def test_combos():
(atoms, constr, bondcombo_def, target_bondcombo, anglecombo_def,
target_anglecombo, dihedralcombo_def,
target_dihedralcombo) = setup_combos()
ref_bondcombo = get_bondcombo(atoms, bondcombo_def)
ref_anglecombo = get_anglecombo(atoms, anglecombo_def)
ref_dihedralcombo = get_dihedralcombo(atoms, dihedralcombo_def)
atoms.calc = EMT()
atoms.set_constraint(constr)
opt = BFGS(atoms, trajectory='opt.traj', logfile='opt.log')
opt.run(fmax=0.01)
new_bondcombo = get_bondcombo(atoms, bondcombo_def)
new_anglecombo = get_anglecombo(atoms, anglecombo_def)
new_dihedralcombo = get_dihedralcombo(atoms, dihedralcombo_def)
err_bondcombo = new_bondcombo - ref_bondcombo
err_anglecombo = new_anglecombo - ref_anglecombo
err_dihedralcombo = new_dihedralcombo - ref_dihedralcombo
print('error in bondcombo:', repr(err_bondcombo))
print('error in anglecombo:', repr(err_anglecombo))
print('error in dihedralcombo:', repr(err_dihedralcombo))
for err in [err_bondcombo, err_anglecombo, err_dihedralcombo]:
assert err < 1e-12
def test_combos():
# XXX https://gitlab.com/ase/ase/-/issues/868
(atoms, constr, bondcombo_def, target_bondcombo, anglecombo_def,
target_anglecombo, dihedralcombo_def,
target_dihedralcombo) = setup_combos()
ref_bondcombo = get_bondcombo(atoms, bondcombo_def)
ref_anglecombo = get_anglecombo(atoms, anglecombo_def)
ref_dihedralcombo = get_dihedralcombo(atoms, dihedralcombo_def)
atoms.calc = EMT()
atoms.set_constraint(constr)
opt = BFGS(atoms)
opt.run(fmax=0.01)
new_bondcombo = get_bondcombo(atoms, bondcombo_def)
new_anglecombo = get_anglecombo(atoms, anglecombo_def)
new_dihedralcombo = get_dihedralcombo(atoms, dihedralcombo_def)
err_bondcombo = new_bondcombo - ref_bondcombo
err_anglecombo = new_anglecombo - ref_anglecombo
err_dihedralcombo = new_dihedralcombo - ref_dihedralcombo
print('error in bondcombo:', repr(err_bondcombo))
print('error in anglecombo:', repr(err_anglecombo))
print('error in dihedralcombo:', repr(err_dihedralcombo))
for err in [err_bondcombo, err_anglecombo, err_dihedralcombo]:
assert err < 1e-12
def relax(atoms, name, calc_mag_state):
# relax only along xy-axis to opitmize lattice
sf = UnitCellFilter(atoms, mask=[1, 1, 0, 0, 0, 0])
opt = BFGS(sf,
trajectory='{0}_relaxed.traj'.format(name),
logfile='{0}_relaxed.log'.format(name))
opt.run(fmax=0.05) # until forces < 0.05 eV/atom
calc.write('relaxed.gpw') #write gpw file for the magnetic relaxations
def opt_emt_bfgs(atoms):
from ase.calculators.emt import EMT
from ase.optimize.bfgs import BFGS
tmpAtoms = atoms.copy()
tmpAtoms.calc = EMT()
geomOpt = BFGS(tmpAtoms, maxstep=0.1, trajectory=None, logfile=None)
geomOpt.run(fmax=0.01, steps=1000)
return tmpAtoms
def preopt_hooke(self, cutoff=1.5, toler=0.2, stepsize=0.05, nsteps=200):
from gocia.calc.hooke import Hooke
from ase.optimize.bfgs import BFGS
tmpAtoms = self.get_allAtoms()
tmpAtoms.calc = Hooke(cutoff=cutoff, tolerAngs=toler, tolerMult=toler)
geomOpt = BFGS(tmpAtoms,
maxstep=stepsize,
trajectory=None,
logfile=None)
