def test_strain():
from math import sqrt
from ase import Atoms
from ase.constraints import StrainFilter
from ase.optimize.mdmin import MDMin
from ase.io import Trajectory
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0,b,b),(b,0,b),(b,b,0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.001)
# HCP:
from ase.build import bulk
cu = bulk('Cu', 'hcp', a=a / sqrt(2))
cu.cell[1,0] -= 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.01)
def test_strain_fcc(asap3):
cu = bulk('Cu', a=a) * (6, 6, 6)
cu.calc = asap3.EMT()
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.001)
def test_strain_hcp(asap3):
cu = bulk('Cu', 'hcp', a=a / sqrt(2))
cu.cell[1, 0] -= 0.05
cu *= (6, 6, 3)
cu.calc = asap3.EMT()
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
opt.run(0.01)
def test_strain_hcp(asap3):
cu = bulk('Cu', 'hcp', a=a / sqrt(2))
cu.cell[1, 0] -= 0.05
cu *= (6, 6, 3)
cu.calc = asap3.EMT()
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.01)
def test_strain_emt():
"""This test checks that the StrainFilter works using the default
built-in EMT calculator."""
import numpy as np
from ase.constraints import StrainFilter
from ase.optimize.mdmin import MDMin
from ase.calculators.emt import EMT
from ase.build import bulk
cu = bulk('Cu', 'fcc', a=3.6)
class EMTPlus(EMT):
def get_stress(self, atoms):
return np.zeros(6)
cu.calc = EMTPlus()
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
opt.run(0.1, steps=2)
def test_vacancy():
from ase import Atoms
from ase.optimize import QuasiNewton
from ase.neb import NEB
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0),
(0, b, b),
(b, 0, b),
(b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [initial] + [initial.copy() for i in range(6)]
images[-1].positions[0] = (0, 0, 0)
for image in images:
image.calc = EMT()
#image.calc = ASAP()
for image in [images[0], images[-1]]:
QuasiNewton(image).run(fmax=0.01)
neb = NEB(images)
neb.interpolate()
for a in images:
print(a.positions[0], a.get_potential_energy())
dyn = MDMin(neb, dt=0.1, trajectory='mep1.traj')
#dyn = QuasiNewton(neb)
print(dyn.run(fmax=0.01, steps=25))
for a in images:
print(a.positions[0], a.get_potential_energy())
"""This test checks that the StrainFilter works using the default
built-in EMT calculator."""
import numpy as np
from ase.constraints import StrainFilter
from ase.optimize.mdmin import MDMin
from ase.calculators.emt import EMT
from ase.structure import bulk
cu = bulk('Cu', 'fcc', a=3.6)
class EMTPlus(EMT):
def get_stress(self, atoms):
return np.zeros(6)
cu.set_calculator(EMTPlus())
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
opt.run(0.1, steps=2)
"""This test checks that the StrainFilter works using the default
built-in EMT calculator."""
from ase.constraints import StrainFilter
from ase.optimize.mdmin import MDMin
from ase.calculators.emt import EMT
from ase.structure import bulk
cu = bulk('Cu', 'fcc', a=3.6)
cu.set_calculator(EMT(fakestress=True))
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
opt.run(0.1, steps=2)
from ase.io import PickleTrajectory
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0,b,b),(b,0,b),(b,b,0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
t = PickleTrajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.001)
# HCP:
from ase.lattice.surface import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1,0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
t = PickleTrajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.01)
from ase.optimize.mdmin import MDMin
from ase.io import PickleTrajectory
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
t = PickleTrajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.001)
# HCP:
from ase.lattice.surface import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
t = PickleTrajectory('Cu.traj', 'w', cu)
opt.attach(t)
opt.run(0.01)
def test_strain_emt():
cu = bulk('Cu', 'fcc', a=3.6)
cu.calc = EMT()
f = StrainFilter(cu)
opt = MDMin(f, dt=0.01)
opt.run(0.1, steps=2)
pass
else:
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0), (0, b, b), (b, 0, b), (b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [initial] + [initial.copy() for i in range(6)]
images[-1].positions[0] = (0, 0, 0)
for image in images:
image.set_calculator(EMT())
#image.set_calculator(ASAP())
for image in [images[0], images[-1]]:
QuasiNewton(image).run(fmax=0.01)
neb = NEB(images)
neb.interpolate()
for a in images:
print a.positions[0], a.get_potential_energy()
dyn = MDMin(neb, dt=0.1, trajectory='mep1.traj')
#dyn = QuasiNewton(neb)
print dyn.run(fmax=0.01, steps=25)
for a in images:
print a.positions[0], a.get_potential_energy()
def test_strain_fcc(asap3):
cu = bulk('Cu', a=a) * (6, 6, 6)
cu.calc = asap3.EMT()
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
opt.run(0.001)
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0),
(0, b, b),
(b, 0, b),
(b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [initial] + [initial.copy() for i in range(6)]
images[-1].positions[0] = (0, 0, 0)
for image in images:
image.set_calculator(EMT())
#image.set_calculator(ASAP())
for image in [images[0], images[-1]]:
QuasiNewton(image).run(fmax=0.01)
neb = NEB(images)
neb.interpolate()
for a in images:
print a.positions[0], a.get_potential_energy()
dyn = MDMin(neb, dt=0.1, trajectory='mep1.traj')
#dyn = QuasiNewton(neb)
print dyn.run(fmax=0.01, steps=25)
for a in images:
print a.positions[0], a.get_potential_energy()
## atoms
atoms = read('POSCAR_1_Kooi')
## calc
calc = LAMMPS(
specorder=['Ge', 'Sb', 'Te'],
parameters={
'units': 'metal',
'boundary': 'p p p',
'box': 'tilt large',
'pair_style': 'deepmd frozen_model.pb',
'pair_coeff': ' ',
'mass': ['1 72.64', '2 121.76', '3 127.60'],
},
files=['frozen_model.pb'],
# keep_tmp_files=True,
)
atoms.set_calculator(calc)
## rlx
# from ase.optimize.bfgslinesearch import BFGSLineSearch as BFGSL
# from ase.optimize.gpmin.gpmin import GPMin
from ase.optimize.mdmin import MDMin
dyn = MDMin(
atoms=atoms,
trajectory='rlx-tmp.traj',
# force_consistent=False,
dt=0.1,
)
dyn.run(fmax=1e-2)
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0),
(0, b, b),
(b, 0, b),
(b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [initial] + [initial.copy() for i in range(6)]
images[-1].positions[0] = (0, 0, 0)
for image in images:
image.set_calculator(EMT())
#image.set_calculator(ASAP())
for image in [images[0], images[-1]]:
QuasiNewton(image).run(fmax=0.01)
neb = NEB(images)
neb.interpolate()
for a in images:
print(a.positions[0], a.get_potential_energy())
dyn = MDMin(neb, dt=0.1, trajectory='mep1.traj')
#dyn = QuasiNewton(neb)
print(dyn.run(fmax=0.01, steps=25))
for a in images:
print(a.positions[0], a.get_potential_energy())