def optimize_lammpslib(struc,
lmp,
parameters=None,
path='tmp',
calc_type=None,
lmp_file=None,
molecule=False,
strain=np.ones([3, 3]),
method='FIRE',
fmax=0.01):
if lmp_file is not None:
lammps = LAMMPSlib(lmp=lmp, lmp_file=lmp_file, log_file='lammps.log', \
molecule=molecule, path=path)
elif calc_type is not None:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, calc_type=calc_type, \
log_file='lammps.log', molecule=molecule, path=path)
else:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, log_file='lammps.log', \
molecule=molecule, path=path)
struc.set_calculator(lammps)
box = mushybox(struc, fixstrain=strain)
if method == 'FIRE':
dyn = FIRE(box)
else:
dyn = LBFGS(box)
dyn.run(fmax=fmax, steps=500)
return struc
def optimize_lammpslib(pbcgb, lmp, parameters, path, method='FIRE', fmax=0.1):
lammps = LAMMPSlib(lmp=lmp,
lmpcmds=parameters,
log_file='lammps.log',
path=path)
pbcgb.set_calculator(lammps)
cell0 = pbcgb.cell
fixstrain = np.zeros((3, 3))
fixstrain[2][2] = 1
box = mushybox(pbcgb, fixstrain=fixstrain)
if method == 'FIRE':
dyn = FIRE(box)
else:
dyn = BFGS(box)
dyn.run(fmax=fmax, steps=500)
return pbcgb
def test_utilities():
eps = 1e-5
atoms = Icosahedron('Cu', 3)
atoms.numbers[[0, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30]] = 79
atoms.center(vacuum=0.0)
atoms.calc = EMT()
with FIRE(atoms, logfile=None) as opt:
opt.run(fmax=0.05)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(atoms, rmax, nbins, elements=c,
distance_matrix=dm, no_dists=True) * inv_norm
assert all(abs(s - calc_rdf) < eps)
AuAu = get_rdf(atoms, rmax, nbins, elements=(79, 79),
distance_matrix=dm, no_dists=True)
assert all(abs(AuAu[-2:] - [0.12126445, 0.]) < eps)
bulk = L1_2(['Au', 'Cu'], size=(3, 3, 3), latticeconstant=2 * np.sqrt(2))
rdf = get_rdf(bulk, 4.2, 5)[0]
calc_rdf = [0., 0., 1.43905094, 0.36948605, 1.34468694]
assert all(abs(rdf - calc_rdf) < eps)
def opt_lammpslib(struc,
lmp,
parameters=None,
mask=None,
logfile='-',
path='tmp',
calc_type=None,
lmp_file=None,
molecule=False,
method='FIRE',
fmax=0.01,
opt_cell=False,
a=0.1,
steps=500):
"""
mask: [1, 1, 1, 1, 1, 1], a, b, c, alpha, beta, gamma
[1, 1, 0, 0, 0, 1]
"""
if lmp_file is not None:
lammps = LAMMPSlib(lmp=lmp, lmp_file=lmp_file, log_file='lammps.log', \
molecule=molecule, path=path)
elif calc_type is not None:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, calc_type=calc_type, \
log_file='lammps.log', molecule=molecule, path=path)
else:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, log_file='lammps.log', \
molecule=molecule, path=path)
#check_symmetry(si, 1.0e-6, verbose=True)
struc.set_calculator(lammps)
struc.set_constraint(FixSymmetry(struc))
if opt_cell:
ecf = ExpCellFilter(struc, mask)
if method == 'FIRE':
dyn = FIRE(ecf, logfile=logfile, a=a)
else:
dyn = LBFGS(ecf, logfile=logfile)
else:
if method == 'FIRE':
dyn = FIRE(struc, logfile=logfile)
else:
dyn = LBFGS(struc, logfile=logfile)
dyn.run(fmax=fmax, steps=steps)
return struc
def optimize(atoms,
sym=True,
box=False,
method='FIRE',
fmax=0.01,
steps=1000,
logfile='ase.log'):
if sym:
atoms.set_constraint(FixSymmetry(atoms))
if box:
ecf = ExpCellFilter(atoms)
if method == 'FIRE':
dyn = FIRE(ecf, logfile=logfile)
else:
dyn = LBFGS(ecf, logfile=logfile)
else:
if method == 'FIRE':
dyn = FIRE(atoms, logfile=logfile)
else:
dyn = FIRE(atoms, logfile=logfile)
dyn.run(fmax=fmax, steps=steps)
atoms.set_constraint()