geomOpt.run(fmax=0.01, steps=nsteps)
print(' - Hookean pre-optimization: RMSD = %.3f Angstroms' %
geom.RMSD(self.get_allAtoms(), tmpAtoms))
self.set_allAtoms(tmpAtoms)
def __init__(self, atoms, restart=None, logfile='-', trajectory=None, maxstep=None,
master=None, initial=None, rmsd_dev=1000.0, molindixes=None, structure=None,
H0=None, fixed_frame=None, parameters=None, mu=None, A=None, known=None):
BFGS.__init__(self, atoms, restart=restart, logfile=logfile, trajectory=trajectory, maxstep=0.04, master=None)
# initial hessian
self.H0 = H0
self.initial=initial
self.rmsd_dev=rmsd_dev
self.molindixes = molindixes
self.structure = structure
self.fixed_frame = fixed_frame
self.parameters = parameters
def preopt_lj(self, fileBaseName='tmp',\
toler=0.2, stepsize=0.05, nsteps=200):
# from ase.calculators.lj import LennardJones
from gocia.calc.lj import LennardJones
from ase.optimize.bfgs import BFGS
tmpAtoms = self.get_allAtoms()
tmpAtoms.calc = LennardJones(tolerAngs=toler, tolerMult=toler)
geomOpt = BFGS(tmpAtoms,
maxstep=stepsize,
trajectory=None,
logfile=None)
geomOpt.run(fmax=0.01, steps=nsteps)
print(' - L-J pre-optimization: RMSD = %.3f Angstroms' %
geom.RMSD(self.get_allAtoms(), tmpAtoms))
self.set_allAtoms(tmpAtoms)
def test_fixinternals():
(atoms, constr, bond_def, target_bond, angle_def, target_angle,
dihedral_def, target_dihedral) = setup_fixinternals()
calc = EMT()
opt = BFGS(atoms, trajectory='opt.traj', logfile='opt.log')
previous_angle = atoms.get_angle(*angle_def)
previous_dihedral = atoms.get_dihedral(*dihedral_def)
print('angle before', previous_angle)
print('dihedral before', previous_dihedral)
print('bond length before', atoms.get_distance(*bond_def))
print('target bondlength', target_bond)
atoms.calc = calc
atoms.set_constraint(constr)
print('-----Optimization-----')
opt.run(fmax=0.01)
new_angle = atoms.get_angle(*angle_def)
new_dihedral = atoms.get_dihedral(*dihedral_def)
new_bondlength = atoms.get_distance(*bond_def)
print('angle after', new_angle)
print('dihedral after', new_dihedral)
print('bondlength after', new_bondlength)
err1 = new_angle - previous_angle
err2 = new_dihedral - previous_dihedral
err3 = new_bondlength - target_bond
print('error in angle', repr(err1))
print('error in dihedral', repr(err2))
print('error in bondlength', repr(err3))
assert err1 < 1e-11
assert err2 < 1e-12
assert err3 < 1e-12
def test_gfn1xtb_bfgs():
"""Perform geometry optimization with GFN1-xTB and BFGS"""
thr = 1.0e-5
atoms = Atoms(
symbols="NHCHC2H3OC2H3ONHCH3",
positions=np.array([
[1.40704587284727, -1.26605342016611, -1.93713466561923],
[1.85007200612454, -0.46824072777417, -1.50918242392545],
[-0.03362432532150, -1.39269245193812, -1.74003582081606],
[-0.56857009928108, -1.01764444489068, -2.61263467107342],
[-0.44096297340282, -2.84337808903410, -1.48899734014499],
[-0.47991761226058, -0.55230954385212, -0.55520222968656],
[-1.51566045903090, -2.89187354810876, -1.32273881320610],
[-0.18116520746778, -3.45187805987944, -2.34920431470368],
