def test_s22():
fragTest = Fragmentation(s22.s22)
minimize = False
#minimize = True
print 'Relaxed:', minimize
fragTest.molecules = []
fragTest.fragments = []
for moleculeName in s22.s22:
data = s22.data[moleculeName]
atoms = Atoms(data['symbols'], data['positions'])
dimer1End = data['dimer atoms'][0]
frag1Atoms = atoms.copy()[:dimer1End]
frag2Atoms = atoms.copy()[dimer1End:]
fragment1 = ReaxFFSystem(moleculeName + '_f1', frag1Atoms, minimize = minimize)
fragment2 = ReaxFFSystem(moleculeName + '_f2', frag2Atoms, minimize = minimize)
system = ReaxFFSystem(moleculeName, atoms, minimize = minimize,
fragment_list = [fragment1.name, fragment2.name])
fragTest.molecules.append(system)
fragTest.fragments += [fragment1, fragment2]
fragTest.fill_data_reference(data_type='s22')
fragTest.run(write=True)
def testSingle(molecule):
#TEST fragmentation
print "Test fragmentation with s22 set"
fragment_names = [molecule+'_f1',molecule+'_f2']
test_f = Fragmentation([molecule])
minimize = False
#minimize = True
print 'Relaxed:', minimize
sys = Atoms(s22_sim_data[molecule]['symbols'],
s22_sim_data[molecule]['positions'])
test_f.molecules = [ReaxFFSystem(molecule,atoms=sys,
fragment_list=fragment_names, minimize=minimize)]
n = s22_sim_data[molecule]['dimer atoms']
atom_fragments = [ sys.copy()[range(n[0])], sys.copy()[range(n[0],n[0]+n[1])] ]
test_f.fragments = [ ReaxFFSystem(name,atoms=a, minimize = minimize)
for name,a in zip(fragment_names,atom_fragments)]
test_f.fill_data_reference(data_type='s22')
test_f.run(write=True)
print test_f.data
def run_s22(reload=False):
h = 0.4
vacuum = 2.0
#molecules = ['Ammonia_dimer']
molecules = s22_molecules
test_f = Fragmentation(molecules)
sys = [Atoms(s22_sim_data[molecule]['symbols'],
s22_sim_data[molecule]['positions'])
for molecule in molecules]
test_f.molecules = [GPAWSystems(molecule,atoms=atoms,
h=h, vacuum=vacuum,
fragment_list=fragment_names(molecule))
for molecule,atoms in zip(molecules,sys)]
atom_fragments_1 = [ system.system.copy()[fragment_n(system.name,1)]
for system in test_f.molecules]
atom_fragments_2 = [ system.system.copy()[fragment_n(system.name,2)]
for system in test_f.molecules]
test_f.fragments = [ GPAWSystems(name+'_f1',atoms=a,h=h, vacuum=vacuum)
for name,a in zip(molecules,atom_fragments_1)]
test_f.fragments += [ GPAWSystems(name+'_f2',atoms=a,h=h, vacuum=vacuum)
for name,a in zip(molecules,atom_fragments_2)]
test_f.fill_data_reference(data_type='s22')
if reload:
test_f.load_data('data.pkl')
test_f.calculate_error()
test_f.calculate_mae()
print test_f.mae
else:
test_f.run(write=True)
def testSingle(moleculeName = "Methane_dimer"):
#TEST fragmentation
print "Test fragmentation with s22 set"
minimize = False
minimize = True
print 'Relaxed:', minimize
fragTest = Fragmentation([moleculeName])
#atoms = s22.create_s22_system(moleculeName)
data = s22.data[moleculeName]
atoms = Atoms(data['symbols'], data['positions'])
dimer1End = s22.data[moleculeName]['dimer atoms'][0]
frag1Atoms = atoms.copy()[:dimer1End]
frag2Atoms = atoms.copy()[dimer1End:]
calculate_charges(frag1Atoms)
calculate_charges(frag2Atoms)
atoms.set_charges(np.append(frag1Atoms.get_charges(), frag2Atoms.get_charges()))
fragment1 = CHARMMSystem(moleculeName + '_f1', frag1Atoms, minimize = minimize)
fragment2 = CHARMMSystem(moleculeName + '_f2', frag2Atoms, minimize = minimize)
system = CHARMMSystem(moleculeName, atoms, minimize = minimize,
