def compare_trajectory(self, i_traj, calc, tables, i_par):
"""
Calculate the energies for the frames in the trajectory
and plot them.
"""
frames = []
energies = []
trajectory = PickleTrajectory(self.trajectories[i_traj])
for i, image in enumerate(trajectory):
e_tb = None
try:
atoms = Atoms(image)
c = copy(calc)
c.tables = tables
atoms.set_calculator(c)
e_tb = atoms.get_potential_energy()
except Exception as ex:
print(ex, file=self.txt)
if e_tb != None:
energies.append(e_tb)
frames.append(i)
delta_E = self.norm_to_isolated_atoms(trajectory[0])
for i in range(len(energies)):
energies[i] += delta_E
self.plot(frames, energies, i_traj, tables, i_par)
def compare_trajectory(self, i_traj, calc, tables, i_par):
"""
Calculate the energies for the frames in the trajectory
and plot them.
"""
frames = []
energies = []
trajectory = PickleTrajectory(self.trajectories[i_traj])
for i, image in enumerate(trajectory):
e_tb = None
try:
atoms = Atoms(image)
c = copy(calc)
c.tables = tables
atoms.set_calculator(c)
e_tb = atoms.get_potential_energy()
except Exception, ex:
print>>self.txt, ex
if e_tb != None:
energies.append(e_tb)
frames.append(i)
def compare_trajectory(self, i_traj, calc, tables, i_par):
"""
Calculate the energies for the frames in the trajectory
and plot them.
"""
frames = []
energies = []
trajectory = PickleTrajectory(self.trajectories[i_traj])
for i, image in enumerate(trajectory):
e_tb = None
try:
atoms = Atoms(image)
c = copy(calc)
c.tables = tables
atoms.set_calculator(c)
e_tb = atoms.get_potential_energy()
except Exception, ex:
print >> self.txt, ex
if e_tb != None:
energies.append(e_tb)
frames.append(i)
def get_isolated_energies(self, trajs, par):
"""
Return the energies of an isolated atoms.
"""
elements = []
energies = {}
for t in trajs:
traj = PickleTrajectory(t)
for atom in traj[0]:
if not atom.symbol in elements:
elements.append(atom.symbol)
el1, el2 = par.split("_")[0:2]
for el in elements:
ss = "%s%s" % (el, el)
if el1 == el2 and el1 == el:
tables = {ss:par, 'rest':'default'}
calc = Hotbit(SCC=True, tables=tables)
else:
calc = Hotbit(SCC=True)
atoms = Atoms(ss, ((0,0,0),(200,0,0)))
atoms.center(vacuum=100)
atoms.set_calculator(calc)
energies[el] = atoms.get_potential_energy() / 2
return energies
def get_isolated_energies(self, trajs, par):
"""
Return the energies of an isolated atoms.
"""
elements = []
energies = {}
for t in trajs:
traj = PickleTrajectory(t)
for atom in traj[0]:
if not atom.symbol in elements:
elements.append(atom.symbol)
el1, el2 = par.split("_")[0:2]
for el in elements:
ss = "%s%s" % (el, el)
if el1 == el2 and el1 == el:
tables = {ss:par, 'rest':'default'}
calc = Hotbit(SCC=True, tables=tables)
else:
calc = Hotbit(SCC=True)
atoms = Atoms(ss, ((0,0,0),(200,0,0)))
atoms.center(vacuum=100)
atoms.set_calculator(calc)
energies[el] = atoms.get_potential_energy() / 2
return energies