[0.06989722340461, -3.23298998903001, -0.60872832703814],
[-1.56668253918793, 0.00552120970194, -0.52884675001441],
[1.99245341064342, -1.73097165236442, -3.08869239114486],
[3.42884244212567, -1.30660069291348, -3.28712665743189],
[3.87721962540768, -0.88843123009431, -2.38921453037869],
[3.46548545761151, -0.56495308290988, -4.08311788302584],
[4.00253374168514, -2.16970938132208, -3.61210068365649],
[1.40187968630565, -2.43826111827818, -3.89034127398078],
[0.40869198386066, -0.49101709352090, 0.47992424955574],
[1.15591901335007, -1.16524842262351, 0.48740266650199],
[0.00723492494701, 0.11692276177442, 1.73426297572793],
[0.88822128447468, 0.28499001838229, 2.34645658013686],
[-0.47231557768357, 1.06737634000561, 1.52286682546986],
[-0.70199987915174, -0.50485938116399, 2.28058247845421],
]),
)
atoms.calc = XTB(method="GFN1-xTB", accuracy=2.0, cache_api=False)
opt = BFGS(atoms)
opt.run(fmax=0.1)
assert approx(atoms.get_potential_energy(), thr) == -951.9006674709672
assert approx(np.linalg.norm(atoms.get_forces(), ord=2),
thr) == 0.2052117803208497
from ase.structure import molecule
from ase.optimize.bfgs import BFGS
from ase.calculators.nwchem import NWChem
from ase.data.g2_1 import molecule_names, atom_names
c = ase.db.connect('g2-1.db')
for name in molecule_names + atom_names:
id = c.reserve(name=name, calculator='nwchem')
if id is None:
continue
atoms = molecule(name)
atoms.calc = NWChem(command='mpiexec -np 4 nwchem PREFIX.nw > PREFIX.out',
geometry='noautosym nocenter noautoz',
task='gradient',
xc='PBE',
grid='nodisk',
tolerances='tight',
basis='def2-qzvppd',
basispar='spherical',
direct='noio',
label=name)
atoms.get_forces()
c.write(atoms, name=name, relaxed=False)
if len(atoms) > 1:
opt = BFGS(atoms, logfile=name + '.nwchem.log')
opt.run(0.01)
c.write(atoms, name=name, relaxed=True)
del c[id]
import ase.io as fio
from gocia.interface import Interface
from ase.calculators.emt import EMT
from ase.optimize.bfgs import BFGS
subs = fio.read('subs-ini.vasp')
subs.calc = EMT()
geomOpt = BFGS(subs, maxstep=0.05)
geomOpt.run(fmax=0.001, steps=200)
fio.write('subs-opt.vasp', subs)
atoms = Atoms('N2', positions=[(0, 0, 0), (0, 0, d_bond + d_disp)])
atoms.set_pbc(False)
atoms.center(vacuum=6.0)
cell_c = np.sum(atoms.get_cell()**2, axis=1)**0.5
N_c = 8 * np.round(cell_c / (0.2 * 8))
calc = GPAW(
gpts=N_c,
nbands=5,
basis='dzp', #TODO xc='PBE'
txt=name + '_gs.txt',
parallel={'band': 1})
atoms.set_calculator(calc)
# QuasiNewton relaxation before we increase the number of bands
qn = BFGS(atoms,
logfile=name + '_gs.log',
trajectory=name + '_gs.traj')
qn.run(0.01, steps=100)
# Converge enough unoccupied bands for dSCF expansion
calc.set(nbands=10,
spinpol=True,
occupations=FermiDirac(0.1),
convergence={
'bands': -2,
'eigenstates': 1.0e-9
})
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del qn, calc, atoms
time.sleep(10)
from ase import io
from ase.calculators.orca import ORCA
from ase.optimize.fire import FIRE
from ase.optimize.bfgs import BFGS
