Lb = float(elem_list[6])
print("lattice constant b = ", Lb)
Lc = float(elem_list[7])
print("lattice constant c = ", Lc)
Lalpha = float(elem_list[8])
print("alpha angle = ", Lalpha)
# First perform a regular SCF run
calc = GPAW(
mode=PW(400),
maxiter=1500,
spinpol=True,
kpts=kpts,
xc=xc,
txt='-',
occupations=FermiDirac(0.02),
mixer=Mixer(0.01, 11, 100.0),
)
atoms = bulk(element, struct, a=La, b=Lb, c=Lc, alpha=Lalpha)
# sc,fcc,bcc,tetragonal,bct,hcp,rhmbohedral,orthorhombic
# mlc, diamond,zincblende,rocksalt,cesiumchloride, fluorite, wurtzite
atoms.set_calculator(calc)
atoms.get_potential_energy()
# Get the valence band maximum
efermi = calc.get_fermi_level()
Nk = len(calc.get_ibz_k_points())
Ns = calc.get_number_of_spins()
eigval = np.array([[calc.get_eigenvalues(kpt=k, spin=s) for k in range(Nk)]
for s in range(Ns)])
a = 5.43095
b = a / 2
c = b / 2
d = b + c
si_nonortho = Atoms(
[Atom('Si',
(0, 0, 0)), Atom('Si', (a / 4, a / 4, a / 4))],
cell=[(a / 2, a / 2, 0), (a / 2, 0, a / 2), (0, a / 2, a / 2)],
pbc=True)
# calculation with full symmetry
calc = GPAW(nbands=-10,
h=0.25,
kpts=(2, 2, 2),
occupations=FermiDirac(width=0.05),
setups={0: 'hch1s'})
si_nonortho.set_calculator(calc)
e = si_nonortho.get_potential_energy()
niter = calc.get_number_of_iterations()
calc.write('si_nonortho_xas_sym.gpw')
# calculation without any symmetry
calc = GPAW(nbands=-10,
h=0.25,
kpts=(2, 2, 2),
occupations=FermiDirac(width=0.05),
setups={0: 'hch1s'},
symmetry='off')
e=e,
linspacestr=linspacestr,
kptdensity=kptdensity,
width=width,
relativistic=relativistic,
constant_basis=constant_basis,
x=x)
if id is None:
continue
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
atoms.calc = GPAW(txt=name + '_' + code + '_' + str(n) + '.txt',
xc='PBE',
kpts=kpts,
occupations=FermiDirac(width),
parallel={'band': 1},
maxiter=777,
idiotproof=False)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
name=name,
mode=mode,
e=e,
linspacestr=linspacestr,
kptdensity=kptdensity,
width=width,
relativistic=relativistic,
constant_basis=constant_basis,
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
from gpaw.mpi import serial_comm
from gpaw.test import equal
from gpaw.xc.rpa import RPACorrelation
from gpaw.xc.fxc import FXCCorrelation
a0 = 5.43
Ni = bulk('Ni', 'fcc')
Ni.set_initial_magnetic_moments([0.7])
calc = GPAW(mode='pw',
kpts=(3, 3, 3),
occupations=FermiDirac(0.001),
setups={'Ni': '10'},
communicator=serial_comm)
Ni.set_calculator(calc)
E = Ni.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=50)
rpa = RPACorrelation(calc, nfrequencies=8, skip_gamma=True)
E_rpa = rpa.calculate(ecut=[50])
fxc = FXCCorrelation(calc, nlambda=16, nfrequencies=8, skip_gamma=True)
E_fxc = fxc.calculate(ecut=[50])
equal(E_rpa, -7.826, 0.01)
equal(E_fxc, -7.826, 0.01)
# Ground state calculation
a = 5.431
atoms = bulk('Si', 'diamond', a=a)
calc = GPAW(mode='pw',
kpts={
'density': 5.0,
'gamma': True
},
parallel={
'band': 1,
'domain': 1
},
xc='LDA',
occupations=FermiDirac(0.001)) # use small FD smearing
atoms.set_calculator(calc)
atoms.get_potential_energy() # get ground state density
