def quench(atoms,name=None,fmax=0.05,method='QN'):
""" Quench given Atoms object with given attached calculator. """
if name==None:
try:
name=atoms.get_chemical_formula(mode="hill")
except:
raise ValueError('name not specified')
traj=ase.PickleTrajectory(name+'_quenching.trj','w',atoms)
if method=='QN':
qn=ase.QuasiNewton(atoms)
elif method=='FIRE':
qn=ase.FIRE(atoms)
qn.attach(traj.write)
qn.run(fmax=fmax)
e=atoms.get_potential_energy()
ase.write(name+'_quenched.xyz',atoms)
return e
def quench(atoms, name=None, fmax=0.05, method='QN'):
""" Quench given Atoms object with given attached calculator. """
if name == None:
try:
name = atoms.get_chemical_formula(mode="hill")
except:
raise ValueError('name not specified')
traj = ase.Trajectory(name + '_quenching.trj', 'w', atoms)
if method == 'QN':
qn = ase.QuasiNewton(atoms)
elif method == 'FIRE':
qn = ase.FIRE(atoms)
qn.attach(traj.write)
qn.run(fmax=fmax)
e = atoms.get_potential_energy()
ase.write(name + '_quenched.xyz', atoms)
return e
def __init__(self, atoms):
'''
'''
self.atoms = atoms
#get density and write cube file
calc = atoms.get_calculator()
ncfile = calc.get_nc()
base, ext = os.path.splitext(ncfile)
x, y, z, density = calc.get_charge_density()
cubefile = base + '_charge_density.cube'
self.densityfile = cubefile
if not os.path.exists(cubefile):
write(cubefile, atoms, data=density * Bohr**3)
#cmd to run for bader analysis. check if output exists so we
#don't run this too often.
acf_file = base + '_ACF.dat'
if not os.path.exists(acf_file):
#mk tempdir
tempdir = tempfile.mkdtemp()
cwd = os.getcwd()
os.chdir(tempdir)
cmd = 'bader %s' % abscubefile
status, output = commands.getstatusoutput(cmd)
if status != 0:
print output
shutil.copy2('ACF.dat', os.path.join(cwd, acf_file))
os.chdir(cwd)
shutil.rmtree(tempdir)
self.charges = []
self.volumes = []
#now parse the output
f = open(acf_file, 'r')
#skip 2 lines
f.readline()
f.readline()
for i, atom in enumerate(self.atoms):
line = f.readline()
fields = line.split()
n = int(fields[0])
x = float(fields[1])
y = float(fields[2])
z = float(fields[3])
chg = float(fields[4])
mindist = float(fields[5])
vol = float(fields[6])
self.charges.append(chg)
self.volumes.append(vol)
f.close()
c = Hotbit(elements={
'H': dir2 + 'H-H.skf',
'C': dir2 + 'C-C.skf'
},
tables={
'HH': dir2 + 'H-H.skf',
'CH': dir2 + 'C-H.skf',
'CC': dir2 + 'C-C.skf'
},
SCC=False)
a.set_calculator(c)
ase.FIRE(a).run(fmax=0.01)
ase.write('C6H6.cfg', a)
###
for i in c.el.get_present():
el = c.el.get_element(i)
sym = el.get_symbol()
orbs = el.get_valence_orbitals()
for orb in orbs:
print sym, orb, el.get_epsilon(orb), el.get_epsilon(orb) * Hartree
x = np.linspace(1.0, 12.0, 1000)
y, dy = c.ia.h['CC'](x)
d = np.transpose(np.append(x.reshape(1, -1), y, axis=0))
np.savetxt('CC_H.out', d)
elements = {
'H': dir2 + 'H-H.skf',
'C': dir2 + 'C-C.skf'
},
tables = {
'HH': dir2 + 'H-H.skf',
'CH': dir2 + 'C-H.skf',
'CC': dir2 + 'C-C.skf'
},
SCC = False
)
a.set_calculator(c)
ase.FIRE(a).run(fmax=0.01)
ase.write('C6H6.cfg', a)
###
for i in c.el.get_present():
el = c.el.get_element(i)
sym = el.get_symbol()
orbs = el.get_valence_orbitals()
for orb in orbs:
print sym, orb, el.get_epsilon(orb), el.get_epsilon(orb)*Hartree
x = np.linspace(1.0, 12.0, 1000)
y, dy = c.ia.h['CC'](x)
d = np.transpose(np.append(x.reshape(1, -1), y, axis=0))
np.savetxt('CC_H.out', d)
def __init__(self, atoms):
"""
"""
self.atoms = atoms
# get density and write cube file
calc = atoms.get_calculator()
ncfile = calc.get_nc()
base, ext = os.path.splitext(ncfile)
x, y, z, density = calc.get_charge_density()
cubefile = base + "_charge_density.cube"
self.densityfile = cubefile
if not os.path.exists(cubefile):
write(cubefile, atoms, data=density * Bohr ** 3)
# cmd to run for bader analysis. check if output exists so we
# don't run this too often.
acf_file = base + "_ACF.dat"
if not os.path.exists(acf_file):
# mk tempdir
tempdir = tempfile.mkdtemp()
cwd = os.getcwd()
os.chdir(tempdir)
cmd = "bader %s" % abscubefile
status, output = commands.getstatusoutput(cmd)
if status != 0:
print output
shutil.copy2("ACF.dat", os.path.join(cwd, acf_file))
os.chdir(cwd)
shutil.rmtree(tempdir)
self.charges = []
self.volumes = []
# now parse the output
f = open(acf_file, "r")
# skip 2 lines
f.readline()
f.readline()
for i, atom in enumerate(self.atoms):
line = f.readline()
fields = line.split()
n = int(fields[0])
x = float(fields[1])
y = float(fields[2])
z = float(fields[3])
chg = float(fields[4])
mindist = float(fields[5])
vol = float(fields[6])
self.charges.append(chg)
self.volumes.append(vol)
f.close()