#Optimise molecule
ethan = io.read('xyz_files/ethan.xyz')
orca_calc= ORCA(
label="orca",
maxiter=200,
task="gradient",
orcasimpleinput="HF-3c"
)
ethan.set_calculator(orca_calc)
#opt = FIRE(ethan, trajectory='ethan.traj')
#opt.run(fmax=0.00241)
opt = BFGS(ethan, trajectory='ethan.traj')
opt.run(fmax=0.0005)
def test_dihedralconstraint():
from math import pi
from ase.calculators.emt import EMT
from ase.constraints import FixInternals
from ase.optimize.bfgs import BFGS
from ase.build import molecule
system = molecule('CH3CH2OH', vacuum=5.0)
system.rattle(stdev=0.3)
# Angles, Bonds, Dihedrals are built up with pairs of constraint
# value and indices defining the constraint
# Fix this dihedral angle to whatever it was from the start
indices = [6, 0, 1, 2]
dihedral1 = system.get_dihedral(*indices)
# Fix angle to whatever it was from the start
indices2 = [6, 0, 1]
angle1 = system.get_angle(*indices2)
# system.set_dihedral(indices, pi/20, mask=[0,1,1,1,1,1,0,0,0])
# Fix bond between atoms 1 and 2 to 1.4
target_bondlength = 1.4
indices_bondlength = [1, 2]
constraint = FixInternals(bonds=[(target_bondlength, indices_bondlength)],
angles=[(angle1 * pi / 180, indices2)],
dihedrals=[(dihedral1 * pi / 180, indices)],
epsilon=1e-10)
print(constraint)
calc = EMT()
opt = BFGS(system, trajectory='opt.traj', logfile='opt.log')
previous_angle = system.get_angle(*indices2)
previous_dihedral = system.get_dihedral(*indices)
print('angle before', previous_angle)
print('dihedral before', previous_dihedral)
print('bond length before', system.get_distance(*indices_bondlength))
print('(target bondlength %s)', target_bondlength)
system.set_calculator(calc)
system.set_constraint(constraint)
print('-----Optimization-----')
opt.run(fmax=0.01)
new_angle = system.get_angle(*indices2)
new_dihedral = system.get_dihedral(*indices)
new_bondlength = system.get_distance(*indices_bondlength)
print('angle after', new_angle)
print('dihedral after', new_dihedral)
print('bondlength after', new_bondlength)
err1 = new_angle - previous_angle
err2 = new_dihedral - previous_dihedral
err3 = new_bondlength - target_bondlength
print('error in angle', repr(err1))
print('error in dihedral', repr(err2))
print('error in bondlength', repr(err3))
assert err1 < 1e-11
assert err2 < 1e-12
assert err3 < 1e-12
#calc.set(xc = 'PBE', lreal = False,
calc.set(
xc='PBE',
mode=PW(400),
# nsw=30, ediff=1e-8, ibrion=2, kpts=[3,3,3])
# ediff=1e-8, ibrion=2, kpts=[3,3,3])
# ibrion=2, kpts=[3,3,3])
kpts=[3, 3, 3])
# Set the calculation mode first.
# Full structure optimization in this case.
# Not all calculators have this type of internal minimizer!
#calc.set(isif=3)
# from ase/GPAW stress example
print("Potential Energy: " + str(cryst.get_potential_energy()))
uf = UnitCellFilter(cryst)
relax = BFGS(uf)
relax.run(fmax=0.05)
stress = cryst.get_stress()
print(stress)
a = cryst.get_cell()[0, 0]
print("optimized lattice constant: " + a)
### EOF ###
import ase.db
from ase.build import molecule
from ase.optimize.bfgs import BFGS
