def test():
atoms, calc = restart(
'/home/hexu/projects/jiahui/STO_bulk_LCAO/STO3_gs.gpw',
fixdensity=True)
kpoints = calc.get_ibz_kpoints()
H, S = get_lcao_hamiltonian()
desc = calc.setups[0].basis.get_description()
def gpawRestart(calc):
from gpaw import restart, PW, Davidson, Mixer, MixerSum, FermiDirac
return restart(
'preCalc_inp.gpw',
mode=PW(calc.pw),
xc=calc.xc,
kpts={
'density': calc.kpt,
'gamma': True
} if isinstance(calc.kpt, int) else calc.kpt,
spinpol=calc.magmom > 0,
convergence={'energy': calc.eConv} #eV/electron
,
mixer=((MixerSum(beta=calc.mixing, nmaxold=calc.nmix, weight=100))
if calc.magmom > 0 else
(Mixer(beta=calc.mixing, nmaxold=calc.nmix, weight=100))),
maxiter=calc.maxsteps,
nbands=-1 * calc.nbands,
occupations=FermiDirac(calc.sigma),
setups='sg15' #(pspDict[calc.psp]).pthFunc[cluster]
,
eigensolver=Davidson(5),
poissonsolver=
None # {'dipolelayer': 'xy'} if isinstance(self,SurfaceJob) else None
,
txt=str(calc) + '.txt',
symmetry={'do_not_symmetrize_the_density':
True} #ERROR IN LI bcc 111 surface
)
def read(self, filename):
self.lrtddft = LrTDDFT(filename + '/' + filename + '.lr.dat.gz')
self.atoms, self.calculator = restart(
filename + '/' + filename, communicator=self.world)
E0 = self.calculator.get_potential_energy()
f = open(filename + '/' + filename + '.exst', 'r')
f.readline()
self.d = f.readline().replace('\n', '').split()[1]
indextype = f.readline().replace('\n', '').split()[1]
if indextype == 'UnconstraintIndex':
iex = int(f.readline().replace('\n', '').split()[1])
self.index = UnconstraintIndex(iex)
else:
direction = f.readline().replace('\n', '').split()[1]
if direction in [str(0), str(1), str(2)]:
direction = int(direction)
else:
direction = None
val = f.readline().replace('\n', '').split()
if indextype == 'MinimalOSIndex':
self.index = MinimalOSIndex(float(val[1]), direction)
else:
emin = float(val[2])
emax = float(val[3].replace(']', ''))
self.index = MaximalOSIndex([emin, emax], direction)
index = self.index.apply(self.lrtddft)
self.results['energy'] = E0 + self.lrtddft[index].energy * Hartree
self.lrtddft.set_calculator(self.calculator)
def createCubeFiles():
atoms, calc = gp.restart( "CO.gpw" )
nbands = calc.get_number_of_bands()
for band in range(nbands):
wf = calc.get_pseudo_wave_function(band=band)
fname = "wavefuncttionCO_%d.cube"%(band)
ase.io.write( fname, atoms, data=wf )
def gpawRestart(self):
from gpaw import restart, PW, Davidson, Mixer, MixerSum, FermiDirac
spinpol = any([x > 0 for x in self.magmomsinit()])
return restart(
'preCalc_inp.gpw',
mode=PW(self.pw),
xc=self.xc,
kpts=self.kpt(),
spinpol=spinpol,
convergence={'energy': self.econv()} #eV/electron
,
mixer=(
(MixerSum(beta=self.mixing(), nmaxold=self.nmix(), weight=100))
if spinpol else
(Mixer(beta=self.mixing(), nmaxold=self.nmix(), weight=100))),
maxiter=self.maxstep(),
nbands=self.nbands(),
occupations=FermiDirac(self.sigma()),
setups=self.psp #(pspDict[calc.psp]).pthFunc[cluster]
,
eigensolver=Davidson(5),
poissonsolver=
None # {'dipolelayer': 'xy'} if isinstance(self,SurfaceJob) else None
,
txt='%d_%s.txt' % (self.pw, self.xc),
symmetry={'do_not_symmetrize_the_density':
True}) #ERROR IN LI bcc 111 surface
def file_ok(gpw_file):
try:
atoms, calc = restart(gpw_file)
atoms.get_potential_energy()
except KeyError as exc:
print(str(exc))
return False
return True
def add_efield(fname, efield=0):
printit('Starting Efield calculation for efiled = {}'.format(efield))
atom, calc = restart('gs_' + fname + '.gpw')
calc.set(txt='gs_efield_{}.txt'.format(efield))
calc.set(external=ConstantElectricField(efield, [0, 0, 1]))
calc.get_potential_energy()
calc.write('gs_' + fname + '_{}.gpw'.format(efield), mode='all')
printit('Efield GS calculation done')
gap, p1, p2 = get_gap(calc)
printit("{} {} {} {}".format(efield, gap, p1, p2), fname="gaps.dat")
printit("efield={} gap={}".format(efield, gap))
def main():
molecule, calc = gp.restart("H2.gpw", txt="H2-relaxed.txt")
print("Getting potential energy")
e2 = molecule.get_potential_energy()
d0 = molecule.get_distance(0, 1)
# Find the minimum energy by Quasi-Newton
relax = QuasiNewton(molecule, logfile="qn.log")
relax.run(fmax=0.05)
d1 = molecule.get_distance(0, 1)
print("Original bondlength: %.2f" % (d0))
print("Optimized bondlength: %.2f" % (d1))
def read(fn, gridref=4, spin_flag=False):
"""Read in from a GPAW restart file, this function requires gpaw.
args:
fn: filename
gridref: the gridrefinemnet flag for get_all_electron_density method
spin_flag: whether to read the spin density also
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Future: remove gpaw dependancy?
"""
from gpaw import restart
prefix, filename = os.path.split(fn)
prefix = os.path.join(prefix, '')
_, calc = restart(fn)
return read_calc(calc, gridref, spin_flag, fn, prefix)
def getXCcontribs(jobID):
jobObject = db2BulkJob(jobID)
if jobObject.dftCode == 'gpaw':
from gpaw import restart
from gpaw.xc.bee import BEEFEnsemble
atoms, calc = restart('inp.gpw',
setups='sg15',
xc='mBEEF',
convergence={'energy': 5e-4},
txt='mbeef.txt')
atoms.get_potential_energy()
beef = BEEFEnsemble(calc)
return beef.mbeef_exchange_energy_contribs()
else:
return np.zeros((8, 8))
def run_task(self,fw_spec):
jobID = fw_spec['jobID']
job = db2object(jobID)
if job.dftcode == 'gpaw':
from gpaw import restart
from gpaw.xc.bee import BEEFEnsemble
atoms,calc = restart('inp.gpw', setups='sg15', xc='mBEEF', convergence={'energy': 5e-4}, txt='mbeef.txt')
atoms.get_potential_energy()
beef = BEEFEnsemble(calc)
xcContribs = beef.mbeef_exchange_energy_contribs()
else:
xcContribs = np.zeros((8,8))
return FWAction( stored_data={'xcContribs': xcContribs}
,mod_spec=[{'_push': {'xcContribs': xcContribs}}])
def run_task(self,fw_spec):
from gpaw import restart
from gpaw.xc.bee import BEEFEnsemble
job,params,atoms = initialize(fw_spec)
atoms.set_calculator(job.PBEcalc())
atoms.get_potential_energy()
atoms.calc.write('inp.gpw', mode='all')
atoms,calc = restart('inp.gpw', setups='sg15', xc='mBEEF', convergence={'energy': 5e-4}, txt='mbeef.txt')
atoms.get_potential_energy()
beef = BEEFEnsemble(calc)
xcContribs = beef.mbeef_exchange_energy_contribs()
ase.io.write('final.traj',atoms)
resultDict = misc.mergeDicts([params,trajDetails(ase.io.read('final.traj'))
,{'xcContribs': pickle.dumps(xcContribs)}])
with open('result.json', 'w') as outfile: json.dumps(resultDict, outfile)
return fireworks.core.firework.FWAction( stored_data=resultDict)
def read_and_check_results():
"""Read energies from .gpw files."""
