def __call__(self):
""" Writes trajectory file for current atoms list. """
from ase import PickleTrajectory
traj = PickleTrajectory('%s_it%i.trj' %(self.name,self.i), 'w')
for image in self.images:
traj.write(image)
self.i+=1
class ExtendedTrajectory:
def __init__(self,filename,atoms,n,mode='w',fixrcm=False):
"""
Trajectory for multiple copies of unit cell.
parameters:
===========
filename: output .traj -file
atoms: hotbit.Atoms object
n: tuple of number of symmetry operations
or list of tuples for the symmetry operations
mode: 'w' write or 'a' append
fixrcm: Write trajectory with center of mass fixed at origin.
"""
self.atoms = atoms
self.n = n
self.ext = self.atoms.extended_copy(n)
self.traj = PickleTrajectory(filename,mode,self.ext) #,properties=['energy'])
self.fixrcm = fixrcm
def set_atoms(self,atoms):
self.atoms = atoms
self.ext = self.atoms.extended_copy(self.n)
self.traj.set_atoms(self.ext)
def write(self):
cp = self.atoms.extended_copy(self.n)
if self.fixrcm:
cp.translate( -cp.get_center_of_mass() )
self.ext.set_positions( cp.get_positions() )
self.traj.write()
class ExtendedTrajectory:
def __init__(self,filename,atoms,n,mode='w',fixrcm=False):
"""
Trajectory for multiple copies of unit cell.
parameters:
===========
filename: output .traj -file
atoms: hotbit.Atoms object
n: tuple of number of symmetry operations
or list of tuples for the symmetry operations
mode: 'w' write or 'a' append
fixrcm: Write trajectory with center of mass fixed at origin.
"""
self.atoms = atoms
self.n = n
self.ext = self.atoms.extended_copy(n)
self.traj = PickleTrajectory(filename,mode,self.ext) #,properties=['energy'])
self.fixrcm = fixrcm
def set_atoms(self,atoms):
self.atoms = atoms
self.ext = self.atoms.extended_copy(self.n)
self.traj.set_atoms(self.ext)
def write(self):
cp = self.atoms.extended_copy(self.n)
if self.fixrcm:
cp.translate( -cp.get_center_of_mass() )
self.ext.set_positions( cp.get_positions() )
self.traj.write()
def __call__(self):
""" Writes trajectory file for current atoms list. """
from ase import PickleTrajectory
traj = PickleTrajectory('%s_it%i.trj' % (self.name, self.i), 'w')
for image in self.images:
traj.write(image)
self.i += 1
def trajToExtTraj(traj, n, *args):
R, T, angle1, angle2, n1, n2, path = args
path_traj = path + 'sphere/md_data/T=%.0f/' %T
checkAndCreateFolder(path_traj)
traj_ext = PickleTrajectory(path_traj + 'md_Ext_R%.3f.traj' %R, 'w')
for a in traj:
c_symb = a.get_chemical_symbols()
posits = a.positions
atoms = Atoms(c_symb, positions = posits, container='Sphere')
atoms.set_container(angle1=angle1,angle2=angle2,n1=n1,n2=n2,mode=4)
traj_ext.write(atoms.extended_copy(n))
def trajToExtTraj(traj, n, *args):
R, T, angle, H, path = args
path_traj = path + 'cylinder/md_data/T=%.0f/' %T
checkAndCreateFolder(path_traj)
traj_ext = PickleTrajectory(path_traj + 'md_Ext_R%.3f.traj' %R,'w')
for a in traj:
c_symb = a.get_chemical_symbols()
posits = a.positions
atoms = Atoms(c_symb, positions = posits, container='Wedge')
atoms.set_container(angle=angle, height=H, physical=False, pbcz=True)
traj_ext.write(atoms.extended_copy(n))
class ExtendedTrajectory:
def __init__(self,filename,atoms,n,mode='w'):
"""
Trajectory for multiple copies of unit cell.
parameters:
===========
filename: output .traj -file
atoms: hotbit.Atoms object
n: tuple of number of symmetry operations
or list of tuples for the symmetry operations
mode: 'w' write or 'a' append
"""
self.atoms = atoms
self.n = n
self.ext = self.atoms.extended_copy(n)
self.traj = PickleTrajectory(filename,mode,self.ext)
def write(self):
cp = self.atoms.extended_copy(self.n)
self.ext.set_positions( cp.get_positions() )
self.traj.write()
import os
from ase import Atom, Atoms
from ase.io import PickleTrajectory
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = PickleTrajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
del traj
traj = PickleTrajectory('1.traj', 'a')
co = traj[-1]
print co.positions
co.positions[:] += 1
traj.write(co)
del traj
t = PickleTrajectory('1.traj', 'a')
print t[-1].positions
print '.--------'
for a in t:
print 1, a.positions[-1,2]
co.positions[:] += 1
t.write(co)
for a in t:
print 2, a.positions[-1,2]
assert len(t) == 7
co[0].number = 1
try:
t.write(co)
return int(self.value - other.value)
if __name__ == '__main__':