# Restart Calculation with fixed density and dense kpoint sampling
calc.set(
kpts={
'density': 15.0,
'gamma': False
}, # dense kpoint sampling
fixdensity=True)
atoms.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=70) # diagonalize Hamiltonian
calc.write('si_large.gpw', 'all') # write wavefunctions
from math import log
from ase import Atoms
from ase.units import Bohr
from gpaw import GPAW, FermiDirac
from gpaw.test import equal
a = 4.0
h = 0.2
hydrogen = Atoms('H', [(a / 2, a / 2, a / 2)], cell=(a, a, a))
hydrogen.calc = GPAW(h=h, nbands=1, convergence={'energy': 1e-7})
e1 = hydrogen.get_potential_energy()
equal(e1, 0.526939, 0.001)
dens = hydrogen.calc.density
c = dens.gd.find_center(dens.nt_sG[0]) * Bohr
equal(abs(c - a / 2).max(), 0, 1e-13)
kT = 0.001
hydrogen.calc.set(occupations=FermiDirac(width=kT))
e2 = hydrogen.get_potential_energy()
equal(e1, e2 + log(2) * kT, 3.0e-7)
sys.__stdout__.write(x)
raise RuntimeError('not silent')
out, err = sys.stdout, sys.stderr
sys.stdout = sys.stderr = Out()
try:
from gpaw import GPAW, FermiDirac
from ase import Atom, Atoms
a = 5.0
h = 0.2
calc = GPAW(h=h,
nbands=1,
kpts=(1, 1, 1),
occupations=FermiDirac(width=1e-9),
xc='PBE',
txt=None)
hydrogen = Atoms([Atom('H', (a / 2, a / 2, a / 2), magmom=0)],
cell=(a, a, a),
calculator=calc)
f = hydrogen.get_forces()
except:
sys.stdout = out
sys.stderr = err
raise
sys.stdout = out
sys.stderr = err
atoms.positions[5:7, 0] = [4 * a + c, 4 * a + c + b]
atoms.positions[:, 1:] = L / 2.
pl_atoms1 = range(4) # Atomic indices of the left principal layer
pl_atoms2 = range(8, 12) # Atomic indices of the right principal layer
pl_cell1 = (L, L, 4 * a) # Cell for the left principal layer
pl_cell2 = pl_cell1 # Cell for the right principal layer
atoms.rotate('x', 'z')
# Attach a GPAW calculator
atoms.set_calculator(
Transport(h=0.3,
xc='PBE',
basis='szp(dzp)',
occupations=FermiDirac(width=0.1),
kpts=(1, 1, 1),
mode='lcao',
save_file=False,
txt='pt_h2_transport.txt',
mixer=Mixer(0.1, 5, weight=100.0),
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1, 1, 13),
mol_atoms=range(4, 8),
lead_restart=False,
scat_restart=False,
edge_atoms=[[0, 3], [0, 11]],
analysis_data_list=['tc'],
data_file='Pt_H2_nsc.dat',
non_sc=True))
from ase import Atoms
from gpaw import GPAW, FermiDirac
from ase.optimize import QuasiNewton
d = 0.74 # bond length
a = 10.0
c = a / 2
atoms = Atoms('H2',
positions=([c - d / 2, c, c], [c + d / 2, c, c]),
cell=(a, a, a))
calc = GPAW(xc="PBE",
eigensolver="dav",
occupations=FermiDirac(0.0, fixmagmom=True),
txt="H2.out",
verbose=1)
atoms.set_calculator(calc)
ene = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
print("Initial energy = %18.10f eV" % ene)
print("d0 = %18.10f angstrom" % d0)
calc.write("H2.gpw")
relax = QuasiNewton(atoms, logfile="relax.qn.log")
relax.run(fmax=0.05)
BH.set_pbc(False)
cf = GPAW(nbands=3, h=.3, txt=txt)
BH.set_calculator(cf)
e1 = BH.get_potential_energy()
niter1 = cf.get_number_of_iterations()
cf.write(fname, 'all')
else:
cf = GPAW(fname, txt=txt)
wf = testSTM(cf)
# finite system with spin
fname = 'BH-spin_Sz2_wfs.gpw'
