def compute_energy(alat, nk, ecut):
"""
Make an input template and select potential and structure, and the path where to run
"""
potname = 'Fe.pbe-nd-rrkjus.UPF'
potpath = os.path.join(os.environ['QE_POTENTIALS'], potname)
pseudopots = {
'Fe':
PseudoPotential(path=potpath,
ptype='uspp',
element='Fe',
functional='GGA',
name=potname),
'Co':
PseudoPotential(path=potpath,
ptype='uspp',
element='Fe',
functional='GGA',
name=potname)
}
struc = make_struc(alat=alat)
kpts = Kpoints(gridsize=[nk, nk, nk], option='automatic', offset=False)
dirname = 'Fe_a_{}_ecut_{}_nk_{}'.format(alat, ecut, nk)
runpath = Dir(
path=os.path.join(os.environ['WORKDIR'], "Lab3/Problem1", dirname))
input_params = PWscf_inparam({
'CONTROL': {
'calculation': 'scf',
'pseudo_dir': os.environ['QE_POTENTIALS'],
'outdir': runpath.path,
'tstress': True,
'tprnfor': True,
'disk_io': 'none',
},
'SYSTEM': {
'ecutwfc': ecut,
'ecutrho': ecut * 8,
'nspin': 2,
'starting_magnetization(1)': 0.7,
'occupations': 'smearing',
'smearing': 'mp',
'degauss': 0.02
},
'ELECTRONS': {
'diagonalization': 'david',
'mixing_beta': 0.5,
'conv_thr': 1e-7,
},
'IONS': {},
'CELL': {},
})
output_file = run_qe_pwscf(runpath=runpath,
struc=struc,
pseudopots=pseudopots,
params=input_params,
kpoints=kpts,
ncpu=2)
output = parse_qe_pwscf_output(outfile=output_file)
return output
def compute_energy(alat, nk, ecut):
"""
Make an input template and select potential and structure, and the path where to run
"""
potname = 'Ge.pz-bhs.UPF'
pseudopath = os.environ['QE_POTENTIALS']
potpath = os.path.join(pseudopath, potname)
pseudopots = {
'Ge':
PseudoPotential(name=potname,
path=potpath,
ptype='uspp',
element='Ge',
functional='LDA')
}
struc = make_struc(alat=alat)
kpts = Kpoints(gridsize=[nk, nk, nk], option='automatic', offset=False)
runpath = Dir(
path=os.path.join(os.environ['WORKDIR'], "Lab2/Problem1", str(alat)))
input_params = PWscf_inparam({
'CONTROL': {
'calculation': 'scf',
'pseudo_dir': pseudopath,
'outdir': runpath.path,
'tstress': True,
'tprnfor': True,
'disk_io': 'none',
},
'SYSTEM': {
'ecutwfc': ecut,
},
'ELECTRONS': {
'diagonalization': 'david',
'mixing_beta': 0.5,
'conv_thr': 1e-7,
},
'IONS': {},
'CELL': {},
})
output_file = run_qe_pwscf(runpath=runpath,
struc=struc,
pseudopots=pseudopots,
params=input_params,
kpoints=kpts)
output = parse_qe_pwscf_output(outfile=output_file)
return output
def compute_energy(alat, nk, ecut, displ=0):
"""
Make an input template and select potential and structure, and the path where to run
"""
pseudopots = {'Pb': PseudoPotential(ptype='uspp', element='Pb', functional='LDA', name='Pb.pz-d-van.UPF'),
'Ti': PseudoPotential(ptype='uspp', element='Ti', functional='LDA', name='Ti.pz-sp-van_ak.UPF'),
'O': PseudoPotential(ptype='uspp', element='O', functional='LDA', name='O.pz-rrkjus.UPF')}
struc = make_struc(alat=alat, displacement=displ)
# fix the Pb and Ti atoms in place during relaxation
constraint = Constraint(atoms={'0': [0,0,0], '1': [0,0,0]})
kpts = Kpoints(gridsize=[nk, nk, nk], option='automatic', offset=True)
dirname = 'PbTiO3_a_{}_ecut_{}_nk_{}_displ_{}'.format(alat, ecut, nk, displ)
runpath = Dir(path=os.path.join(os.environ['WORKDIR'], "Lab3/Problem2", dirname))
input_params = PWscf_inparam({
'CONTROL': {
'calculation': 'scf',
'pseudo_dir': os.environ['QE_POTENTIALS'],
'outdir': runpath.path,
'tstress': True,
'tprnfor': True,
'disk_io': 'none'
},
'SYSTEM': {
'ecutwfc': ecut,
'ecutrho': ecut * 8,
},
'ELECTRONS': {
'diagonalization': 'david',
'mixing_beta': 0.7,
'conv_thr': 1e-7,
},
'IONS': {
'ion_dynamics': 'bfgs'
},
'CELL': {},
})
output_file = run_qe_pwscf(runpath=runpath, struc=struc, pseudopots=pseudopots,
params=input_params, kpoints=kpts, constraint=constraint, ncpu=2)