fd = sys.stdout
E = {}
fd.write('E = {')
for formula in systems:
try:
atoms, calc = restart(formula, txt=None)
except (KeyError, IOError):
#print formula
continue
nspins = calc.get_number_of_spins()
fa = calc.get_occupation_numbers(spin=0)
assert ((fa.round() - fa)**2).sum() < 1e-14
if nspins == 2:
fb = calc.get_occupation_numbers(spin=1)
assert ((fb.round() - fb)**2).sum() < 1e-9
if len(atoms) == 1:
M = data[formula]['magmom']
else:
M = sum(data[formula]['magmoms'])
assert abs((fa-fb).sum() - M) < 1e-9
e = calc.get_potential_energy()
fd.write("'%s': %.3f, " % (formula, e))
fd.flush()
E[formula] = e
dE = [] # or maybe {} ?
fd.write('}\ndE = [')
for formula in dimers:
try:
trajectory = PickleTrajectory(formula + '.traj', 'r')
except IOError:
continue
energies = [a.get_potential_energy() for a in trajectory]
dE.append((formula, (energies)))
fd.write("('%s', (" % formula)
fd.write(', '.join(['%.4f' % (energy - E[formula])
for energy in energies]))
fd.write(')),\n ')
fd.write(']\n')
return E, dE
def read_and_check_results():
"""Read energies from .gpw files."""
fd = sys.stdout
E = {}
fd.write('E = {')
for formula in systems:
try:
atoms, calc = restart(formula, txt=None)
except (KeyError, IOError):
#print formula
continue
nspins = calc.get_number_of_spins()
fa = calc.get_occupation_numbers(spin=0)
assert ((fa.round() - fa)**2).sum() < 1e-14
if nspins == 2:
fb = calc.get_occupation_numbers(spin=1)
assert ((fb.round() - fb)**2).sum() < 1e-9
if len(atoms) == 1:
M = data[formula]['magmom']
else:
M = sum(data[formula]['magmoms'])
assert abs((fa-fb).sum() - M) < 1e-9
e = calc.get_potential_energy()
fd.write("'%s': %.3f, " % (formula, e))
fd.flush()
E[formula] = e
dE = [] # or maybe {} ?
fd.write('}\ndE = [')
for formula in dimers:
try:
trajectory = PickleTrajectory(formula + '.traj', 'r')
except IOError:
continue
energies = [a.get_potential_energy() for a in trajectory]
dE.append((formula, (energies)))
fd.write("('%s', (" % formula)
fd.write(', '.join(['%.4f' % (energy - E[formula])
for energy in energies]))
fd.write(')),\n ')
fd.write(']\n')
return E, dE
def __init__(self, atoms=None, calc=None, gpw_fname=None):
if not _has_gpaw:
raise ImportError("GPAW was not imported. Please install gpaw.")
if atoms is None or calc is None:
atoms, calc=restart(gpw_fname, fixdensity=False, txt='nscf.txt')
self.atoms=atoms
self.calc=calc
#self.wfs=self.calc.wfs
#self.h=self.calc.hamiltonian
#self.kpt_u = self.wfs.kpt_u
self.cell = self.atoms.get_cell()
#self.wann_centers=get_bf_centers(self.atoms)
self.positions=self.cell.scaled_positions(get_bf_centers(self.atoms))
#if calc.get_spin_polarized():
# self.positions=np.vstack([self.positions, self.positions])
self.efermi=self.calc.get_fermi_level()
self.R2kfactor= -2.0j* np.pi
#self.nbasis=len(self.positions)
self.norb=len(self.positions)
self.nbasis=self.norb*2
def band_calc(fname):
printit('Starting Band structure calculation')
atom, calc = restart(fname)
path = atom.cell.bandpath([[0, 0, 0], [0, 0.5, 0], [0, 1, 0]], npoints=100)
calc.set(fixdensity=True)
calc.set(symmetry='off')
calc.set(kpts=path.kpts)
calc.get_potential_energy()
printit('Band structure calculation Done')
gap, p1, p2 = gap(calc)
printit("{} {}".format(fname, gap), fname="gaps.dat")
e_kn = np.array([calc.get_eigenvalues(k) for k in range(len(kpts))])
efermi = calc.get_fermi_level()
plt.figure(figsize=(5, 6))
x = path.get_linear_kpoint_axis()[0]
for i in range(nbands):
plt.plot(x, e_kn[:, i])
for j in path.get_linear_kpoint_axis()[1]:
plt.plot([0, X[-1]], [0, 0], 'k-')
plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
plt.tight_layout()
plt.savefig(fname + '.png', dpi=300)
def test(atoms):
e0 = atoms.get_potential_energy()
f0 = atoms.get_forces()
m0 = atoms.get_magnetic_moments()
eig00 = atoms.calc.get_eigenvalues(spin=0)
eig01 = atoms.calc.get_eigenvalues(spin=1)
wf0 = atoms.calc.get_pseudo_wave_function(band=1)
# Write the restart file(s):
atoms.calc.write('tmp1.gpw')
atoms.calc.write('tmp2.gpw', 'all')
# Try restarting:
atoms, calc = restart('tmp2.gpw', txt=None)
wf1 = calc.get_pseudo_wave_function(band=1)
e1 = atoms.get_potential_energy()
f1 = atoms.get_forces()
m1 = atoms.get_magnetic_moments()
eig10 = calc.get_eigenvalues(spin=0)
eig11 = calc.get_eigenvalues(spin=1)
print(e0, e1)
equal(e0, e1, 1e-10)
print(f0, f1)
for ff0, ff1 in zip(f0, f1):
err = np.linalg.norm(ff0 - ff1)
assert err <= 1e-10
print(m0, m1)
for mm0, mm1 in zip(m0, m1):
equal(mm0, mm1, 1e-10)
print('A', eig00, eig10)
for eig0, eig1 in zip(eig00, eig10):
equal(eig0, eig1, 1e-10)
print('B', eig01, eig11)
for eig0, eig1 in zip(eig01, eig11):
equal(eig0, eig1, 1e-10)
equal(abs(wf1 - wf0).max(), 0, 1e-14)
# Check that after restart everything is writable
calc.write('tmp3.gpw')
calc.write('tmp4.gpw', 'all')
def XCcontribsScript():
import cPickle, json, ase
from gpaw import restart
from gpaw.xc.bee import BEEFEnsemble
params, optAtoms = initialize(
) # Remove old .out/.err files, load from fw_spec, and write 'init.traj'
pbeParams = copy.deepcopy(params)
pbeParams['xc'] = 'PBE'
atoms.set_calculator(makeCalc(pbeParams))
atoms.get_potential_energy()
atoms.calc.write('inp.gpw', mode='all')
atoms, calc = restart('inp.gpw',
setups='sg15',
xc='mBEEF',
convergence={'energy': 5e-4},
txt='mbeef.txt')
atoms.get_potential_energy()
beef = BEEFEnsemble(calc)
xcContribs = beef.mbeef_exchange_energy_contribs()
################################
print "Storing Results..."