from ase.data.g2_1 import molecule_names, atom_names
from gpaw import GPAW, PW, Mixer, FermiDirac
c = ase.db.connect('g2-1.db')
for name in molecule_names + atom_names:
id = c.reserve(name=name, calculator='gpaw')
if id is None:
continue
atoms = molecule(name)
atoms.cell = [12, 13.01, 14.02]
atoms.center()
atoms.calc = GPAW(mode=PW(800),
xc='PBE',
occupations=FermiDirac(0.0, fixmagmom=True),
txt=name + '.txt')
if name in ['Na2', 'NaCl', 'NO', 'ClO', 'Cl', 'Si']:
atoms.calc.set(eigensolver='dav', mixer=Mixer(0.05, 2))
atoms.get_forces()
c.write(atoms, id=id, name=name, relaxed=False)
if len(atoms) > 1:
opt = BFGS(atoms, logfile=name + '.gpaw.log')
opt.run(0.01)
c.write(atoms, name=name, relaxed=True)
#system.set_dihedral(indices, pi/20, mask=[0,1,1,1,1,1,0,0,0])
# Fix bond between atoms 1 and 2 to 1.4
target_bondlength = 1.4
indices_bondlength = [1, 2]
constraint = FixInternals(bonds=[(target_bondlength, indices_bondlength)],
angles=[(angle1, indices2)],
dihedrals=[(dihedral1, indices)],
epsilon=1e-10)
print(constraint)
calc = EMT()
opt = BFGS(system, trajectory='opt.traj', logfile='opt.log')
previous_angle = system.get_angle(indices2)
previous_dihedral = system.get_dihedral(indices)
print('angle before', previous_angle)
print('dihedral before', previous_dihedral)
print('bond length before', system.get_distance(*indices_bondlength))
print('(target bondlength %s)', target_bondlength)
system.set_calculator(calc)
system.set_constraint(constraint)
print('-----Optimization-----')
opt.run(fmax=0.01)
new_angle = system.get_angle(indices2)
relativistic=relativistic)
if id is None:
continue
# set calculator
atoms.calc = GPAW(
txt=label + '.txt',
xc='PBE',
kpts=kpts,
maxiter=777,
eigensolver='dav',
parallel={'band': 1},
idiotproof=False,
)
atoms.calc.set(**kwargs) # remaining calc keywords
if optimize:
opt = BFGS(atoms, logfile=label + '.opt',
trajectory=label + '.traj')
opt.run(fmax=0.01)
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
name=name, adsorbate=adsorbate, category=category,
site=site,
ecut=ecut,
kptdensity=kptdensity, width=width,
relativistic=relativistic,
niter=atoms.calc.get_number_of_iterations(),
time=time.time()-t)
traj.write(atoms)
del c[id]
def test_dihedralconstraint():
from ase.calculators.emt import EMT
from ase.constraints import FixInternals
from ase.optimize.bfgs import BFGS
from ase.build import molecule
system = molecule('CH3CH2OH', vacuum=5.0)
system.rattle(stdev=0.3)
# Angles, Bonds, Dihedrals are built up with pairs of constraint
# value and indices defining the constraint
# Linear combinations of bond lengths are built up similarly with the
# coefficients appended to the indices defining the constraint
# Fix this dihedral angle to whatever it was from the start
indices = [6, 0, 1, 2]
dihedral1 = system.get_dihedral(*indices)
# Fix angle to whatever it was from the start
indices2 = [6, 0, 1]
angle1 = system.get_angle(*indices2)
# Fix bond between atoms 1 and 2 to 1.4
target_bondlength = 1.4
indices_bondlength = [1, 2]
