def mass_save(sims, cut, destination_dir, analysis_type='last'):
if not isgenerator(sims) or not isinstance(sims, list):
sims = [sims]
for sim in sims:
name = str(sim.atoms.id)
new_dir_path = os.path.join(destination_dir, str(sim.name))
if not os.path.exists(new_dir_path):
os.mkdir(os.path.join(destination_dir, sim.name))
d = sim_unpack(sim)
if analysis_type == 'min':
pel = []
for atoms in d['traj']:
if atoms._calc is not None:
pel.append(atoms.get_potential_energy())
index = int(np.argmin(pel))
print index
print pel[index]
elif analysis_type == 'last':
index = -1
save_config(new_dir_path, name, d, index)
plot_pdf(atoms=d['traj'][index], show=False,
save_file=os.path.join(new_dir_path, name), **d)
plot_angle(cut, show=False, save_file=os.path.join(new_dir_path, name),
index=index, **d)
plot_coordination(cut, show=False,
save_file=os.path.join(new_dir_path, name),
index=index, **d)
plot_radial_bond_length(cut, show=False,
save_file=os.path.join(new_dir_path, name),
index=index, **d)
def mass_save(sims, cut, destination_dir, analysis_type='last'):
if not isgenerator(sims) or not isinstance(sims, list):
sims = [sims]
for sim in sims:
name = str(sim.atoms.id)
new_dir_path = os.path.join(destination_dir, str(sim.name))
if not os.path.exists(new_dir_path):
os.mkdir(os.path.join(destination_dir, sim.name))
d = sim_unpack(sim)
if analysis_type == 'min':
pel = []
for atoms in d['traj']:
if atoms._calc is not None:
pel.append(atoms.get_potential_energy())
index = int(np.argmin(pel))
print index
print pel[index]
elif analysis_type == 'last':
index = -1
save_config(new_dir_path, name, d, index)
plot_pdf(atoms=d['traj'][index],
show=False,
save_file=os.path.join(new_dir_path, name),
**d)
plot_angle(cut,
show=False,
save_file=os.path.join(new_dir_path, name),
index=index,
**d)
plot_coordination(cut,
show=False,
save_file=os.path.join(new_dir_path, name),
index=index,
**d)
plot_radial_bond_length(cut,
show=False,
save_file=os.path.join(new_dir_path, name),
index=index,
**d)
def mass_plot(sims, cut, analysis_type='last'):
if not isgenerator(sims) and not isinstance(sims, list):
sims = [sims]
for sim in sims:
d = sim_unpack(sim)
if analysis_type == 'min':
pel = []
for atoms in d['traj']:
if atoms._calc is not None:
pel.append(atoms.get_potential_energy())
index = np.argmin(pel)
print index
print pel[index]
elif analysis_type == 'last':
index = -1
ase_view(**d)
plot_pdf(atoms=d['traj'][index], **d)
plot_angle(cut, index=index, **d)
plot_coordination(cut, index=index, **d)
plot_radial_bond_length(cut, index=index, **d)
def mass_plot(sims, cut, analysis_type='last'):
if not isgenerator(sims) and not isinstance(sims, list):
sims = [sims]
for sim in sims:
d = sim_unpack(sim)
if analysis_type == 'min':
pel = []
for atoms in d['traj']:
if atoms._calc is not None:
pel.append(atoms.get_potential_energy())
index = np.argmin(pel)
print index
print pel[index]
elif analysis_type == 'last':
index = -1
ase_view(**d)
plot_pdf(atoms=d['traj'][index], **d)
plot_angle(cut, index=index, **d)
plot_coordination(cut, index=index, **d)
plot_radial_bond_length(cut, index=index, **d)