#-------------------------------
ase.io.write('final.traj', atoms)
resultDict = mergeDicts([
params,
trajDetails(ase.io.read('final.traj')), {
'xcContribs': cPickle.dumps(xcContribs)
}
])
with open('result.json', 'w') as outfile:
outfile.write(json.dumps(resultDict))
if rank() == 0:
with open('result.json', 'r') as outfile:
json.loads(outfile.read()) #test that dictionary isn't 'corrupted'
log(params, atoms)
return 0
def load_gpaw_restart(
self,
infile,
**kwargs,
):
from gpaw import restart
atoms, calc = restart(infile)
try: # check if the wavefunction exists
wfs = calc.wfs
except:
print('ERROR: No wavefunctions found in the GPAW restart file {}'.
format(filename))
print("Make sure to write the GPAW file with mode='all'!")
raise NoWavefunctionFound
#end try
if self.density:
# run SCF to re-populate density
print('Running SCF to re-populate density')
calc.scf.converged = False
calc.results.pop('energy')
E = calc.get_potential_energy()
#end def
self.load_gpaw_calc(calc, atoms)
# Find optimal k parameter
k, calc = convergeK(atoms, tol=1e-4, kstart=4)
print(f'Optimal k-parameter: k={k}')
# Perform a ground state energy calculation to get the ground state density
atoms.get_potential_energy()
# Save the calculator
calc.write('Al_calc.gpw')
# if world.rank == 0:
print('Calculator saved')
#### Electronic band structure
# if world.rank == 0:
print('Electronic structure calculation started')
atoms, calc = restart('Al_calc.gpw')
# kpts = {'size': (60,60,60), 'path': 'GXWKGLUWLK,UX'}
kpts = {'path': 'GXWKGLUWLK,UX', 'npoints': 60}
calc.set(kpts = kpts, fixdensity=True, symmetry='off')
# calc = GPAW(
# 'Al_calc.gpw',
# nbands=16, # Include more bands than convergence since metallic
# fixdensity=True, # Fixate the density
# symmetry='off', # Check all points along the path
# kpts={'path': 'GXWKL', 'npoints': 60},
# convergence={'bands': 8},
# txt='Al_calc.txt'
# )
# calc.get_potential_energy() # Converge the system
# # if world.rank == 0:
calc.write(formula)
# add total energy to users tags
cmr_params['U_potential_energy'] = e
# write the information 'as in' corresponding trajectory file
# plus cmr_params into cmr file
write(cmrfile, system, cmr_params=cmr_params)
del calc
if recalculate:
# now calculate PBE energies on LDA orbitals
# molecule
formula = symbol + '2'
system, calc = restart(formula, txt=None)
ediff = calc.get_xc_difference('PBE')
cmrfile = formula + '.cmr'
# add new results to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable('U_potential_energy_PBE', data['U_potential_energy'] + ediff)
data.write(cmrfile)
del calc
# atom
formula = symbol
system, calc = restart(formula, txt=None)
is_initial = Is_initial)
if __name__ == "__main__":
#Main arguments:
e_cut = 500
nbands = -25
xc = 'PBE'
k_pts = 10
smear = 0.1
system_name = str(sys.argv[7])
if os.path.isfile('./' + system_name + '_relaxed.gpw'):
#Recover past done calculations if available
bulk_mat, calc = restart(system_name + '_relaxed.gpw', txt = None)
bulk_mat.set_calculator(calc)
else:
#Initialize new calculations
db = connect(sys.argv[8])
bulk_mat = db.get_atoms(id = sys.argv[9])
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_atoms(bulk_mat, e_cut, nbands, k_pts, smear, a, initial_magmom, 1, str(sys.argv[6]))
from gpaw import restart
from gpaw.lrtddft import LrTDDFT, photoabsorption_spectrum
atoms, calc = restart('na2_gs_unocc.gpw')
# Calculate the omega matrix
lr = LrTDDFT(calc, xc='LDA', jend=5)
# Use only 5 unoccupied states
# Save the omega matrix
lr.write('Omega_Na2.gz')
# Diagonalize the matrix
lr.diagonalize()
# Analyse 5 lowest excitations
lr.analyse(range(5))
photoabsorption_spectrum(lr, 'Na2_spectrum.dat', e_min=0.0, e_max=10)
from __future__ import print_function
from ase.io import write
from gpaw import restart
basename = 'CO'
# load binary file and get calculator
atoms, calc = restart(basename + '.gpw')
# loop over all wfs and write their cube files
nbands = calc.get_number_of_bands()
for band in range(nbands):
wf = calc.get_pseudo_wave_function(band=band)
fname = '{0}_{1}.cube'.format(basename, band)
print('writing wf', band, 'to file', fname)
write(fname, atoms, data=wf)
from ase.io import write
from gpaw import restart
basename = 'CO'
# load nc binary file and get calculator
atoms, calc = restart(basename + '.gpw')
# loop over all wfs and write their cube files
nbands = calc.get_number_of_bands()
for band in range(nbands):
wf = calc.get_pseudo_wave_function(band=band)
fname=basename + '_' + '%d' % (band) + '.cube'
print 'writing wf', band, 'to file', fname
write(fname, atoms, data=wf)
from gpaw import restart
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)
print "experimental bond length:"
print "hydrogen molecule energy: %5.2f eV" % e2
print "bondlength : %5.2f Ang" % d0
# 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
print "PBE energy minimum:"
print "hydrogen molecule energy: %5.2f eV" % e2
print "bondlength : %5.2f Ang" % d0
from gpaw import restart
# J.Phys.: Condens. Matter 18 (2006) 41-54
pw91vasp = {'NO': -0.95,
'N2': 0.00,
'O2': 0.00,
'NRu001': -0.94,
'ORu001': -2.67,
'Ru001': 0.00}
pbe = {}
pw91 = {}
for name in ['NO', 'O2', 'N2', 'Ru001', 'NRu001', 'ORu001']:
a, calc = restart(name, txt=None)
pbe[name] = a.get_potential_energy()
pw91[name] = pbe[name] + calc.get_xc_difference('PW91')
for data, text in [(pbe, 'PBE'),
(pw91, 'PW91 (non-selfconsitent)'),
(pw91vasp, 'PW91 (VASP)')]:
print ('%22s %.3f %.3f %.3f' %
(text,
data['NRu001'] - data['Ru001'] - data['N2'] / 2,
data['ORu001'] - data['Ru001'] - data['O2'] / 2,
data['NO'] - data['N2'] / 2 - data['O2'] / 2))
Eini = mol.get_potential_energy()
Iini = calc.get_number_of_iterations()
print ('%10s: %12.6f eV in %3d iterations' %
('init(cg)', Eini, Iini))
equal(Eini, Eini0, 1E-8)
equal(Iini, Iini0, 12)
calc.write('N2.gpw', mode='all')
del calc, mol
E = {}
I = {}
for esolver in esolvers:
mol, calc = restart('N2.gpw', txt=None)
if (calc.wfs.dtype!=complex or
calc.wfs.kpt_u[0].psit_nG.dtype!=complex):
raise AssertionError('ERROR: restart failed to read complex WFS')
calc.scf.reset()
calc.set(convergence={'eigenstates': 1E-10})
calc.set(eigensolver=esolver)
E[esolver]=mol.get_potential_energy()
I[esolver]=calc.get_number_of_iterations()
print ('%10s: %12.6f eV in %3d iterations' %
(esolver, E[esolver], I[esolver]))
def get_M(self, modes, log=None, q=0):
"""Calculate el-ph coupling matrix for given modes(s).