# Fix linear combination of two bond lengths with atom indices 0-8 and
# 0-6 with weighting coefficients 1.0 and -1.0 to the current value.
# In other words, fulfil the following constraint:
# 1 * system.get_distance(0, 8) -1 * system.get_distance(0, 6) = const.
bondcombo_def = [[0, 8, 1.0], [0, 6, -1.0]]
def get_bondcombo(system, bondcombo_def):
return sum([
defin[2] * system.get_distance(defin[0], defin[1])
for defin in bondcombo_def
])
target_bondcombo = get_bondcombo(system, bondcombo_def)
constraint = FixInternals(bonds=[(target_bondlength, indices_bondlength)],
angles_deg=[(angle1, indices2)],
dihedrals_deg=[(dihedral1, indices)],
bondcombos=[(target_bondcombo, bondcombo_def)],
epsilon=1e-10)
print(constraint)
calc = EMT()
opt = BFGS(system, trajectory='opt.traj', logfile='opt.log')
previous_angle = system.get_angle(*indices2)
previous_dihedral = system.get_dihedral(*indices)
previous_bondcombo = get_bondcombo(system, bondcombo_def)
print('angle before', previous_angle)
print('dihedral before', previous_dihedral)
print('bond length before', system.get_distance(*indices_bondlength))
print('(target bondlength %s)', target_bondlength)
print('linear bondcombination before', previous_bondcombo)
system.calc = calc
system.set_constraint(constraint)
print('-----Optimization-----')
opt.run(fmax=0.01)
new_angle = system.get_angle(*indices2)
new_dihedral = system.get_dihedral(*indices)
new_bondlength = system.get_distance(*indices_bondlength)
new_bondcombo = get_bondcombo(system, bondcombo_def)
print('angle after', new_angle)
print('dihedral after', new_dihedral)
print('bondlength after', new_bondlength)
print('linear bondcombination after', new_bondcombo)
err1 = new_angle - previous_angle
err2 = new_dihedral - previous_dihedral
err3 = new_bondlength - target_bondlength
err4 = new_bondcombo - previous_bondcombo
print('error in angle', repr(err1))
print('error in dihedral', repr(err2))
print('error in bondlength', repr(err3))
print('error in bondcombo', repr(err4))
assert err1 < 1e-11
assert err2 < 1e-12
assert err3 < 1e-12
assert err4 < 1e-12
from ase import Atoms
from ase.lattice import bulk
from ase.optimize.bfgs import BFGS
from ase.constraints import UnitCellFilter
from gpaw import GPAW
from gpaw import PW
import numpy as np
cell = bulk('Si', 'fcc', a=6.0).get_cell()
# Experimental Lattice constant is a=5.421 A
a = Atoms('Si2',
cell=cell,
pbc=True,
scaled_positions=((0, 0, 0), (0.25, 0.25, 0.25)))
calc = GPAW(
xc='PBE',
mode=PW(400),
# mode=PW(400, cell=a.get_cell()), # fix no of planewaves!
kpts=(4, 4, 4),
# convergence={'eigenstates': 1.e-10}, # converge tightly!
txt='stress.txt')
a.set_calculator(calc)
uf = UnitCellFilter(a)
relax = BFGS(uf)
relax.run(fmax=0.05) # Consider much tighter fmax!
a = np.dot(a.get_cell()[0], a.get_cell()[0])**0.5 * 2**0.5
print('Relaxed lattice parameter: a = %s A' % a)
from ase import Atoms
from ase.lattice import bulk
from ase.optimize.bfgs import BFGS
from ase.constraints import UnitCellFilter
from gpaw import GPAW
from gpaw import PW
import numpy as np
cell = bulk('Si', 'fcc', a=6.0).get_cell()
# Experimental Lattice constant is a=5.421 A
a = Atoms('Si2', cell=cell, pbc=True,
scaled_positions=((0,0,0), (0.25,0.25,0.25)))
calc = GPAW(xc='PBE',
mode=PW(400),
#mode=PW(400, cell=a.get_cell()), # fix no of planewaves!
kpts=(4,4,4),
#convergence={'eigenstates': 1.e-10}, # converge tightly!
txt='stress.txt')
a.set_calculator(calc)
uf = UnitCellFilter(a)
relax = BFGS(uf)
relax.run(fmax=0.05) # Consider much tighter fmax!
a = np.dot(a.get_cell()[0], a.get_cell()[0])**0.5 * 2**0.5
print 'Relaxed lattice parameter: a = %s A' % a
def optimise_positions(self, fmax=0.01, use_precon=None, use_armijo=None):
""" Relax atoms positions with the fixed cell to a given force
threshold """
if use_precon is None:
use_precon = self.parameters.use_precon
if use_armijo is None:
