from ase.build import bulk
from gpaw import GPAW, PW, FermiDirac
calc = GPAW(mode=PW(600),
xc='PBE',
occupations=FermiDirac(0.01),
kpts=(32, 32, 16),
symmetry='off',
parallel={
'band': 1,
'domain': 1
},
txt='gs_Co.txt')
bulk = bulk('Co', 'hcp')
bulk.set_initial_magnetic_moments([1.0, 1.0])
bulk.set_calculator(calc)
bulk.get_potential_energy()
calc.write('gs_Co.gpw', mode='all')
# making dimer.traj
traj = Trajectory('dimer.traj', 'w') # create Trajectory object
dx = 0.1 #scaling factor
list1 = [0, 0, 0] # position of first atom
list2 = [0, 0, 0.5] # will store new position of second atom
vec_2 = np.array(list2) - np.array(list1) # vector pointing from 1 to 2
norm_2 = np.linalg.norm(vec_2, ord=2) # get norm
vec_2 = [x / norm_2 for x in vec_2] # get unit vector
for i in range(4):
ss = [dx * x for x in vec_2] #scale vector
list2 = np.array(list2) + np.array(ss) # move second atom
dimer = Atoms('CC', positions=[list1, list2]) # create ASE atom object
dimer.calc = Espresso(pseudopotentials=pseudopotentials)
dft_energy = dimer.get_potential_energy()
traj.write(dimer,
energy=(dft_energy)) # write dft energy to trajectory file
dx += 0.1
# making bulk.traj
#https://wiki.fysik.dtu.dk/ase/tutorials/deltacodesdft/deltacodesdft.html?highlight=dft%20calculatin#ase.utils.deltacodesdft.delta
pseudopotentials = {'C': 'C.pbe-n-kjpaw_psl.1.0.0.UPF'}
for symbol in ['C']:
traj = Trajectory('bulk.traj'.format(symbol), 'w')
for s in range(94, 108, 2):
bulk = dcdft[symbol]
bulk.set_cell(bulk.cell * (s / 100.0)**(1.0 / 3.0), scale_atoms=True)
bulk.calc = Espresso(pseudopotentials=pseudopotentials, kpts=(6, 6, 6))
dft_energy = bulk.get_potential_energy()
print s, dft_energy
traj.write(bulk, energy=(dft_energy))
spin='none',
k_grid=(9,9,9),
vdw_correction_hirshfeld="True",
relativistic=('atomic_zora','scalar'),
#use_dipole_correction='True',
compute_forces="true",
output=['mulliken'],
# elsi_restart=("write",1)
)
bulk = Atoms('Pd',
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1,
calculator=calc) # use EMT potential
bulk.get_potential_energy()
#traj.write(bulk)
energy_bulk=bulk.get_potential_energy()
print ("potential-energy-bulk", energy_bulk)
#print (energy_bulk)
############SURFACE################################
from ase.io import write
## Edit these
atomic_species='Pd'
a2 = a
unit_cell_depth=3
unit_cell_width=3
slab_depth=4
vacuum_region_size=10.0
def optimize_lattice_constant(bulk,
lattice="fcc",
a0=4.0,
xc="PBEsol",
encut=400,
ediff=1.0e-5,
ediffg=1.0e-6,
npar=1,
nsim=1):
"""
function to do bulk optimization
"""
from ase import Atoms
from ase.calculators.vasp import Vasp
import os, shutil
#
# directry things
#
cudir = os.getcwd()
workdir = os.path.join(cudir, "lattice_opt")
os.makedirs(workdir)
os.chdir(workdir)
os.system("mkdir work_bulk")
#
# compuational condition for Vasp
#
prec = "normal"
potim = 0.1
nelmin = 5
kpts = [3, 3, 3]
gamma = True
nsw = 200
isif = 6 # or 6---freezing ions
xc = xc.lower()
if xc == "pbe" or xc == "pbesol" or xc == "rpbe":
pp = "pbe"
elif xc == "pw91":
pp = "pw91"
elif xc == "lda":
pp = "lda"
else:
print("xc error")
calc = Vasp(prec=prec,
xc=xc,
pp=pp,
ispin=1,
ismear=1,
sigma=0.2,
isif=isif,
nelmin=nelmin,
encut=encut,
ibrion=2,
nsw=nsw,
potim=potim,
ediff=ediff,
ediffg=ediffg,
kpts=kpts,
gamma=gamma,
isym=0,
npar=npar,
nsim=nsim,
lreal=False)
bulk.set_calculator(calc)
bulk.get_potential_energy()
cell = bulk.cell # optimized cell size
os.chdir(cudir)
shutil.rmtree(workdir)