XXX:
kwarg "q=0" is an ugly hack for k-points.
There shuold be loops over q!
Note that modes must be given as a dictionary with mode
frequencies in eV and corresponding mode vectors in units
of 1/sqrt(amu), where amu = 1.6605402e-27 Kg is an atomic mass unit.
In short frequencies and mode vectors must be given in ase units.
::
d d ~
< w | -- v | w' > = < w | -- v | w'>
dP dP
_
\ ~a d . ~a
+ ) < w | p > -- /_\H < p | w' >
/_ i dP ij j
a,ij
_
\ d ~a . ~a
+ ) < w | -- p > /_\H < p | w' >
/_ dP i ij j
a,ij
_
\ ~a . d ~a
+ ) < w | p > /_\H < -- p | w' >
/_ i ij dP j
a,ij
"""
if log is None:
timer = nulltimer
elif log == '-':
timer = StepTimer(name='EPCM')
else:
timer = StepTimer(name='EPCM', out=open(log, 'w'))
modes1 = modes.copy()
#convert to atomic units
amu = 1.6605402e-27 # atomic unit mass [Kg]
me = 9.1093897e-31 # electron mass [Kg]
modes = {}
for k in modes1.keys():
modes[k / Hartree] = modes1[k] / np.sqrt(amu / me)
dvt_Gx, ddH_aspx = self.get_gradient()
from gpaw import restart
atoms, calc = restart('eq.gpw', txt=None)
spos_ac = atoms.get_scaled_positions()
if calc.wfs.S_qMM is None:
calc.initialize(atoms)
calc.initialize_positions(atoms)
wfs = calc.wfs
nao = wfs.setups.nao
bfs = wfs.basis_functions
dtype = wfs.dtype
spin = 0 # XXX
M_lii = {}
timer.write_now('Starting gradient of pseudo part')
for f, mode in modes.items():
mo = []
M_ii = np.zeros((nao, nao), dtype)
for a in self.indices:
mo.append(mode[a])
mode = np.asarray(mo).flatten()
dvtdP_G = np.dot(dvt_Gx, mode)
bfs.calculate_potential_matrix(dvtdP_G, M_ii, q=q)
tri2full(M_ii, 'L')
M_lii[f] = M_ii
timer.write_now('Finished gradient of pseudo part')
P_aqMi = calc.wfs.P_aqMi
# Add the term
# _
# \ ~a d . ~a
# ) < w | p > -- /_\H < p | w' >
# /_ i dP ij j
# a,ij
Ma_lii = {}
for f, mode in modes.items():
Ma_lii[f] = np.zeros_like(M_lii.values()[0])
timer.write_now('Starting gradient of dH^a part')
for f, mode in modes.items():
mo = []
for a in self.indices:
mo.append(mode[a])
mode = np.asarray(mo).flatten()
for a, ddH_spx in ddH_aspx.items():
ddHdP_sp = np.dot(ddH_spx, mode)
ddHdP_ii = unpack2(ddHdP_sp[spin])
Ma_lii[f] += dots(P_aqMi[a][q], ddHdP_ii, P_aqMi[a][q].T)
timer.write_now('Finished gradient of dH^a part')
timer.write_now('Starting gradient of projectors part')
spos_ac = self.atoms.get_scaled_positions() % 1.0
dP_aMix = self.get_dP_aMix(spos_ac, wfs, q, timer)
timer.write_now('Finished gradient of projectors part')
dH_asp = pickle.load(open('v.eq.pckl'))[1]
Mb_lii = {}
for f, mode in modes.items():
Mb_lii[f] = np.zeros_like(M_lii.values()[0])
for f, mode in modes.items():
for a, dP_Mix in dP_aMix.items():
dPdP_Mi = np.dot(dP_Mix, mode[a])
dH_ii = unpack2(dH_asp[a][spin])
dPdP_MM = dots(dPdP_Mi, dH_ii, P_aqMi[a][q].T)