use_armijo = self.parameters.use_armijo
if use_precon:
precon = Exp(A=3, use_pyamg=False)
else:
precon = None
if self.parameters.optimizer == 'BFGS':
relax = BFGS(self.atoms)
elif self.parameters.optimizer == 'FIRE':
relax = PreconFIRE(self.atoms, precon=precon)
elif self.parameters.optimizer == 'ase-FIRE':
relax = ASEFIRE(self.atoms)
elif self.parameters.optimizer == 'LBFGS':
relax = PreconLBFGS(self.atoms,
precon=precon,
use_armijo=use_armijo)
elif self.parameters.optimizer == 'ase-LBFGS':
relax = ASELBFGS(self.atoms)
else:
parprint("ERROR: unknown optimizer {}. "
"Reverting to BFGS".format(self.parameters.optimizer))
relax = BFGS(self.atoms)
name = self.atoms.get_chemical_formula()
relax.attach(
lambda: self.atoms.calc.write(name + '_relax.gpw', mode='all'))
relax.attach(lambda: write_atat_input(self.atoms, 'str_last.out'))
relax.run(fmax=fmax, steps=100)
if not relax.converged():
relax = ASELBFGS(self.atoms)
relax.run(fmax=fmax, steps=100)
if not relax.converged():
max_force = self.atoms.get_forces()
max_force = np.sqrt((max_force**2).sum(axis=1).max())
print('WARNING: optimisation not converged.' +
' Maximum force: %.4f' % max_force)
niter = ndiv * int(np.ceil(2 * period / (ndiv * timestep)))
if __name__ == '__main__':
if not os.path.isfile(name + '_gs.gpw'):
# Calculator for quick ground state relaxation
atoms = Atoms('N2', positions=[(0, 0, 0), (0, 0, d_bond + d_disp)])
atoms.set_pbc(False)
atoms.center(vacuum=6.0)
cell_c = np.sum(atoms.get_cell()**2, axis=1)**0.5
N_c = 8 * np.round(cell_c / (0.2 * 8))
calc = GPAW(gpts=N_c, nbands=5, basis='dzp', #TODO xc='PBE'
txt=name + '_gs.txt', parallel={'band': 1})
atoms.set_calculator(calc)
# QuasiNewton relaxation before we increase the number of bands
qn = BFGS(atoms, logfile=name + '_gs.log', trajectory=name + '_gs.traj')
qn.run(0.01, steps=100)
# Converge enough unoccupied bands for dSCF expansion
calc.set(nbands=10, spinpol=True, occupations=FermiDirac(0.1),
convergence={'bands': -2, 'eigenstates': 1.0e-9})
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del qn, calc, atoms
time.sleep(10)
while not os.path.isfile(name + '_gs.gpw'):
print 'Node %d waiting for %s...' % (world.rank, name + '_gs.gpw')
time.sleep(10)
world.barrier()
if atoms.get_initial_magnetic_moments().any(): # spin-polarization
kwargs.update({'spinpol': True})
kwargs.update({'fix_magmom': True})
atoms.calc = espresso(outdir=label,
xc='PBE',
pw=pw*Rydberg,
dw=dw*Rydberg,
sigma=0.0,
mode='scf',
# will overwrite disk_io parameter if True
output={'avoidio':True},
convergence={'mixing': 0.05, 'maxsteps':500,},
dontcalcforces=True,
)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.calc.results = {'energy': atoms.get_potential_energy()}
c.write(atoms, name=name, relaxed=False, pw=pw, dw=dw,
time=time.time()-t)
# no optimization: espresso does not conform yet to ASE interface style
if 0 and len(atoms) > 1:
opt = BFGS(atoms,
logfile=name + '_' + code + '.log',
trajectory=name + '_' + code + '.traj')
t = time.time()
opt.run(0.005)
atoms.get_potential_energy()
c.write(atoms, name=name, relaxed=True, pw=pw, dw=dw,
time=time.time()-t)
del c[id]
import ase.db
from ase.structure import molecule
from ase.optimize.bfgs import BFGS
from ase.calculators.nwchem import NWChem
from ase.data.g2_1 import molecule_names, atom_names
c = ase.db.connect('g2-1.db')
for name in molecule_names + atom_names:
id = c.reserve(name=name, calculator='nwchem')
if id is None:
continue
atoms = molecule(name)
atoms.calc = NWChem(command='mpiexec -np 4 nwchem PREFIX.nw > PREFIX.out',
geometry='noautosym nocenter noautoz',
task='gradient',
xc='PBE',
grid='nodisk',
tolerances='tight',
basis='def2-qzvppd',
basispar='spherical',
direct='noio',
label=name)
atoms.get_forces()
c.write(atoms, name=name, relaxed=False)
if len(atoms) > 1:
opt = BFGS(atoms, logfile=name + '.nwchem.log')
opt.run(0.01)
c.write(atoms, name=name, relaxed=True)
del c[id]