import info # import ourselves to make info.Foo reachable
# Create a molecule with an info attribute
info = dict(
creation_date='2011-06-27',
chemical_name='Hydrogen',
# custom classes also works provided that it is
# imported and pickleable...
foo=info.Foo(7),
)
molecule = Atoms('H2', positions=[(0., 0., 0.), (0., 0., 1.1)], info=info)
assert molecule.info == info
# Copy molecule
atoms = molecule.copy()
assert atoms.info == info
# Save molecule to trajectory
traj = PickleTrajectory('info.traj', 'w', atoms=molecule)
traj.write()
del traj
# Load molecule from trajectory
t = PickleTrajectory('info.traj')
atoms = t[-1]
assert atoms.info == info
import numpy as np
from ase.io import read, PickleTrajectory
from ase.lattice import bulk
from ase.calculators.emt import EMT
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print '%.4f %.3f' % (a0, c0 / a0)
for i in range(3):
traj = PickleTrajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 4):
for c in c0 * np.linspace(1 - eps, 1 + eps, 4):
ni = bulk('Ni', 'hcp', a=a, covera=c / a)
ni.set_calculator(EMT())
ni.get_potential_energy()
traj.write(ni)
configs = read('Ni.traj@:')
energies = [config.get_potential_energy() for config in configs]
ac = [(config.cell[0, 0], config.cell[2, 2]) for config in configs]
from ase.optimize import polyfit
p = polyfit(ac, energies)
from scipy.optimize import fmin_bfgs
a0, c0 = fmin_bfgs(p, (a0, c0))
print '%.4f %.3f' % (a0, c0 / a0)
assert abs(a0 - 2.466) < 0.001
assert abs(c0 / a0 - 1.632) < 0.005
import numpy as np
from ase.lattice import bulk
from ase.optimize import BFGS
from ase.io import PickleTrajectory
from ase.constraints import StrainFilter
from gpaw import GPAW, PW
co = bulk('Co')
co.set_initial_magnetic_moments([1.6, 1.6])
co.calc = GPAW(mode=PW(700),
xc='PBE',
kpts=(8, 8, 4),
txt='co.txt')
BFGS(StrainFilter(co)).run(0.005)
a0 = co.cell[0, 0]
c0 = co.cell[2, 2]
traj = PickleTrajectory('co.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 3):
for c in c0 * np.linspace(1 - eps, 1 + eps, 3):
co.set_cell(bulk('Co', a=a, covera=c / a).cell, scale_atoms=True)
co.get_potential_energy()
traj.write(co)
return int(self.value - other.value)
if __name__ == '__main__':
import info # import ourselves to make info.Foo reachable
# Create a molecule with an info attribute
info = dict(creation_date='2011-06-27',
chemical_name='Hydrogen',
# custom classes also works provided that it is
# imported and pickleable...
foo=info.Foo(7),
)
molecule = Atoms('H2', positions=[(0., 0., 0.), (0., 0., 1.1)], info=info)
assert molecule.info == info
# Copy molecule
atoms = molecule.copy()
assert atoms.info == info
# Save molecule to trajectory
traj = PickleTrajectory('info.traj', 'w', atoms=molecule)
traj.write()
del traj
# Load molecule from trajectory
t = PickleTrajectory('info.traj')
atoms = t[-1]
assert atoms.info == info
import numpy as np
from ase.lattice import bulk
from ase.optimize import BFGS
from ase.io import PickleTrajectory
from ase.constraints import StrainFilter
from gpaw import GPAW, PW
co = bulk("Co")
co.set_initial_magnetic_moments([1.6, 1.6])
co.calc = GPAW(mode=PW(700), xc="PBE", kpts=(8, 8, 4), txt="co.txt")
BFGS(StrainFilter(co)).run(0.005)
a0 = co.cell[0, 0]
c0 = co.cell[2, 2]
traj = PickleTrajectory("co.traj", "w")
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 3):
for c in c0 * np.linspace(1 - eps, 1 + eps, 3):
co.set_cell(bulk("Co", a=a, covera=c / a).cell, scale_atoms=True)
co.get_potential_energy()
traj.write(co)
from ase.test import NotAvailable
if sys.platform in ['win32']:
raise NotAvailable('Fails on Windows https://trac.fysik.dtu.dk/projects/ase/ticket/62')
import os
from ase import Atom, Atoms
from ase.io import PickleTrajectory
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = PickleTrajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
del traj
traj = PickleTrajectory('1.traj', 'a')
co = traj[-1]
print co.positions
co.positions[:] += 1
traj.write(co)
del traj
t = PickleTrajectory('1.traj', 'a')
print t[-1].positions
print '.--------'
for a in t:
print 1, a.positions[-1,2]
co.positions[:] += 1
t.write(co)
for a in t:
atoms.get_charges = calc.notimpl
# get total energy at first ionic step
en = get_total_energy(s)
if en is not None:
calc.set_energy(en)
else:
print >>stderr, 'no total energy found'
exit(3)
print(atoms)
traj = PickleTrajectory(argv[2], 'w')
traj.write(atoms)
a = s.readline()
while a != '':
while a[:7] != 'CELL_PA' and a[:7] != 'ATOMIC_' and a != '':
a = s.readline()
if a == '':
break
if a[0] == 'A':
coord = a.split('(')[-1]
for i in range(natoms):
pos[i][:] = s.readline().split()[1:4]
if coord == 'alat)':
atoms.set_positions(pos * alat)
elif coord == 'bohr)':
import numpy as np
from ase import Atoms
from ase.calculators.emt import EMT
from ase.io import PickleTrajectory
Cu = Atoms('Cu', pbc=(1, 0, 0), calculator=EMT())
traj = PickleTrajectory('Cu.traj', 'w')
for a in np.linspace(2.0, 4.0, 20):
Cu.set_cell([a, 1, 1], scale_atoms=True)
traj.write(Cu)