Mb_lii[f] -= dPdP_MM + dPdP_MM.T
# XXX The minus sign here is quite subtle.
# It is related to how the derivative of projector
# functions in GPAW is calculated.
# More thorough explanations, anyone...?
# Units of M_lii are Hartree/(Bohr * sqrt(m_e))
for mode in M_lii.keys():
M_lii[mode] += Ma_lii[mode] + Mb_lii[mode]
# conversion to eV. The prefactor 1 / sqrt(hb^2 / 2 * hb * f)
# has units Bohr * sqrt(me)
M_lii_1 = M_lii.copy()
M_lii = {}
for f in M_lii_1.keys():
M_lii[f * Hartree] = M_lii_1[f] * Hartree / np.sqrt(2 * f)
return M_lii
from ase.io import write
from gpaw import restart
slab, calc = restart('ontop.gpw', txt=None)
AuAl = slab.copy()
AuAl_density = calc.get_pseudo_density()
# Remove gold atom and do a clean slab calculation:
del slab[4]
slab.get_potential_energy()
Al_density = calc.get_pseudo_density()
# Remove Al atoms and do a calculation for Au only:
slab, calc = restart('ontop.gpw', txt=None)
del slab[:4]
calc.set(kpts=None)
slab.get_potential_energy()
Au_density = calc.get_pseudo_density()
diff = AuAl_density - Au_density - Al_density
write('diff.cube', AuAl, data=diff)
write('diff.plt', AuAl, data=diff)
import numpy as np
from gpaw import restart
slab, calc = restart("ontop.gpw", txt=None)
AuAl_density = calc.get_pseudo_density()
# Remove gold atom and do a clean slab calculation:
del slab[-1]
slab.get_potential_energy()
Al_density = calc.get_pseudo_density()
# Remove Al atoms and do a calculation for Au only:
slab, calc = restart("ontop.gpw", txt=None)
del slab[:-1]
calc.set(kpts=None)
slab.get_potential_energy()
Au_density = calc.get_pseudo_density()
diff = AuAl_density - Au_density - Al_density
np.save("densitydiff.npy", diff)
eps = g.e_j[-1]
world.barrier()
a = 10
Ne = Atoms([Atom(atom, (0, 0, 0))], cell=(a, a, a), pbc=False)
Ne.center()
calc = GPAW(nbands=10, h=0.2, xc=xcname)
Ne.set_calculator(calc)
e = Ne.get_potential_energy()
response = calc.hamiltonian.xc.xcs["RESPONSE"]
response.calculate_delta_xc()
KS, dxc = response.calculate_delta_xc_perturbation()
if xcname == "GLLB":
equal(KS + dxc, 24.71, 1e-1)
else:
equal(KS + dxc, 27.70, 1e-2)
eps3d = calc.wfs.kpt_u[0].eps_n[3]
calc.write("Ne_temp.gpw")
atoms, calc = restart("Ne_temp.gpw")
KS2, dxc2 = response.calculate_delta_xc_perturbation()
equal(KS, KS2, 1e-5)
equal(dxc2, dxc, 1e-5)
# Hardness of Ne 24.71eV by GLLB+Dxc, experimental I-A = I = 21.56eV
if world.rank == 0:
equal(eps, eps3d, 1e-3)
if xcname == "GLLB":
equal(24.71, KS2 + dxc2, 1e-1)
kpts=(3, 1, 1),
# basis='dzp',
txt="Na4_fd.txt",
)
atoms.set_calculator(calc)
etot_fd = atoms.get_potential_energy()
niter_fd = calc.get_number_of_iterations()
print "Etot:", etot_fd, "eV in fd-mode"
calc.write("Na4_fd.gpw")
del atoms, calc
equal(etot_fd, -1.99055, energy_tolerance)
equal(niter_fd, 17, niter_tolerance)
if os.path.isfile("Na4_fd.gpw"):
# LCAO calculation based on grid kpts calculation
atoms, calc = restart(
"Na4_fd.gpw",
# basis='dzp',
mode="lcao",
txt="Na4_lcao.txt",
)
etot_lcao = atoms.get_potential_energy()
niter_lcao = calc.get_number_of_iterations()
print "Etot:", etot_lcao, "eV in lcao-mode"
calc.write("Na4_lcao.gpw")
del atoms, calc
equal(etot_lcao, -1.9616, energy_tolerance)
equal(niter_lcao, 6, niter_tolerance)
from ase import Atoms
from gpaw import GPAW, restart
from gpaw.xc.sic import SIC
from gpaw.test import equal
a = 6.0
atom = Atoms('H', magmoms=[1.0], cell=(a, a, a))
molecule = Atoms('H2', positions=[(0, 0, 0), (0, 0, 0.737)], cell=(a, a, a))
atom.center()
molecule.center()
calc = GPAW(xc='LDA-PZ-SIC',
eigensolver='rmm-diis',
txt='h2.sic.txt',
setups='hgh')
atom.set_calculator(calc)
e1 = atom.get_potential_energy()
molecule.set_calculator(calc)
e2 = molecule.get_potential_energy()
F_ac = molecule.get_forces()
de = 2 * e1 - e2
#equal(de, 4.5, 0.1)
# Test forces ...
calc.write('H2.gpw', mode='all')
atoms, calc = restart('H2.gpw')
e2b = atoms.get_potential_energy()
equal(e2, e2b, 0.0001)
if world.rank == 0:
basis = BasisMaker('Li', 'szp').generate(1, 1)
basis.write_xml()
world.barrier()
if setup_paths[0] != '.':
setup_paths.insert(0, '.')
if 1:
a = 2.7
bulk = Atoms('Li', pbc=True, cell=[a, a, a])
calc = GPAW(gpts=(8, 8, 8), kpts=(4, 4, 4), mode='lcao', basis='szp')
bulk.set_calculator(calc)
e = bulk.get_potential_energy()
niter = calc.get_number_of_iterations()
calc.write('temp.gpw')
atoms, calc = restart('temp.gpw')
H_skMM, S_kMM = get_lcao_hamiltonian(calc)
eigs = calc.get_eigenvalues(kpt=2)
if world.rank == 0:
eigs2 = np.linalg.eigvals(np.linalg.solve(S_kMM[2], H_skMM[0, 2])).real
eigs2.sort()
assert abs(sum(eigs - eigs2)) < 1e-8
energy_tolerance = 0.00003
niter_tolerance = 0
equal(e, -1.82847, energy_tolerance)
equal(niter, 5, niter_tolerance)
from ase import Atoms
from ase.io import write
from ase.visualize import view
from gpaw import restart
from gpaw.wannier import Wannier
atoms, calc = restart('benzene.gpw')
h**o = calc.get_pseudo_wave_function(band=14)
write('h**o.cube', atoms, data=h**o)
write('h**o.plt', atoms, data=h**o)
# Initialize the Wannier class
w = Wannier(calc)
w.localize()
centers = w.get_centers()
view(atoms + Atoms(symbols='X15', positions=centers))
# Find the index of the center with the lowest y-coordinate:
nsigma = centers[:, 1].argmin()
sigma = w.get_function(calc, nsigma)
write('benzene.xyz', atoms)
write('sigma.cube', atoms, data=sigma)
write('sigma.plt', atoms, data=sigma)
xc='PBE',
nbands=-2,
kpts=(8, 8, 8),
occupations=FermiDirac(0.1),
txt='cubulk_dos.txt')
copper.set_calculator(calc)
copper.get_potential_energy()
calc.write('cu.gpw', mode='all')
from ase import *
from ase.dft.dos import DOS
from gpaw import GPAW, restart
import pylab as p
slab, calc = restart('cu.gpw')
e, dos = calc.get_dos(spin=0, npts=2001, width=0.1)
e_f = calc.get_fermi_level()
#db = connect('cu_dos.db')
#db.write(slab, number_of_atoms = 1)
#
#for obj in db.select(number_of_atoms = 1):
# print(obj)
bs = calc.band_structure()
bs.plot(filename='bandstructure.png', show=True, emax=10.0)
plt.figure(0)
plt.plot(dos, e)
plt.plot([0, 5], e_f * np.ones(2))
# Normal ground state calculation
atoms = bulk('Si')
calc = GPAW(h=0.24, kpts=(4,4,4),
convergence={'eigenstates' : 1e-4, 'density' : 1e-3},
)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# "Bandstructure" calculation (only Gamma point here)
kpts = np.array(((0, 0, 0),))
calc.set(fixdensity=True, kpts=kpts)
atoms.get_potential_energy()
calc.write('Si_gamma.gpw', mode='all')
# Analyse symmetries of wave functions
atoms, calc = restart('Si_gamma.gpw', txt=None)
# Find symmetries (in Gamma-point calculations calculator does not
# use symmetry)
sym = Symmetry(calc.wfs.setups.id_a, atoms.cell, atoms.pbc)
sym.analyze(atoms.get_scaled_positions())
def find_classes(op_all_scc):
# Find classes of group represented by matrices op_all_scc
# and return representative operations
op_scc = [op_all_scc[0]]
for op1 in op_all_scc[1:]:
new_class = True
for op2 in op_all_scc:
op_tmp = (np.dot(np.dot(op2, op1), np.linalg.inv(op2).astype(int)))
# Check whether operation op1 belongs to existing class
def get_M(self, modes, log=None, q=0):
"""Calculate el-ph coupling matrix for given modes(s).