fragment_list = [fragment1.name, fragment2.name])
fragTest.molecules = [system]
fragTest.fragments = [fragment1, fragment2]
fragTest.fill_data_reference(data_type='s22')
fragTest.run(write=True)
import ase.io
ase.io.write('molecule.xyz', atoms)
print fragTest.data
def main():
#TEST atomization
print "Test atomization"
molecule_names = ['CH4']
test = Fragmentation(molecule_names)
test.molecules = [
GPAWSystems(name, h=0.3, vacuum=2.0, xc='PBE')
for name in molecule_names
]
atom_names = []
for gs in test.molecules:
atom_names.extend(gs.system.get_chemical_symbols())
test.fragments = [
GPAWSystems(name, h=0.3, vacuum=2.0, xc='PBE')
for name in set(atom_names)
]
test.fill_data_reference(data_type='g22')
test.run()
error = 5.64039227514 - test.mae
print 'Test error: {0} eV'.format(error)
#TEST fragmentation
print "Test fragmentation with s22 set"
molecule = 'Ammonia_dimer'
fragment_names = [molecule + '_f1', molecule + 'f2']
test_f = Fragmentation([molecule])
sys = Atoms(s22_sim_data[molecule]['symbols'],
s22_sim_data[molecule]['positions'])
test_f.molecules = [
GPAWSystems(molecule,
atoms=sys,
h=0.4,
vacuum=2.0,
fragment_list=fragment_names)
]
n = s22_sim_data[molecule]['dimer atoms']
atom_fragments = [
sys.copy()[range(n[0])],
sys.copy()[range(n[0], n[0] + n[1])]
]
test_f.fragments = [
GPAWSystems(name, atoms=a, h=0.4, vacuum=2.0)
for name, a in zip(fragment_names, atom_fragments)
]
test_f.fill_data_reference(data_type='s22')
test_f.run(write=True)
error = 266.704827694 - test_f.mae
print 'Test error: {0} eV'.format(error)
def test_s22():
fragTest = Fragmentation(s22.s22)
minimize = False
minimize = True
print 'Relaxed:', minimize
fragTest.molecules = []
fragTest.fragments = []
testSet = [
#'Ammonia_dimer',
#'Water_dimer',
#'Formic_acid_dimer',
#'Formamide_dimer',
#'Uracil_dimer_h-bonded',
#'2-pyridoxine_2-aminopyridine_complex',
#'Adenine-thymine_Watson-Crick_complex',
'Methane_dimer',
#'Ethene_dimer',
'Benzene-methane_complex',
#'Benzene_dimer_parallel_displaced',
#'Pyrazine_dimer',
#'Uracil_dimer_stack',
#'Indole-benzene_complex_stack',
#'Adenine-thymine_complex_stack',
#'Ethene-ethyne_complex',
#'Benzene-water_complex',
#'Benzene-ammonia_complex',
#'Benzene-HCN_complex',
#'Benzene_dimer_T-shaped',
#'Indole-benzene_T-shape_complex',
'Phenol_dimer'
]
for moleculeName in testSet:
data = s22.data[moleculeName]
atoms = Atoms(data['symbols'], data['positions'])
dimer1End = data['dimer atoms'][0]
frag1Atoms = atoms.copy()[:dimer1End]
frag2Atoms = atoms.copy()[dimer1End:]
fragment1 = COMPASSSystem(moleculeName + '_f1',
frag1Atoms,
minimize=minimize)
fragment2 = COMPASSSystem(moleculeName + '_f2',
frag2Atoms,
minimize=minimize)
system = COMPASSSystem(moleculeName,
atoms,
minimize=minimize,
fragment_list=[fragment1.name, fragment2.name])
fragTest.molecules.append(system)
fragTest.fragments += [fragment1, fragment2]
fragTest.fill_data_reference(data_type='s22')
fragTest.run(write=True)
def test_s22():
fragTest = Fragmentation(s22.s22)
minimize = False
#minimize = True
print 'Relaxed:', minimize
fragTest.molecules = []
fragTest.fragments = []
testSet = [
'Ammonia_dimer',
'Water_dimer',
'Formic_acid_dimer',
'Formamide_dimer',
'Uracil_dimer_h-bonded',
'2-pyridoxine_2-aminopyridine_complex',
'Adenine-thymine_Watson-Crick_complex',
'Methane_dimer',
'Ethene_dimer',
'Benzene-methane_complex',
'Benzene_dimer_parallel_displaced',
'Pyrazine_dimer',
'Uracil_dimer_stack',
'Indole-benzene_complex_stack',
'Adenine-thymine_complex_stack',
'Ethene-ethyne_complex',
'Benzene-water_complex',
'Benzene-ammonia_complex',
'Benzene-HCN_complex',
'Benzene_dimer_T-shaped',
'Indole-benzene_T-shape_complex',
'Phenol_dimer'
]
for moleculeName in testSet:
atoms = s22.create_s22_system(moleculeName)
dimer1End = s22.data[moleculeName]['dimer atoms'][0]
frag1Atoms = atoms.copy()[:dimer1End]
frag2Atoms = atoms.copy()[dimer1End:]
calculate_charges(frag1Atoms)
calculate_charges(frag2Atoms)
atoms.set_charges(np.append(frag1Atoms.get_charges(), frag2Atoms.get_charges()))
fragment1 = CHARMMSystem(moleculeName + '_f1', frag1Atoms, minimize = minimize)
fragment2 = CHARMMSystem(moleculeName + '_f2', frag2Atoms, minimize = minimize)
system = CHARMMSystem(moleculeName, atoms, minimize = minimize,
fragment_list = [fragment1.name, fragment2.name])
fragTest.molecules.append(system)
fragTest.fragments += [fragment1, fragment2]
fragTest.fill_data_reference(data_type='s22')
fragTest.run(write=True)
def run_s22(reload=False):
h = 0.4
vacuum = 2.0
#molecules = ['Ammonia_dimer']
molecules = s22_molecules
test_f = Fragmentation(molecules)
sys = [
Atoms(s22_sim_data[molecule]['symbols'],
s22_sim_data[molecule]['positions']) for molecule in molecules
]
test_f.molecules = [
GPAWSystems(molecule,
atoms=atoms,
h=h,
vacuum=vacuum,
fragment_list=fragment_names(molecule))
for molecule, atoms in zip(molecules, sys)
]
atom_fragments_1 = [
system.system.copy()[fragment_n(system.name, 1)]
for system in test_f.molecules
]
atom_fragments_2 = [
system.system.copy()[fragment_n(system.name, 2)]
for system in test_f.molecules
]
test_f.fragments = [
GPAWSystems(name + '_f1', atoms=a, h=h, vacuum=vacuum)
for name, a in zip(molecules, atom_fragments_1)
]
test_f.fragments += [
GPAWSystems(name + '_f2', atoms=a, h=h, vacuum=vacuum)
for name, a in zip(molecules, atom_fragments_2)
]
test_f.fill_data_reference(data_type='s22')
if reload:
test_f.load_data('data.pkl')
test_f.calculate_error()
test_f.calculate_mae()
print test_f.mae
else:
test_f.run(write=True)
def main():
#TEST atomization
print "Test atomization"
molecule_names = ['CH4']
test = Fragmentation(molecule_names)
test.molecules = [GPAWSystems(name,h=0.3,vacuum=2.0,xc='PBE')
for name in molecule_names]
atom_names = []
for gs in test.molecules:
atom_names.extend(gs.system.get_chemical_symbols())
test.fragments = [GPAWSystems(name,h=0.3,vacuum=2.0,xc='PBE')
for name in set(atom_names)]
test.fill_data_reference(data_type='g22')
test.run()
error = 5.64039227514 - test.mae
print 'Test error: {0} eV'.format(error)
#TEST fragmentation
print "Test fragmentation with s22 set"
molecule = 'Ammonia_dimer'
fragment_names = [molecule+'_f1',molecule+'f2']
test_f = Fragmentation([molecule])
sys = Atoms(s22_sim_data[molecule]['symbols'],
s22_sim_data[molecule]['positions'])
test_f.molecules = [GPAWSystems(molecule,atoms=sys,
h=0.4, vacuum=2.0,
fragment_list=fragment_names)]
n = s22_sim_data[molecule]['dimer atoms']
atom_fragments = [ sys.copy()[range(n[0])], sys.copy()[range(n[0],n[0]+n[1])] ]
test_f.fragments = [ GPAWSystems(name,atoms=a,h=0.4, vacuum=2.0)
for name,a in zip(fragment_names,atom_fragments)]
test_f.fill_data_reference(data_type='s22')
test_f.run(write=True)
error = 266.704827694 - test_f.mae
print 'Test error: {0} eV'.format(error)