def test_pubchem():
from ase.data.pubchem import pubchem_search, pubchem_conformer_search
from ase.data.pubchem import pubchem_atoms_search
from ase.data.pubchem import pubchem_atoms_conformer_search
# check class functionality
data = pubchem_search('ammonia', mock_test=True)
data.get_atoms()
data.get_pubchem_data()
# XXX maybe verify some of this data?
# check the various entry styles and the functions that return atoms
pubchem_search(cid=241, mock_test=True).get_atoms()
pubchem_atoms_search(smiles='CCOH', mock_test=True)
pubchem_atoms_conformer_search('octane', mock_test=True)
# (maybe test something about some of the returned atoms)
# check conformer searching
confs = pubchem_conformer_search('octane', mock_test=True)
for conf in confs:
pass
try: # check that you can't pass in two args
pubchem_search(name='octane', cid=222, mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
try: # check that you must pass at least one arg
pubchem_search(mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
return ASE_new_positions
'''
Main Program Begins Here
'''
#TRAPPE
#Collect TRAPPE input params
TRAPPE_fname = 'trappe_parameters_99.txt'
TRAPPE_atoms, TRAPPE_bonds, TRAPPE_name = get_TRAPPE_params(TRAPPE_fname)
#ASE
#Convert Smiles string into Atoms object.
SMILES = 'O=C(C=C)OCCCCCCCC'
atoms = pubchem_atoms_search(smiles=SMILES)
#Determine psuedo-atoms of molecule and remove hydrogens.
psuedo_atoms = get_psuedoatoms(atoms,TRAPPE_atoms,TRAPPE_bonds)
ana = Analysis(psuedo_atoms) #Create geometry analysis object from Atoms object.
organized_ASE_atoms = Order_atoms_wrt_TRAPPE(psuedo_atoms,ana,TRAPPE_bonds,TRAPPE_atoms)
#Center the psuedo_atoms. FEASST requires atom[0] to be located within origin!
for atm in organized_ASE_atoms:
if atm[0] == 1:
center_about = np.copy(atm[-1])
break
for atm in organized_ASE_atoms:
positions=[[0, L / 2, L / 2]],
cell=[d, L, L],
pbc=[1, 0, 0])
add_to_dict(AseAtomsAdaptor.get_structure(wire), metal + '_Wire')
"""
for metal in ['Au', 'Pt', 'Mo']:
atoms = bulk(metal, cubic=True)
if metal == 'Fe':
atoms *= (1, 2, 2)
atoms.set_cell([atoms.cell[0][0]] + [12] * 2)
atoms.center()
add_to_dict(AseAtomsAdaptor.get_structure(atoms), metal + '_wire')
# this code is about to get pretty serious if you are trying to follow it
atoms = pubchem_atoms_search('ethane')
vector = atoms[1].position - atoms[0].position
methyl = Atoms([atoms[a] for a in [1, 6, 5, 7]])
del atoms[7]
del atoms[6]
del atoms[5]
del atoms[1]
methyl.rotate(120, v=vector, center=methyl[0].position)
atoms += methyl
del atoms[7]
del atoms[3]
atoms.rotate(180, v=vector)
atoms.positions -= atoms[0].position
bl = np.linalg.norm(vector)
add_to_dict(atoms, 'water', 300)
# CO2
atoms = make_box_of_molecules(molecule('CO2'), 25, [20] * 3)
print(len(atoms))
add_to_dict(atoms, 'CO2', 70 + 273.15)
# Al
atoms = read('Al.xyz')
add_to_dict(atoms, 'Al', 10000)
# natural gas
CH4 = pubchem_atoms_search('methane')
C2H6 = pubchem_atoms_search('ethane')
C3H8 = pubchem_atoms_search('propane')
atoms = make_box_of_molecules([CH4, C2H6, C3H8], [18, 6, 6], [15] * 3)
add_to_dict(atoms, 'LNG', 273.15 - 162)
# Battery
with open('Li-ion_electrolyte_interface_318.txt', 'r') as f:
txt = f.read()
lattice = txt.split('lattice vectors (au):')[1]
lattice, positions = txt.split('Atom types and positions (au):')
lattice = lattice.splitlines()[1:]
lattice = [[float(b) * Bohr for b in a.split()] for a in lattice]
struct = AseAtomsAdaptor.get_structure(atoms)
add_to_dict(struct)
atoms = molecule('HF')
for atom in atoms:
if atom.symbol == 'F':
atom.symbol = 'Br'
atoms.set_distance(0, 1, 1.43)
atoms.set_cell([10, 10, 10])
atoms.center()
struct = AseAtomsAdaptor.get_structure(atoms)
add_to_dict(struct)
atoms = pubchem_atoms_search(cid=807) # I2
atoms.set_cell([10, 10, 10])
atoms.center()
struct = AseAtomsAdaptor.get_structure(atoms)
add_to_dict(struct, 'I2')
# nano-particles
import ase
from ase.cluster.cubic import FaceCenteredCubic
surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)]
layers = [3, 3, 3]
lc = 3.61000
atoms = FaceCenteredCubic('Cu',
from ase.data.pubchem import pubchem_search, pubchem_conformer_search
from ase.data.pubchem import pubchem_atoms_search
from ase.data.pubchem import pubchem_atoms_conformer_search
# check class functionality
data = pubchem_search('ammonia', mock_test=True)
atoms = data.get_atoms()
entry_data = data.get_pubchem_data()
# check the various entry styles and the functions that return atoms
atoms = pubchem_search(cid=241, mock_test=True).get_atoms()
atoms = pubchem_atoms_search(smiles='CCOH', mock_test=True)
atoms = pubchem_atoms_conformer_search('octane', mock_test=True)
# check conformer searching
confs = pubchem_conformer_search('octane', mock_test=True)
for conf in confs:
pass
try: # check that you can't pass in two args
atoms = pubchem_search(name='octane', cid=222, mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
try: # check that you must pass at least one arg
atoms = pubchem_search(mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass