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 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)
