charge=0, mult=1) h = Reactant(name='H', atoms=[h3], charge=0, mult=2) reac = ReactantComplex(hydrogen, h) prod_h2 = Product(name='H2', atoms=[h1, h2], charge=0, mult=1) prod_h = Product(name='H', atoms=[h3], charge=0, mult=2) fbond = FormingBond(atom_indexes=(1, 2), species=reac) bbond = BreakingBond(atom_indexes=(0, 1), species=reac, reaction=Reaction(hydrogen, h, prod_h2, prod_h)) assert fbond.curr_dist == 1.0 assert 0.6 < fbond.final_dist < 0.8 assert 2.0 < bbond.final_dist < 2.5 assert bbond.curr_dist == 0.7
def test_get_ts_guess_2dscan(): ch3cl_f = Reactant(name='CH3Cl_F-', charge=-1, mult=1, atoms=[ Atom('F', -4.14292, -0.24015, 0.07872), Atom('Cl', 1.63463, 0.09787, -0.02490), Atom('C', -0.14523, -0.00817, 0.00208), Atom('H', -0.47498, -0.59594, -0.86199), Atom('H', -0.45432, -0.49900, 0.93234), Atom('H', -0.56010, 1.00533, -0.04754) ]) ch3f_cl = Product(name='CH3Cl_F-', charge=-1, mult=1, atoms=[ Atom('F', 1.63463, 0.09787, -0.02490), Atom('Cl', -4.14292, -0.24015, 0.07872), Atom('C', -0.14523, -0.00817, 0.00208), Atom('H', -0.47498, -0.59594, -0.86199), Atom('H', -0.45432, -0.49900, 0.93234), Atom('H', -0.56010, 1.00533, -0.04754) ]) # H H # F- C--Cl -> F--C Cl- # H H H H pes = pes_2d.PES2d(reactant=ReactantComplex(ch3cl_f), product=ProductComplex(ch3f_cl), r1s=np.linspace(4.0, 1.5, 9), r1_idxs=(0, 2), r2s=np.linspace(1.78, 4.0, 8), r2_idxs=(1, 2)) pes.calculate(name='SN2_PES', method=xtb, keywords=xtb.keywords.low_opt) assert pes.species[0, 1] is not None assert -13.13 < pes.species[0, 1].energy < -13.11 assert pes.species.shape == (9, 8) assert pes.rs.shape == (9, 8) assert type(pes.rs[0, 1]) == tuple assert pes.rs[1, 1] == (np.linspace(4.0, 1.5, 9)[1], np.linspace(1.78, 4.0, 8)[1]) # Fitting the surface with a 2D polynomial up to order 3 in r1 and r2 i.e. # r1^3r2^3 pes.fit(polynomial_order=3) assert pes.coeff_mat is not None assert pes.coeff_mat.shape == (4, 4) # Includes r1^0 etc. pes.print_plot(name='pes_plot') assert os.path.exists('pes_plot.png') os.remove('pes_plot.png') # Products should be made on this surface assert pes.products_made() # Get the TS guess from this surface calling all the above functions reactant = ReactantComplex(ch3cl_f) fbond = FormingBond(atom_indexes=(0, 2), species=reactant) fbond.final_dist = 1.5 bbond = BreakingBond(atom_indexes=(1, 2), species=reactant, reaction=Reaction(ch3cl_f, ch3f_cl)) bbond.final_dist = 4.0 ts_guess = pes_2d.get_ts_guess_2d(reactant=reactant, product=ProductComplex(ch3f_cl), bond1=fbond, bond2=bbond, polynomial_order=3, name='SN2_PES', method=xtb, keywords=xtb.keywords.low_opt, dr=0.3) assert ts_guess is not None assert ts_guess.n_atoms == 6 assert ts_guess.energy is None assert 1.9 < ts_guess.get_distance(0, 2) < 2.1 assert 1.9 < ts_guess.get_distance(1, 2) < 2.0
def test_find_tss(): os.chdir(os.path.join(here, 'data', 'locate_ts')) Config.num_conformers = 1 # Spoof ORCA install Config.ORCA.path = here # Don't run the calculation without a working XTB install if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'): return Config.XTB.path = shutil.which('xtb') Config.ORCA.implicit_solvation_type = 'cpcm' Config.make_ts_template = False Config.num_complex_sphere_points = 2 Config.num_complex_random_rotations = 1 # SN2 example flouride = Reactant(name='F-', smiles='[F-]') methyl_chloride = Reactant(name='CH3Cl', smiles='ClC') chloride = Product(name='Cl-', smiles='[Cl-]') methyl_flouride = Product(name='CH3F', smiles='CF') reaction = Reaction(flouride, methyl_chloride, chloride, methyl_flouride, name='sn2', solvent_name='water') # Will work in data/locate_ts/transition_states reaction.locate_transition_state() assert reaction.ts is not None os.chdir(os.path.join(here, 'data', 'locate_ts', 'transition_states')) for filename in os.listdir(os.getcwd()): if filename.endswith(('.inp', '.png')): os.remove(filename) assert reaction.ts.is_true_ts() reaction.ts.save_ts_template(folder_path=os.getcwd()) assert os.path.exists('template0.obj') # There should now be a saved template templates = get_ts_templates(folder_path=os.getcwd()) assert len(templates) == 1 template = templates[0] assert template.solvent.name == 'water' assert template.mult == 1 assert template.charge == -1 assert template.graph.number_of_nodes() == 6 # Tidy the generated files os.remove('template0.obj') os.chdir(here)