def check_db(db, params):
if debug:
print "%10s %10s %10s ( %10s )" \
% ( "bond", "value", "reference", "error" )
for mol, values in db.iteritems():
#if mol == 'H2O':
if 1:
if debug:
print mol
a = molecule(mol)
a.center(vacuum=10.0)
a.set_pbc(False)
#print a.get_chemical_symbols()
calc = Hotbit(
charge_density = 'Slater',
SCC = True,
width = 1e-6,
txt = 'mio.out',
**params)
a.set_calculator(calc)
#calc.ia.plot_table('H', 'H')
#calc.rep.get_repulsion('H', 'H').plot()
OPT(a, logfile='opt.log').run(fmax=FMAX)
#print a.get_charges()
for name, ( ( i1, i2 ), refvalue ) in values.iteritems():
value = a.get_distance(i1, i2)
if debug:
print '%10s %10.3f %10.3f ( %10.3f )' % \
( name, value, refvalue, abs(value-refvalue) )
assert abs(value-refvalue) < 0.01
import numpy as np
import ase
from ase.units import Hartree
from hotbit import Hotbit
###
dir1 = '/Users/pas/Sourcen/hotbit/param/'
#dir2 = '/Users/pas/Sourcen/hotbit/param/'
dir2 = '/Users/pas/Sourcen/mdcore/data/slater_koster_tables/Frauenheim/download-2009-10-23/mio-0-1/'
###
a = ase.molecule('C6H6')
a.center(vacuum=6.0)
c = Hotbit(elements={
'H': dir2 + 'H-H.skf',
'C': dir2 + 'C-C.skf'
},
tables={
'HH': dir2 + 'H-H.skf',
'CH': dir2 + 'C-H.skf',
'CC': dir2 + 'C-C.skf'
},
SCC=False)
a.set_calculator(c)
ase.FIRE(a).run(fmax=0.01)
import numpy as np
import ase
from ase.units import Hartree
from hotbit import Hotbit
###
dir1 = '/Users/pas/Sourcen/hotbit/param/'
#dir2 = '/Users/pas/Sourcen/hotbit/param/'
dir2 = '/Users/pas/Sourcen/mdcore/data/slater_koster_tables/Frauenheim/download-2009-10-23/mio-0-1/'
###
a = ase.molecule('C6H6')
a.center(vacuum=6.0)
c = Hotbit(
elements = {
'H': dir2 + 'H-H.skf',
'C': dir2 + 'C-C.skf'
},
tables = {
'HH': dir2 + 'H-H.skf',
'CH': dir2 + 'C-H.skf',
'CC': dir2 + 'C-C.skf'
},
SCC = False
)
a.set_calculator(c)
import os
import numpy as np
from time import time
from ase import molecule
from gpaw import GPAW
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs
if not os.path.isfile('C6H6.gpw'):
atoms = molecule('C6H6')
atoms.center(vacuum=2.5)
calc = GPAW(h=0.2, basis='szp', width=0.05, convergence={'bands': 17})
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C6H6.gpw', 'all')
calc = GPAW('C6H6.gpw', txt=None, basis='sz')
ibzk_kc = calc.wfs.ibzk_kc
nk = len(ibzk_kc)
Ef = calc.get_fermi_level()
eps_kn = np.asarray([calc.get_eigenvalues(k) for k in range(nk)])
eps_kn -= Ef
V_knM, H_kMM, S_kMM, P_aqMi = get_phs(calc, s=0)
H_kMM -= Ef * S_kMM
pwf = ProjectedWannierFunctions(V_knM,
h_lcao=H_kMM,
s_lcao=S_kMM,
eigenvalues=eps_kn,
import os
import numpy as np
from time import time
from ase import molecule
from gpaw import GPAW
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs
if not os.path.isfile('C6H6.gpw'):
atoms = molecule('C6H6')
atoms.center(vacuum=2.5)
calc = GPAW(h=0.2, basis='szp', width=0.05, convergence={'bands':17})
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C6H6.gpw', 'all')
calc = GPAW('C6H6.gpw', txt=None, basis='sz')
ibzk_kc = calc.wfs.ibzk_kc
nk = len(ibzk_kc)
Ef = calc.get_fermi_level()
eps_kn = np.asarray([calc.get_eigenvalues(k) for k in range(nk)])
eps_kn -= Ef
V_knM, H_kMM, S_kMM, P_aqMi = get_phs(calc, s=0)
H_kMM -= Ef * S_kMM
pwf = ProjectedWannierFunctions(V_knM,
h_lcao=H_kMM,
s_lcao=S_kMM,
eigenvalues=eps_kn,
def run_molecule(adsorbate, geometry, xc, code):
parameters = initialize_parameters(code, 0.01, h)
parameters['xc'] = xc
molecules = {
'None': ('NO', 8),
'N': ('N2', 8),
'O': ('O2', 8),
}
for name, nbands in [molecules[adsorbate]]:
if code != 'elk':
parameters['nbands'] = nbands
if geometry == 'fix':
mol = read_trajectory(code + '_' + name + '.traj')
else:
mol = molecule(name)
mol.center(vacuum=3.0 + add_vacuum)
if name == 'NO':
mol.translate((0, 0.1, 0))
#
if code == 'gpaw':
from gpaw import GPAW as Calculator
from gpaw.mpi import rank
parameters['txt'] = code + '_' + name + '.txt'
from gpaw.mixer import Mixer, MixerSum
#if name == 'N2':
# parameters['mixer'] = Mixer(beta=0.1, nmaxold=5, metric='new', weight=100.0)
#else:
# #parameters['eigensolver'] = 'cg'
# parameters['mixer'] = MixerSum(beta=0.2, nmaxold=5, metric='new', weight=100.0)
if code == 'dacapo':
from ase.calculators.dacapo import Dacapo as Calculator
rank = 0
parameters['txtout'] = code + '_' + name + '.txt'
if code == 'abinit':
from ase.calculators.abinit import Abinit as Calculator
rank = 0
parameters['label'] = code + '_' + name
if code == 'elk':
from ase.calculators.elk import ELK as Calculator
rank = 0
elk_dir = 'elk_' + str(parameters['rgkmax'])
conv_param = 1.0
parameters['dir'] = elk_dir + '_' + name
#
calc = Calculator(**parameters)
#
mol.set_calculator(calc)
try:
if geometry == 'fix':
mol.get_potential_energy()
traj = PickleTrajectory(code + '_' + name + '.traj', mode='w')
traj.write(mol)
else:
opt = QuasiNewton(mol,
logfile=code + '_' + name + '.qn',
trajectory=code + '_' + name + '.traj')
opt.run(fmax=fmax)
except:
raise