XXX:
kwarg "q=0" is an ugly hack for k-points.
There shuold be loops over q!
Note that modes must be given as a dictionary with mode
frequencies in eV and corresponding mode vectors in units
of 1/sqrt(amu), where amu = 1.6605402e-27 Kg is an atomic mass unit.
In short frequencies and mode vectors must be given in ase units.
::
d d ~
< w | -- v | w' > = < w | -- v | w'>
dP dP
_
\ ~a d . ~a
+ ) < w | p > -- /_\H < p | w' >
/_ i dP ij j
a,ij
_
\ d ~a . ~a
+ ) < w | -- p > /_\H < p | w' >
/_ dP i ij j
a,ij
_
\ ~a . d ~a
+ ) < w | p > /_\H < -- p | w' >
/_ i ij dP j
a,ij
"""
if log is None:
timer = nulltimer
elif log == '-':
timer = StepTimer(name='EPCM')
else:
timer = StepTimer(name='EPCM', out=open(log, 'w'))
modes1 = modes.copy()
#convert to atomic units
amu = 1.6605402e-27 # atomic unit mass [Kg]
me = 9.1093897e-31 # electron mass [Kg]
modes = {}
for k in modes1.keys():
modes[k / Hartree] = modes1[k] / np.sqrt(amu / me)
dvt_Gx, ddH_aspx = self.get_gradient()
from gpaw import restart
atoms, calc = restart('eq.gpw', txt=None)
if calc.wfs.S_qMM is None:
calc.initialize(atoms)
calc.initialize_positions(atoms)
wfs = calc.wfs
nao = wfs.setups.nao
bfs = wfs.basis_functions
dtype = wfs.dtype
spin = 0 # XXX
M_lii = {}
timer.write_now('Starting gradient of pseudo part')
for f, mode in modes.items():
mo = []
M_ii = np.zeros((nao, nao), dtype)
for a in self.indices:
mo.append(mode[a])
mode = np.asarray(mo).flatten()
dvtdP_G = np.dot(dvt_Gx, mode)
bfs.calculate_potential_matrix(dvtdP_G, M_ii, q=q)
tri2full(M_ii, 'L')
M_lii[f] = M_ii
timer.write_now('Finished gradient of pseudo part')
P_aqMi = calc.wfs.P_aqMi
# Add the term
# _
# \ ~a d . ~a
# ) < w | p > -- /_\H < p | w' >
# /_ i dP ij j
# a,ij
Ma_lii = {}
for f, mode in modes.items():
Ma_lii[f] = np.zeros_like(M_lii.values()[0])
timer.write_now('Starting gradient of dH^a part')
for f, mode in modes.items():
mo = []
for a in self.indices:
mo.append(mode[a])
mode = np.asarray(mo).flatten()
for a, ddH_spx in ddH_aspx.items():
ddHdP_sp = np.dot(ddH_spx, mode)
ddHdP_ii = unpack2(ddHdP_sp[spin])
Ma_lii[f] += dots(P_aqMi[a][q], ddHdP_ii, P_aqMi[a][q].T)
timer.write_now('Finished gradient of dH^a part')
timer.write_now('Starting gradient of projectors part')
dP_aMix = self.get_dP_aMix(calc.spos_ac, wfs, q, timer)
timer.write_now('Finished gradient of projectors part')
dH_asp = pickle.load(open('v.eq.pckl', 'rb'))[1]
Mb_lii = {}
for f, mode in modes.items():
Mb_lii[f] = np.zeros_like(M_lii.values()[0])
for f, mode in modes.items():
for a, dP_Mix in dP_aMix.items():
dPdP_Mi = np.dot(dP_Mix, mode[a])
dH_ii = unpack2(dH_asp[a][spin])
dPdP_MM = dots(dPdP_Mi, dH_ii, P_aqMi[a][q].T)
Mb_lii[f] -= dPdP_MM + dPdP_MM.T
# XXX The minus sign here is quite subtle.
# It is related to how the derivative of projector
# functions in GPAW is calculated.
# More thorough explanations, anyone...?
# Units of M_lii are Hartree/(Bohr * sqrt(m_e))
for mode in M_lii.keys():
M_lii[mode] += Ma_lii[mode] + Mb_lii[mode]
# conversion to eV. The prefactor 1 / sqrt(hb^2 / 2 * hb * f)
# has units Bohr * sqrt(me)
M_lii_1 = M_lii.copy()
M_lii = {}
for f in M_lii_1.keys():
M_lii[f * Hartree] = M_lii_1[f] * Hartree / np.sqrt(2 * f)
return M_lii
from ase import Atoms, Atom
from gpaw import GPAW, restart
atoms, calc = restart('H2_gs.gpw')
atoms.center(vacuum=6.0)
calc.set(nbands=20)
calc.set(txt='H2.out')
atoms.set_calculator(calc)
e2 = atoms.get_potential_energy()
calc.write('H2.gpw')
lr = LrTDDFT(calc, xc="LDA")
lr.write("Omega_H2.gz")
photoabsorption_spectrum(lr, 'H2_spectrum.dat', e_min=0.0, e_max=10)
mol.center(vacuum=3.0)
mol.set_calculator(calc)
Eini = mol.get_potential_energy()
Iini = calc.get_number_of_iterations()
print ("%10s: %12.6f eV in %3d iterations" % ("init(cg)", Eini, Iini))
equal(Eini, Eini0, 1e-8)
calc.write("N2.gpw", mode="all")
del calc, mol
E = {}
I = {}
for esolver in esolvers:
mol, calc = restart("N2.gpw", txt=None)
if calc.wfs.dtype != complex or calc.wfs.kpt_u[0].psit_nG.dtype != complex:
raise AssertionError("ERROR: restart failed to read complex WFS")
calc.scf.reset()
calc.set(convergence={"eigenstates": 3.5e-9})
calc.set(eigensolver=esolver)
E[esolver] = mol.get_potential_energy()
I[esolver] = calc.get_number_of_iterations()
print ("%10s: %12.6f eV in %3d iterations" % (esolver, E[esolver], I[esolver]))
for esolver in esolvers:
print esolver
from __future__ import print_function
from sys import argv
import matplotlib.pyplot as plt
from ase.dft import STM
from gpaw import restart
filename = argv[1]
z0 = 8
bias = 1.0
atoms, calc = restart(filename, txt=None)
stm = STM(atoms, symmetries=[0, 1, 2])
c = stm.get_averaged_current(bias, z0)
print('Average current at z=%f: %f' % (z0, c))
# Get 2d array of constant current heights:
x, y, h = stm.scan(bias, c)
print('Min: %.2f Ang, Max: %.2f Ang' % (h.min(), h.max()))
plt.contourf(x, y, h, 40)
plt.hot()
plt.colorbar()
plt.show()
from ase.structure import molecule
from ase.io import write
from ase.parallel import parprint
from gpaw import GPAW, restart
from gpaw.elf import ELF
from gpaw.test import equal
from gpaw.mpi import rank, world
atoms = molecule('CO')
atoms.center(2.0)
txt=sys.stdout
txt=None
try:
atoms, calc = restart('CO.gpw', txt=txt)
energy = atoms.get_potential_energy()
except:
