def retrieve(self, formula, filename):
system = read(filename)
energy = system.get_potential_energy()
return energy
def retrieve(self, formula, filename):
system = read(filename)
energy = system.get_potential_energy()
return energy
from sgt import ElaSticDistortion, loadObject
from ase.calculators import Exciting
from ase import read
exciting = Exciting(bin='/fshome/chm/git/exciting/bin/excitingser',
kpts=(4, 4, 4),
xctype='GGArevPBE')
atoms = read('AlBulk.xml', format='exi')
#print atoms.get_cell()
distortions = ElaSticDistortion(structure=atoms,
calculator=exciting,
order=2,
maxstrain=0.02,
distortions=11)
#distortions.print_distortions()
distortions.calculate()
distortions.save("distwenergy")
print "--- no SCC ---"
calc = Hotbit(
charge_density = 'Slater',
SCC = SCC,
verbose = True,
verbose_SCC = True,
mixer = {
'name': 'anderson',
'convergence': 1e-6,
'mixing_constant': 0.01 },
maxiter = 1000,
txt = 'mio.out',
**params)
a = read('formamide.xyz')
a.center(vacuum=10.0)
a.set_pbc(False)
a.set_calculator(calc)
OPT(a, logfile='opt.log').run(fmax=FMAX)
iO = 0
iC = 1
iN = 2
iHC = 3
iHN = 4
assert a[iO].get_symbol() == 'O'
assert a[iC].get_symbol() == 'C'
assert a[iN].get_symbol() == 'N'
def transition_barrier(calc,quench,guess,cell=None,pbc=None,constraints=None,\
M=None,name=None,fmax=0.05,steps=1000000):
import ase
method=ase.NEB
if type(guess)!=type([]) and type(guess)!=type(''):
# all Atoms properties should be set for Atoms-type guess
images=guess
path=method(images)
else:
if type(guess)==type(''):
assert guess.split('.')[-1]=='trj' and M==None
# for some reason copying has to be done...
images=[]
for image in ase.PickleTrajectory(guess):
images.append(image.copy())
path=method(images)
else:
assert type(guess)==type([]) and M!=None
images=[]
first=ase.read(guess[0])
images.append(first)
for i in range(M-2):
images.append(first.copy())
last=ase.read(guess[1])
images.append(last)
path=method(images)
path.interpolate()
# now coordinates are set; set other properties
assert cell!=None and pbc!=None
for image in images:
image.set_pbc(pbc)
image.set_cell(cell,fix=True)
if constraints!=None:
image.set_constraint(constraints)
# attach calculators
if type(calc)==type([]):
for image,clc in zip(images,calc):
image.set_calculator(clc)
else:
for image in images:
image.set_calculator(calc.copy())
for image in images:
image.center()
if quench:
e1=quench_atoms(images[0],'initial')
print 'First image quenched. Energy=',e1
eM=quench_atoms(images[-1],'final')
print 'Last image quenched. Energy=',eM
# solve the transition path
writer=TrajectoryWriter(images)
minimizer=ase.QuasiNewton(path)
minimizer.attach(writer)
minimizer.run(fmax=fmax,steps=steps)
# output of the final path
traj = ase.PickleTrajectory('%s_converged.trj' %name, 'w')
path.write(traj)
return images
def transition_barrier(calc,quench,guess,cell=None,pbc=None,constraints=None,\
M=None,name=None,fmax=0.05,steps=1000000):
import ase
method = ase.NEB
if type(guess) != type([]) and type(guess) != type(''):
# all Atoms properties should be set for Atoms-type guess
images = guess
path = method(images)
else:
if type(guess) == type(''):
assert guess.split('.')[-1] == 'trj' and M == None
# for some reason copying has to be done...
images = []
for image in ase.Trajectory(guess):
images.append(image.copy())
path = method(images)
else:
assert type(guess) == type([]) and M != None
images = []
first = ase.read(guess[0])
images.append(first)
for i in range(M - 2):
images.append(first.copy())
last = ase.read(guess[1])
images.append(last)
path = method(images)
path.interpolate()
# now coordinates are set; set other properties
assert cell != None and pbc != None
for image in images:
image.set_pbc(pbc)
image.set_cell(cell, fix=True)
if constraints != None:
image.set_constraint(constraints)
# attach calculators
if type(calc) == type([]):
for image, clc in zip(images, calc):
image.set_calculator(clc)
else:
for image in images:
image.set_calculator(calc.copy())
for image in images:
image.center()
if quench:
e1 = quench_atoms(images[0], 'initial')
print('First image quenched. Energy=', e1)
eM = quench_atoms(images[-1], 'final')
print('Last image quenched. Energy=', eM)
# solve the transition path
writer = TrajectoryWriter(images)
minimizer = ase.QuasiNewton(path)
minimizer.attach(writer)
minimizer.run(fmax=fmax, steps=steps)
# output of the final path
traj = ase.Trajectory('%s_converged.trj' % name, 'w')
path.write(traj)
return images
import os
import ase
from dftd_interface import d3_pbc as dftd3
from dftd_interface import d2_pbc as dftd2
import numpy
print 'single cell'
system = ase.read('./test/POSCAR5', format='vasp')
c, d = dftd3(system ,'pbe')
print repr(c)
print d
print 'mupltiple cell'
system = ase.read('./test/POSCAR6', format='vasp')
c, d = dftd3(system ,'pbe')
print repr(c)
print d
print 'reference'
os.system('./test/dftd3 ./test/POSCAR5.xyz -func pbe -noprint -grad')
from sgt import ElaSticDistortion,loadObject
from ase.calculators import Exciting
from ase import read
exciting=Exciting(bin='/fshome/chm/git/exciting/bin/excitingser', kpts=(4, 4, 4), xctype='GGArevPBE')
atoms=read('AlBulk.xml',format='exi')
#print atoms.get_cell()
distortions=ElaSticDistortion(structure=atoms,
calculator=exciting,
order=2,
maxstrain=0.02,
distortions=11)
#distortions.print_distortions()
distortions.calculate()
distortions.save("distwenergy")