def run(self, formula, system, filename):
"""Calculate energy of specified system and save to file."""
system.get_potential_energy()
# Won't create .bak file:
traj = PickleTrajectory(open(filename, 'w'), 'w')
traj.write(system)
traj.close()
def run(self, formula, system, filename):
"""Calculate energy of specified system and save to file."""
system.get_potential_energy()
# Won't create .bak file:
traj = PickleTrajectory(open(filename, 'w'), 'w')
traj.write(system)
traj.close()
def run(self, formula, system, filename):
"""Calculate bond length of a dimer.
This will calculate total energies for varying atomic
separations close to the g2 bond length, allowing
determination of bond length by fitting.
"""
if len(system) != 2:
raise ValueError('Not a dimer')
traj = PickleTrajectory(open(filename, 'w'), 'w')
pos = system.positions
d = np.linalg.norm(pos[1] - pos[0])
for x in range(-2, 3):
system.set_distance(0, 1, d * (1.0 + x * 0.02))
traj.write(system)
traj.close()
def run(self, formula, system, filename):
"""Calculate bond length of a dimer.
This will calculate total energies for varying atomic
separations close to the g2 bond length, allowing
determination of bond length by fitting.
"""
if len(system) != 2:
raise ValueError('Not a dimer')
traj = PickleTrajectory(open(filename, 'w'), 'w')
pos = system.positions
d = np.linalg.norm(pos[1] - pos[0])
for x in range(-2, 3):
system.set_distance(0, 1, d * (1.0 + x * 0.02))
traj.write(system)
traj.close()