calc = GPAW(h=0.24, txt=txt)
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.write('CO.gpw', 'all')
elf = ELF(calc)
elf.update()
elf_G = elf.get_electronic_localization_function(gridrefinement=1)
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
nt_G = calc.density.nt_sG[0]
taut_G = elf.taut_sG[0]
nt_grad2_G = elf.nt_grad2_sG[0]
poissonsolver=PoissonSolver(nn="M"),
occupations=FermiDirac(width=0.01),
kpts=(3, 3, 3),
convergence={"eigenstates": 9.2e-11, "bands": 8},
xc=xc,
eigensolver="cg",
)
bulk.set_calculator(calc)
e[xc] = {"direct": bulk.get_potential_energy()}
niter[xc] = {"direct": calc.get_number_of_iterations()}
print(calc.get_ibz_k_points())
old_eigs = calc.get_eigenvalues(kpt=3)
calc.write("Si_gs.gpw")
del bulk
del calc
bulk, calc = restart("Si_gs.gpw", fixdensity=True, kpts=[[0, 0, 0], [1.0 / 3, 1.0 / 3, 1.0 / 3]])
e[xc] = {"restart": bulk.get_potential_energy()}
niter[xc] = {"restart": calc.get_number_of_iterations()}
if world.rank == 0:
os.remove("Si_gs.gpw")
diff = calc.get_eigenvalues(kpt=1)[:6] - old_eigs[:6]
if world.rank == 0:
print("occ. eig. diff.", diff)
error = max(abs(diff))
assert error < 5e-6
for mode in e[xc].keys():
equal(e[xc][mode], e_ref[xc][mode], energy_tolerance)
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()
from ase import *
from ase.dft import Wannier
from gpaw import restart
atoms, calc = restart('poly.gpw', txt=None)
# Make wannier functions using (one) extra degree of freedom
wan = Wannier(nwannier=6, calc=calc, fixedenergy=1.5)
wan.localize()
wan.save('poly.pickle')
wan.translate_all_to_cell((2, 0, 0))
for i in range(wan.nwannier):
wan.write_cube(i, 'polyacetylene_%i.cube' % i)
# Print Kohn-Sham bandstructure
ef = calc.get_fermi_level()
f = open('KSbands.txt', 'w')
for k, kpt_c in enumerate(calc.get_ibz_k_points()):
for eps in calc.get_eigenvalues(kpt=k):
print >> f, kpt_c[0], eps - ef
# Print Wannier bandstructure
f = open('WANbands.txt', 'w')
for k in np.linspace(-.5, .5, 100):
for eps in np.linalg.eigvalsh(wan.get_hamiltonian_kpoint([k, 0, 0])).real:
print >> f, k, eps - ef
xc=xc,
nbands=8,
eigensolver=eigensolver,
parallel={'band': band})
atoms.set_calculator(calc)
atoms.get_potential_energy()
# And calculate the discontinuity potential with accurate band gap
response = calc.hamiltonian.xc.xcs['RESPONSE']
response.calculate_delta_xc(homolumo=homolumo / Ha)
calc.write('CGLLBSC.gpw')
# Redo the band structure calculation
atoms, calc = restart('CGLLBSC.gpw',
kpts={
'path': 'GX',
'npoints': 12
},
fixdensity=True,
symmetry='off',
convergence=dict(bands=8))
atoms.get_potential_energy()
response = calc.hamiltonian.xc.xcs['RESPONSE']
KS, dxc = response.calculate_delta_xc_perturbation()
KSb.append(KS)
dxcb.append(dxc)
assert abs(KS + dxc - 5.41) < 0.10
# M. Kuisma et. al, Phys. Rev. B 82, 115106,
# QP gap for C, 5.41eV, expt. 5.48eV
assert abs(KSb[0] - KSb[1]) < 1e-6
assert abs(KSb[0] - KSb[2]) < 1e-6
assert abs(dxcb[0] - dxcb[1]) < 1e-6
convergence={
'eigenstates': 1e-4,
'density': 1e-3
},
)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# "Bandstructure" calculation (only Gamma point here)
kpts = np.array(((0, 0, 0), ))
calc.set(fixdensity=True, kpts=kpts)
atoms.get_potential_energy()
calc.write('Si_gamma.gpw', mode='all')
# Analyse symmetries of wave functions
atoms, calc = restart('Si_gamma.gpw', txt=None)
# Find symmetries (in Gamma-point calculations calculator does not
# use symmetry)
sym = Symmetry(calc.wfs.setups.id_a, atoms.cell, atoms.pbc)
sym.analyze(atoms.get_scaled_positions())
def find_classes(op_all_scc):
# Find classes of group represented by matrices op_all_scc
# and return representative operations
op_scc = [op_all_scc[0]]
for op1 in op_all_scc[1:]:
new_class = True
for op2 in op_all_scc:
op_tmp = (np.dot(np.dot(op2, op1), np.linalg.inv(op2).astype(int)))
h=0.18,
xc=xcname,
basis='dzp',
mixer=Mixer(0.6))
Ne.set_calculator(calc)
e = Ne.get_potential_energy()
response = calc.hamiltonian.xc.xcs['RESPONSE']
response.calculate_delta_xc()
KS, dxc = response.calculate_delta_xc_perturbation()
if xcname == 'GLLB':
equal(KS + dxc, 24.89, 1.5e-1)
else:
equal(KS + dxc, 27.70, 6.0e-2)
eps3d = calc.wfs.kpt_u[0].eps_n[3]
calc.write('Ne_temp.gpw')
atoms, calc = restart('Ne_temp.gpw')
KS2, dxc2 = response.calculate_delta_xc_perturbation()
equal(KS, KS2, 1e-5)
equal(dxc2, dxc, 1e-5)
# Hardness of Ne 24.71eV by GLLB+Dxc, experimental I-A = I = 21.56eV
#
# Not sure where 24.71 comes from, but with better grid and better
# stencil, result becomes 24.89. --askhl
if world.rank == 0:
equal(eps, eps3d, 1e-3)
if xcname == 'GLLB':
equal(24.89, KS2 + dxc2, 1.2e-1)
atoms = bulk('Fe', 'bcc', a=a)
atoms.set_initial_magnetic_moments([2.2,])
calc = GPAW(h=0.20,
eigensolver=RMM_DIIS(),
mixer=MixerSum(0.1,3),
nbands=6,
kpts=(4,4,4),
parallel={'band' : 2, 'domain' : (2,1,1)},
maxiter=4)
atoms.set_calculator(calc)
try:
atoms.get_potential_energy()
except ConvergenceError:
pass
for mode in modes:
calc.write('tmp.%s' % mode, mode='all')
# Continue calculation for few iterations
for mode in modes:
atoms, calc = restart('tmp.%s' % mode,
eigensolver=RMM_DIIS(),
mixer=MixerSum(0.1,3),
parallel={'band' : 2, 'domain' : (1,1,2)},
maxiter=4)
try:
atoms.get_potential_energy()
except ConvergenceError:
pass