BH.set_initial_magnetic_moments([1, 1])
if not load:
BH.set_pbc(False)
cf = GPAW(occupations=FermiDirac(0.1, fixmagmom=True),
nbands=5,
h=0.3,
txt=txt)
BH.set_calculator(cf)
e2 = BH.get_potential_energy()
niter2 = cf.get_number_of_iterations()
cf.write(fname, 'all')
else:
cf = GPAW(fname, txt=txt)
testSTM(cf)
# periodic system
if not load:
BH.set_pbc(True)
cp = GPAW(spinpol=True,
from ase.build import bulk
from gpaw import GPAW, PW, FermiDirac
from ase.units import Bohr, Hartree
# Hydrogen atom:
atoms = bulk("Si", "diamond", a=10.2631*Bohr)
atoms.write("TEMP_Si.xsf")
# gpaw calculator:
ecutwfc = 15.0*Hartree
calc = GPAW( mode=PW(ecutwfc),
setups="hgh",
xc="LDA_X+LDA_C_VWN",
eigensolver="dav",
spinpol=False,
occupations=FermiDirac(0),
kpts={"size": (3, 3, 3)},
txt="-")
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
calc.write("TEMP_Si.gpw")
print("===================================================")
print("Total energy : %18.10f eV = %18.10f Hartree" % (e1,e1/Hartree))
print("===================================================")
kpts += kshift
atoms = bulk('MgO', 'rocksalt', a=4.212)
if mode == 'pw':
calc = GPAW(mode=PW(800),
basis='dzp',
xc='PBE',
maxiter=300,
kpts=kpts,
parallel={
'band': 1,
'domain': 1
},
setups={'Mg': '2'},
occupations=FermiDirac(0.01))
atoms.set_calculator(calc)
E1 = atoms.get_potential_energy()
from gpaw.xc.hybridg import HybridXC
exx = HybridXC('EXX', method='acdf')
E_hf1 = E1 + calc.get_xc_difference(exx)
else:
calc = GPAW(h=0.12,
basis='dzp',
kpts=kpts,
xc='PBE',
setups={'Mg': '2'},
parallel={
'domain': 1,
'band': 1
#Initialize new calculations
bulk_mat = bulk('Fe', 'bcc', a)
bulk_mat.set_initial_magnetic_moments([initial_magmom])
bulk_mat = bulk_mat * (atoms, atoms, atoms)
if (str(sys.argv[8]) == 'True'):
del bulk_mat[[atom.index for atom in bulk_mat if atom.index == 0]]
calc = GPAW(mode=PW(e_cut),
nbands=nbands,
xc='PBE',
spinpol=True,
kpts=(k_pts, k_pts, k_pts),
occupations=FermiDirac(smear),
txt=system_name + '.out')
bulk_mat.set_calculator(calc)
#Save the initial state of the calculations
#calc.write('Fe_relaxer_initial.gpw')
save_atoms(bulk_mat, e_cut, nbands, k_pts, smear, a, initial_magmom, 1,
str(sys.argv[6]))
saver = Gpw_save(calc, system_name + '_relaxed.gpw')
traj = Trajectory(system_name + '_relaxed.traj', 'w', bulk_mat)
ucf = UnitCellFilter(bulk_mat)
relaxer = BFGS(ucf, logfile=system_name + '.txt')
relaxer.attach(traj)
relaxer.attach(saver)
relaxer.run(fmax=0.025)
from ase.units import Bohr
from ase.structure import bulk
from gpaw import GPAW, FermiDirac
from gpaw.atom.basis import BasisMaker
from gpaw.response.df import DF
from gpaw.mpi import serial_comm, rank, size
from gpaw.utilities import devnull
if rank != 0:
sys.stdout = devnull
# GS Calculation One
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(h=0.2, kpts=(4, 4, 4), occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C.gpw', 'all')
# Macroscopic dielectric constant calculation
q = np.array([0.0, 0.00001, 0.])
w = np.linspace(0, 24., 241)
df = DF(calc='C.gpw',
q=q,
w=(0., ),
eta=0.001,
ecut=50,
hilbert_trans=False,