def evaluate(args):
x = str(args['xc'][0])
be = bool(str(args['beefensemble'][0]))
pe = bool(str(args['printensemble'][0]))
kpoints = tuple(float(args['kpts'][0][0]), float(args['kpts'][0][1]),
float(args['kpts'][0][2]))
p = float(args['pw'][0])
d = float(args['dw'][0])
sp = bool(args['spinpol'][0])
pflags = str(args['parflags'][0])
odir = str(args['outdir'][0])
calcargs = dict(
xc=x,
beefensemble=be,
printensemble=pe,
kpts=kpoints, #only need 1 kpt in z-direction
pw=p,
dw=d,
spinpol=sp,
parflags=pflags,
outdir=odir)
calc = espresso(**calcargs)
atoms = io.read(
'Pt_111.json') #Read in the structure built by the other script
atoms.set_calculator(calc)
energy = atoms.get_potential_energy(
) #this is the potential energy of the electrons as computed by DFT. It will be closely related to the enthalpy.
f = open('converged.log', 'w')
f.write(str(energy))
f.close()
return calc
txt=myGpaw.symstr+'.out',
occupations=FermiDirac(width=0.05),
# nbands=-2,
convergence={'energy': 0.0005, # eV / electron
'density': 1.0e-4,
'eigenstates': 4.0e-8, # eV^2 / electron
'bands': 'CBM+2.0',
'forces': float('inf')}, # eV / Ang Max
)
atoms.calc = calc
e2 = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
calc.write(myGpaw.symstr+'.gpw')
fd = open('optimization.txt', 'w')
print('experimental bond length:', file=fd)
print('experimental energy: %5.2f eV' % e2, file=fd)
print('bondlength : %5.2f Ang' % d0, file=fd)
# # Find the theoretical bond length:
relax = QuasiNewton(atoms, logfile='qn.log', trajectory=myGpaw.symstr+'.emt.traj')
relax.run(fmax=0.05)
e2 = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
# calc.write(myGpaw.symstr+'relax.gpw')
print(file=fd)
print('PBE energy minimum:', file=fd)
print('PBE minimal energy: %5.2f eV' % e2, file=fd)
from __future__ import print_function
from gpaw import restart
from ase.parallel import paropen as open
from ase.optimize import QuasiNewton
molecule, calc = restart('H2.gpw', txt='H2-relaxed.txt')
e2 = molecule.get_potential_energy()
d0 = molecule.get_distance(0, 1)
fd = open('optimization.txt', 'w')
print('experimental bond length:', file=fd)
print('hydrogen molecule energy: %5.2f eV' % e2, file=fd)
print('bondlength : %5.2f Ang' % d0, file=fd)
# Find the theoretical bond length:
relax = QuasiNewton(molecule, logfile='qn.log')
relax.run(fmax=0.05)
e2 = molecule.get_potential_energy()
d0 = molecule.get_distance(0, 1)
print(file=fd)
print('PBE energy minimum:', file=fd)
print('hydrogen molecule energy: %5.2f eV' % e2, file=fd)
print('bondlength : %5.2f Ang' % d0, file=fd)
fd.close()
xc='PBE',
hund=True,
eigensolver='rmm-diis', # This solver can parallelize over bands
occupations=FermiDirac(0.0, fixmagmom=True),
txt='H.out',
)
atom.set_calculator(calc)
e1 = atom.get_potential_energy()
calc.write('H.gpw')
# Hydrogen molecule:
d = 0.74 # Experimental bond length
molecule = Atoms('H2',
positions=([c - d / 2, c, c],
[c + d / 2, c, c]),
cell=(a, a, a))
calc.set(txt='H2.out')
calc.set(hund=False) # No hund rule for molecules
molecule.set_calculator(calc)
e2 = molecule.get_potential_energy()
calc.write('H2.gpw')
fd = open('atomization.txt', 'w')
print(' hydrogen atom energy: %5.2f eV' % e1, file=fd)
print(' hydrogen molecule energy: %5.2f eV' % e2, file=fd)
print(' atomization energy: %5.2f eV' % (2 * e1 - e2), file=fd)
fd.close()
'npoints': 60
},
symmetry='off',
convergence={'bands': 'CBM+2.0'},
txt=myGpaw.symstr + '_bs.out')
# Plot the band structure
bs = bs_calc.band_structure().subtract_reference()
bs.plot(filename=myGpaw.symstr + 'bs.png', emin=-6, emax=6)
# Get the accurate H**O and LUMO from the band structure calculator
h**o, lumo = bs_calc.get_homo_lumo()
# Calculate the discontinuity potential using the ground state calculator and
# the accurate H**O and LUMO
response = calc.hamiltonian.xc.response
dxc_pot = response.calculate_discontinuity_potential(h**o, lumo)
# Calculate the discontinuity using the band structure calculator
bs_response = bs_calc.hamiltonian.xc.response
KS_gap, dxc = bs_response.calculate_discontinuity(dxc_pot)
# Fundamental band gap = Kohn-Sham band gap + derivative discontinuity
QP_gap = KS_gap + dxc