e = calc.hamiltonian.Etot
equal(e, -0.372602008394, 0.000001)
calc = GPAW(h=0.30, nbands=3, setups={'Na': '1'}, convergence=conv)
atoms.set_calculator(calc)
e0 = atoms.get_potential_energy()
niter0 = calc.get_number_of_iterations()
f0 = atoms.get_forces()
m0 = atoms.get_magnetic_moments()
eig00 = calc.get_eigenvalues(spin=0)
eig01 = calc.get_eigenvalues(spin=1)
# Write the restart file(s)
for mode in modes:
calc.write('tmp.%s' % mode)
del atoms, calc
# Try restarting from all the files
for mode in modes:
atoms, calc = restart('tmp.%s' % mode)
# Force new calculation
calc.scf.converged = False
e1 = atoms.get_potential_energy()
f1 = atoms.get_forces()
m1 = atoms.get_magnetic_moments()
eig10 = calc.get_eigenvalues(spin=0)
eig11 = calc.get_eigenvalues(spin=1)
print(e0, e1)
equal(e0, e1, 2e-3)
print(f0, f1)
for ff0, ff1 in zip(f0, f1):
err = np.linalg.norm(ff0 - ff1)
# for forces we use larger tolerance
equal(err, 0.0, 4e-2)
print(m0, m1)
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()
from gpaw import restart
from ase.dft import Wannier
atoms, calc = restart('benzene.gpw', txt=None)
# Make wannier functions of occupied space only
wan = Wannier(nwannier=15, calc=calc)
wan.localize()
for i in range(wan.nwannier):
wan.write_cube(i, 'benzene15_%i.cube' % i)
# Make wannier functions using (three) extra degrees of freedom.
wan = Wannier(nwannier=18, calc=calc, fixedstates=15)
wan.localize()
wan.save('wan18.pickle')
for i in range(wan.nwannier):
wan.write_cube(i, 'benzene18_%i.cube' % i)
convergence=conv)
atoms.set_calculator(calc)
e0 = atoms.get_potential_energy()
niter0 = calc.get_number_of_iterations()
f0 = atoms.get_forces()
m0 = atoms.get_magnetic_moments()
eig00 = calc.get_eigenvalues(spin=0)
eig01 = calc.get_eigenvalues(spin=1)
# Write the restart file(s)
for mode in modes:
calc.write('tmp.%s' % mode)
del atoms, calc
# Try restarting from all the files
for mode in modes:
atoms, calc = restart('tmp.%s' % mode)
# Force new calculation
calc.scf.converged = False
e1 = atoms.get_potential_energy()
f1 = atoms.get_forces()
m1 = atoms.get_magnetic_moments()
eig10 = calc.get_eigenvalues(spin=0)
eig11 = calc.get_eigenvalues(spin=1)
print e0, e1
equal(e0, e1, 2e-3)
print f0, f1
for ff0, ff1 in zip(f0, f1):
err = np.linalg.norm(ff0-ff1)
# for forces we use larger tolerance
equal(err, 0.0, 4e-2)
print m0, m1
from ase.structure import molecule
from ase.io import write
from ase.parallel import parprint
from gpaw import GPAW, restart
from gpaw.elf import ELF
from gpaw.test import equal
from gpaw.mpi import rank, world
atoms = molecule("CO")
atoms.center(2.0)
txt = sys.stdout
txt = None
try:
atoms, calc = restart("CO.gpw", txt=txt)
energy = atoms.get_potential_energy()
except:
calc = GPAW(h=0.24, txt=txt)
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.write("CO.gpw", "all")
elf = ELF(calc)
elf.update()
elf_G = elf.get_electronic_localization_function(gridrefinement=1)
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
nt_G = calc.density.nt_sG[0]
taut_G = elf.taut_sG[0]
nt_grad2_G = elf.nt_grad2_sG[0]
'mode': mode,
'h': h,
}
cmrfile = formula + '.cmr'
system1 = molecule(formula)
system1.center(vacuum=vacuum)
# first calculation: LDA lcao
calc = GPAW(mode=mode, xc=xc, h=h, txt=None)
system1.set_calculator(calc)
e = system1.get_potential_energy()
calc.write(formula)
# read gpw file
system2, calc2 = restart(formula, txt=None)
# write the information 'as in' gpw file into db file
# (called *db to avoid conflict with the *cmr file below)
if 1: # not used in this example
calc2.write(formula + '.db', cmr_params=cmr_params)
# write the information 'as in' corresponding trajectory file into cmr file
write(cmrfile, system2, cmr_params=cmr_params)
# add the xc tag to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable('xc', xc)
data.write(cmrfile)
# perform PBE calculation on LDA density
ediff = calc2.get_xc_difference('PBE')
#!/usr/bin/env python
from ase import Atoms
from gpaw import GPAW, restart
from gpaw.test import equal
from gpaw.utilities.kspot import CoreEigenvalues
a = 7.0
calc = GPAW(h=0.1)
system = Atoms('Ne', calculator=calc)
system.center(vacuum=a / 2)
e0 = system.get_potential_energy()
niter0 = calc.get_number_of_iterations()
calc.write('Ne.gpw')
del calc, system
atoms, calc = restart('Ne.gpw')
calc.restore_state()
e_j = CoreEigenvalues(calc).get_core_eigenvalues(0)
assert abs(e_j[0] - (-30.344066)) * 27.21 < 0.1 # Error smaller than 0.1 eV
energy_tolerance = 0.0004
equal(e0, -0.0107707223, energy_tolerance)
pbc=True, cell=(a, a, a))
n = 20
calc = GPAW(gpts=(n, n, n),
nbands=8*3,
occupations=FermiDirac(width=0.01),
verbose=1,
kpts=(1, 1, 1))
bulk.set_calculator(calc)
e1 = bulk.get_potential_energy()
niter1 = calc.get_number_of_iterations()
eigs = calc.get_eigenvalues(kpt=0)
calc.write('temp.gpw')
del bulk
del calc
bulk, calc = restart('temp.gpw', fixdensity=True)
#calc.scf.reset()
e2 = bulk.get_potential_energy()
try: # number of iterations needed in restart
niter2 = calc.get_number_of_iterations()
except: pass
eigs2 = calc.get_eigenvalues(kpt=0)
print 'Orginal', eigs
print 'Fixdensity', eigs2
print 'Difference', eigs2-eigs
assert np.fabs(eigs2 - eigs)[:-1].max() < 3e-5
energy_tolerance = 0.0005
niter_tolerance = 0
equal(e1, -36.7664, energy_tolerance)