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 retrieve(self, formula, filename):
traj = PickleTrajectory(filename, 'r')
distances = np.array(
[np.linalg.norm(a.positions[1] - a.positions[0]) for a in traj])
energies = np.array([a.get_potential_energy() for a in traj])
polynomial = np.polyfit(distances, energies, 2) # or maybe 3rd order?
# With 3rd order it is not always obvious which root is right
pderiv = np.polyder(polynomial, 1)
d0 = np.roots(pderiv)
e0 = np.polyval(energies, d0)
return distances, energies, d0, e0, polynomial
def read(self, filename, filetype=None):
"""Read from a file"""
ftfe = filetype_from_ending(filename)
aft = ase_filetype(filename)
if ftfe == 'vmol':
self.read_viewmol(filename)
elif aft == 'traj':
PickleTrajectory.__init__(self, filename)
elif aft == 'gpaw-text':
# this is strange code, but I don't know how to create the full
# slice XXXXX
last = read_gpaw_text(filename)
self.__init__(atoms=last)
s = slice(-1)
rest = read_gpaw_text(filename, s)
rest.append(last)
self.append(rest)
else:
raise NotImplementedError('unknown file type "' + aft + '"')
def read(self, filename, filetype=None):
"""Read from a file"""
ftfe = filetype_from_ending(filename)
aft = ase_filetype(filename)
if ftfe == 'vmol':
self.read_viewmol(filename)
elif aft == 'traj':
PickleTrajectory.__init__(self, filename)
elif aft == 'gpaw-text':
# this is strange code, but I don't know how to create the full
# slice XXXXX
last = read_gpaw_text(filename)
self.__init__(atoms=last)
s = slice(-1)
rest = read_gpaw_text(filename, s)
rest.append(last)
self.append(rest)
else:
raise NotImplementedError('unknown file type "'+ aft +'"')
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 __iter__(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.__iter__(self)
else:
return self.images.__iter__()
def __getitem__(self, i=-1):
if hasattr(self, 'offsets'):
return PickleTrajectory.__getitem__(self, i)
else:
return self.images[i]
def __len__(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.__len__(self)
else:
return len(self.images)
def next(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.next(self)
else:
return self.images.next()
def __iter__(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.__iter__(self)
else:
return self.images.__iter__()
def __getitem__(self, i=-1):
if hasattr(self, 'offsets'):
return PickleTrajectory.__getitem__(self, i)
else:
return self.images[i]
def __len__(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.__len__(self)
else:
return len(self.images)
def next(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.next(self)
else:
return self.images.next()
import os
import sys
from ase import Atoms, Atom, QuasiNewton, PickleTrajectory
from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol
s = Cluster([Atom('H'), Atom('H', (0, 0, 3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)
vfname = 'traj.vmol'
pfname = 'traj.pickle'
vmt = ViewmolTrajectory(s, vfname)
traj = PickleTrajectory(pfname, 'w', s)
#c.attach(vmt.add, 100000)
#sys.exit()
# Find the theoretical bond length:
dyn = QuasiNewton(s)
dyn.attach(traj.write)
dyn.attach(vmt.add)
dyn.run(fmax=0.05)
traj = PickleTrajectory(pfname, 'r')
vfname2 = 'pickle.vmol'
write_viewmol(traj, vfname2)
def __next__(self):
if hasattr(self, 'offsets'):
return PickleTrajectory.next(self)
else:
return next(self.images)