output = parse_qe_pwscf_output(outfile=output_file)
return output
def compute_energy(alat, nk, ecut):
"""
Make an input template and select potential and structure, and the path where to run
"""
start_time=time.time()
potname = 'Au.pbe-n-kjpaw_psl.1.0.0.UPF'
pseudopath = os.environ['QE_POTENTIALS']
potpath = os.path.join(pseudopath, potname)
pseudopots = {'Au': PseudoPotential(name=potname, path=potpath, ptype='paw', element='Au', functional='PBE')}
struc = make_struc(alat=alat)
kpts = Kpoints(gridsize=[nk, nk, nk], option='automatic', offset=False)
runpath = Dir(path=os.path.join(os.environ['WORKDIR'], "final_project/bulk_cohesive_energy_QE/alat_convergence/", str(alat)))
input_params = PWscf_inparam({
'CONTROL': {
# 'calculation': 'scf',
'calculation':'vc-relax',
'pseudo_dir': pseudopath,
'outdir': runpath.path,
'tstress': True,
'tprnfor': True,
'disk_io': 'none',
},
'SYSTEM': {
'ecutwfc': ecut,
},
'ELECTRONS': {
'diagonalization': 'david',
'mixing_beta': 0.5,
'conv_thr': 1e-7,
},
'IONS': {},
'CELL': {},
})
output_file = run_qe_pwscf(runpath=runpath, struc=struc, pseudopots=pseudopots,
params=input_params, kpoints=kpts,ncpu=4)
output = parse_qe_pwscf_output(outfile=output_file)
end_time=(time.time()-start_time)
print('running time is',end_time)
return output
def compute_energy(nk,
ecut,
elements,
formula,
spacegroup,
sc=1,
directory="final_project",
ncpu=8,
functional="GGA"):
"""
Make an input template and select potential and structure, and the path where to run
"""
# Base Metal
if ('Cu' in elements):
e1 = 'Cu'
if (functional == "GGA"):
pot1 = 'Cu.rel-pbe-spn-kjpaw_psl.1.0.0.UPF'
elif (functional == "LDA"):
pot1 = 'Cu.pz-dn-rrkjus_psl.0.2.UPF'
#pot1 = 'Cu.rel-pbe-spn-kjpaw_psl.1.0.0.UPF'
# Alloying agent
if ('Sn' in elements):
e2 = 'Sn'
if (functional == "GGA"):
pot2 = 'Sn.rel-pbe-dn-kjpaw_psl.1.0.0.UPF'
elif (functional == "LDA"):
pot2 = 'Sn.pz-dn-rrkjus_psl.0.2.UPF'
if ('Cu' not in elements):
e1 = 'Sn'
if (functional == "GGA"):
pot1 = 'Sn.rel-pbe-dn-kjpaw_psl.1.0.0.UPF'
elif (functional == "LDA"):
pot1 = 'Sn.pz-dn-rrkjus_psl.0.2.UPF'
# Put it together
pot1path = './pseudopot/' + pot1
if (len(elements) == 1):
pseudopots = {
e1:
PseudoPotential(path=pot1path,
ptype='paw',
element=e1,
functional='GGA',
name=pot1)
}
elif (len(elements) == 2):
pot2path = './pseudopot/' + pot2
pseudopots = {
e1:
PseudoPotential(path=pot1path,
ptype='paw',
element=e1,
functional='GGA',
name=pot1),
e2:
PseudoPotential(path=pot2path,
ptype='paw',
element=e2,
functional='GGA',
name=pot2)
}
# Get structure
struc = make_struc(formula, spacegroup, sc)
kpts = Kpoints(gridsize=[nk, nk, nk], option='automatic', offset=False)
# Directory
dirname = '{}_{}_{}_{}_{}'.format(formula, spacegroup, nk, sc, ecut)
# Path
runpath = Dir(path=os.path.join(os.environ['WORKDIR'], "final_project/" +
directory, dirname))
# Create input
input_params = PWscf_inparam({
'CONTROL': {
'calculation': 'scf',
#'pseudo_dir': os.environ['QE_POTENTIALS'],
'pseudo_dir': '/home/bond/Work/final_project/pseudopot',
'outdir': runpath.path,
'tstress': True,
'tprnfor': True,
'disk_io': 'none',
},
'SYSTEM': {
'ecutwfc': ecut,
'ecutrho': ecut * 10,
'nspin': 4,
'starting_magnetization(1)': 0,
'starting_magnetization(2)': 0,
'occupations': 'smearing',
'smearing': 'mp',
'degauss': 0.02,
'ntyp': 2,
'lspinorb': True
},
'ELECTRONS': {
'diagonalization': 'david',
'mixing_beta': 0.5,
'conv_thr': 1e-7,
},
'IONS': {},
'CELL': {},
})
# Run and parse
#print(struc)
#exit(1)
output_file = run_qe_pwscf(runpath=runpath,
struc=struc,
pseudopots=pseudopots,
params=input_params,
kpoints=kpts,
ncpu=ncpu)
output = parse_qe_pwscf_output(outfile=output_file, col=True)
return output