fd = open('band.txt', 'w')
print(file=fd)
print(f'Kohn-Sham band gap: {KS_gap:.5f} eV', file=fd)
print(f'Discontinuity from GLLB-sc: {dxc:.5f} eV', file=fd)
print(f'Fundamental band gap: {QP_gap:.5f} eV', file=fd)
fd.close()
from __future__ import print_function
import numpy as np
from ase.utils.bee import get_ensemble_energies
from ase.parallel import paropen as open
from gpaw import GPAW
atom = GPAW('H.gpw', txt=None).get_atoms()
molecule = GPAW('H2.gpw', txt=None).get_atoms()
e1 = atom.get_potential_energy()
e2 = molecule.get_potential_energy()
ea = 2 * e1 - e2
fd = open('ensemble_energies.txt', 'w')
print('PBE:', ea, 'eV', file=fd)
e1i = get_ensemble_energies(atom)
e2i = get_ensemble_energies(molecule)
eai = 2 * e1i - e2i
n = len(eai)
ea0 = np.sum(eai) / n
sigma = (np.sum((eai - ea0)**2) / n)**0.5
print('Best fit:', ea0, '+-', sigma, 'eV', file=fd)
fd.close()
fd = open('ensemble.dat', 'w')
for e in eai:
print(e, file=fd)
fd.close()
from __future__ import print_function
import numpy as np
from ase.utils.bee import get_ensemble_energies
from ase.parallel import paropen as open
from gpaw import GPAW
atom = GPAW('H.gpw', txt=None).get_atoms()
molecule = GPAW('H2.gpw', txt=None).get_atoms()
e1 = atom.get_potential_energy()
e2 = molecule.get_potential_energy()
ea = 2 * e1 - e2
fd = open('ensemble_energies.txt', 'w')
print('PBE:', ea, 'eV', file=fd)
e1i = get_ensemble_energies(atom)
e2i = get_ensemble_energies(molecule)
eai = 2 * e1i - e2i
n = len(eai)
ea0 = np.sum(eai) / n
sigma = (np.sum((eai - ea0)**2) / n)**0.5
print('Best fit:', ea0, '+-', sigma, 'eV', file=fd)
fd.close()
fd = open('ensemble.dat', 'w')
for e in eai:
print(e, file=fd)
fd.close()
from gpaw import restart
from ase.parallel import paropen as open
from ase.optimize import QuasiNewton
molecule, calc = restart("../01_atomization_energies/H2.gpw", txt="LOG_H2-relaxed.txt")
e2 = molecule.get_potential_energy()
d0 = molecule.get_distance(0, 1) # distance between H atoms
fd = open("LOG_optimization.txt", "w")
print("experimental bond length:", file=fd)
print("hydrogen molecule energy: %5.2f eV" % e2, file=fd)
print("bondlength : %5.2f Ang" % d0, file=fd)
# Find the theoretical bond length:
relax = QuasiNewton(molecule, logfile="LOG_qn.txt")
relax.run(fmax=0.05)
e2 = molecule.get_potential_energy()
d0 = molecule.get_distance(0, 1)
print(file=fd)
print("PBE energy minimum:", file=fd)
print("hydrogen molecule energy: %5.2f eV" % e2, file=fd)
print("bondlength : %5.2f Ang" % d0, file=fd)
fd.close()
# gpaw calculator:
calc = GPAW(
mode=PW(),
xc="PBE",
hund=True,
eigensolver="rmm-diis", # This solver can parallelize over bands
occupations=FermiDirac(0.0, fixmagmom=True),
txt="H.out",
)
atom.set_calculator(calc)
e1 = atom.get_potential_energy()
calc.write("H.gpw")
# Hydrogen molecule:
d = 0.74 # Experimental bond length
molecule = Atoms("H2", positions=([c - d / 2, c, c], [c + d / 2, c, c]), cell=(a, a, a))
calc.set(txt="H2.out")
calc.set(hund=False) # No hund rule for molecules
molecule.set_calculator(calc)
e2 = molecule.get_potential_energy()
calc.write("H2.gpw")
fd = open("atomization.txt", "w")
print(" hydrogen atom energy: %5.2f eV" % e1, file=fd)
print(" hydrogen molecule energy: %5.2f eV" % e2, file=fd)
print(" atomization energy: %5.2f eV" % (2 * e1 - e2), file=fd)
fd.close()
calc = GPAW(mode=PW(),
xc="PBE",
hund=True,
eigensolver="rmm-diis", # This solver can parallelize over bands
occupations=FermiDirac(0.0, fixmagmom=True),
txt="H.out",
)
atom.set_calculator(calc)
e1 = atom.get_potential_energy()
calc.write("H.gpw")
# Hydrogen molecule:
d = 0.74 # Experimental bond length
molecule = Atoms("H2",
positions=([c - d / 2, c, c],
[c + d / 2, c, c]),
cell=(a, a, a))
calc.set(txt="H2.out")
calc.set(hund=False) # No hund rule for molecules
molecule.set_calculator(calc)
e2 = molecule.get_potential_energy()
calc.write("H2.gpw")
fd = open("LOG_atomization.txt", "w")
print(" hydrogen atom energy: %5.2f eV" % e1, file=fd)
print(" hydrogen molecule energy: %5.2f eV" % e2, file=fd)
print(" atomization energy: %5.2f eV" % (2 * e1 - e2), file=fd)
fd.close()