import ase.units as units
from numpy import array, linspace
import matplotlib.pyplot as plt
import numpy
# Create the MgO crystal
a = 4.194
cryst = Crystal(
crystal(['Mg', 'O'], [(0, 0, 0), (0.5, 0.5, 0.5)],
spacegroup=225,
cellpar=[a, a, a, 90, 90, 90]))
# Create the calculator running on one, eight-core node.
# This is specific to the setup on my cluster.
# You have to adapt this part to your environment
calc = ClusterVasp(nodes=1, ppn=8)
# Assign the calculator to the crystal
cryst.set_calculator(calc)
# Set the calculation parameters
calc.set(prec='Accurate',
xc='PBE',
lreal=False,
nsw=30,
ediff=1e-8,
ibrion=2,
kpts=[3, 3, 3])
# Set the calculation mode first.
# Full structure optimization in this case.
def secban(msg):
print()
print(max(0,(60-len(msg))//2-1)*' ',msg)
print(60*'-')
banner('Structure optimization on MgO')
a = 4.291
MgO = crystal(['Mg', 'O'], [(0, 0, 0), (0.5, 0.5, 0.5)], spacegroup=225,
cellpar=[a, a, a, 90, 90, 90])
##################################
# Provide your own calculator here
##################################
calc=ClusterVasp(nodes=1,ppn=8)
# The calculator must be runnable in an isolated directory
# Without disturbing other running instances of the same calculator
# They are run in separate processes (not threads!)
MgO.set_calculator(calc)
calc.set(prec = 'Accurate', xc = 'PBE', lreal = False, isif=2, nsw=20, ibrion=2, kpts=[1,1,1])
print("Residual pressure: %.3f GPa" % (MgO.get_pressure()/GPa))
calc.clean()
banner('Volume scan on MgO (+/- 5%)')
systems=[]
for av in numpy.linspace(a*0.95,a*1.05,5):
systems.append(crystal(['Mg', 'O'], [(0, 0, 0), (0.5, 0.5, 0.5)], spacegroup=225,
print(n+1,end='')
while not r.get_calculator().calc_finished() :
print('.',end='')
sys.stdout.flush()
sleep(10)
print(end=' ')
sys.stdout.flush()
print()
a=4 ; c=crystal('Si',[(0,0,0)],spacegroup=221,cellpar=[a,a,a,90,90,90])
spglib.get_spacegroup(c)
block=False
calc = ClusterVasp(block=block)
calc.set(prec = 'Accurate', xc = 'PBE', lreal = False,
nsw=30, ediff=1e-8, ibrion=2, kpts=[3,3,3])
calc.set(isif=3)
c.set_calculator(calc)
l=ParCalculate(c,calc,cleanup=False,block=block)
s = l[0]
wait_for_results(l)
print(s.get_forces(), s.get_cell(), s.get_stress(), s.get_pressure())
print(n+1,end='')
while not r.get_calculator().calc_finished() :
print('.',end='')
sys.stdout.flush()
sleep(10)
print(end=' ')
sys.stdout.flush()
print()
a=4 ; c=crystal('Si',[(0,0,0)],spacegroup=221,cellpar=[a,a,a,90,90,90])
spglib.get_spacegroup(c)
block=False
calc = ClusterVasp(block=block)
calc.set(prec = 'Accurate', xc = 'PBE', lreal = False,
nsw=30, ediff=1e-8, ibrion=2, kpts=[3,3,3])
calc.set(isif=3)
c.set_calculator(calc)
l=ParCalculate(c,calc,cleanup=False,block=block)
s = l[0]
wait_for_results(l)
print(s.get_forces(), s.get_cell(), s.get_stress(), s.get_pressure())