return atoms
def test_ethene_rotation(tmpdir):
tmpdir.chdir()
# Optimise molecule
initial = molecule('C2H6')
smart_cell(initial, vac=4.0, h=0.01)
initial.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
qn = QuasiNewton(initial, 'initial.traj')
qn.run(fmax=0.01)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
final.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
final.get_potential_energy()
# Generate blank images
images = [initial]
nimage = 7
for i in range(nimage):
image = initial.copy()
image.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
images.append(image)
images.append(final)
# Run IDPP interpolation
neb = NEBEspresso(images)
neb.interpolate('idpp')
# Run NEB calculation
qn = QuasiNewton(neb, logfile='ethane_linear.log', trajectory='neb.traj')
qn.run(fmax=0.05)
nt = NEBTools(neb.images)
print('fmax: ', nt.get_fmax())
print('Ef, dE: ', nt.get_barrier())
from ase.optimize.fire import FIRE as QuasiNewton
from ase.io import read
# Read the previous configurations
initial = read('N2.traj')
final = read('2N.traj')
# Make 9 images (note the use of copy)
configs = [initial.copy() for i in range(8)] + [final]
# As before, fix the Cu atoms
constraint = FixAtoms(mask=[atom.symbol != 'N' for atom in initial])
for config in configs:
config.calc = EMT()
config.set_constraint(constraint)
# Make the NEB object, interpolate to guess the intermediate steps
band = NEB(configs)
band.interpolate()
relax = QuasiNewton(band)
# Do the calculation
relax.run()
# Compare intermediate steps to initial energy
e0 = initial.get_potential_energy()
for config in configs:
d = config[-2].position - config[-1].position
print(np.linalg.norm(d), config.get_potential_energy() - e0)
write('initial.traj', initial)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
write('final.traj', final)
# Generate blank images
images = [initial]
nimage = 7
for i in range(nimage):
images.append(initial.copy())
images.append(final)
# Run IDPP interpolation
neb = NEB(images)
neb.interpolate()
calcs = NEBEspresso(neb, kpts='gamma', pw=300, dw=4000)
# Run NEB calculation
qn = QuasiNewton(neb, logfile='ethane_linear.log')
for j in range(nimage):
traj = Trajectory('neb%d.traj' % j, 'w', images[j + 1])
qn.attach(traj)
qn.run(fmax=0.05)
sg = randint(2, 230)
crystal = molecular_crystal(sg, ['H2O'], [randint(1, 4)],
1.0) #, lattice=para)
if crystal.valid:
struc = Atoms(
crystal.spg_struct[2],
cell=crystal.spg_struct[0],
scaled_positions=crystal.spg_struct[1],
)
break
#struc = struc.repeat((2,2,2))
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, mol=True)
struc.set_calculator(lammps)
box = mushybox(struc)
dyn = FIRE(box)
dyn.run(fmax=0.00, steps=1100)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
Eng = struc.get_potential_energy() * 96 / len(struc) * 3
Vol = struc.get_volume() / len(struc) * 3
stress = np.max(struc.get_stress())
struc = sort(struc)
try:
spg = get_symmetry_dataset(struc, symprec=1e-1)['number']
except:
spg = 1
final.positions[2:5] = initial.positions[[3, 4, 2]]
# Generate blank images.
images = [initial]
for i in range(9):
images.append(initial.copy())
for image in images:
image.calc = EMT()
images.append(final)
neb = NEB(images, climb=True)
neb.interpolate(method='idpp') #idpp插值，设置初猜
# set calculator
for atoms in images:
atoms.calc = EMT()
atoms.get_potential_energy()
# Optimize:
py_fname = os.path.splitext(sys.argv[0])[0]
traj_fname = "{}.traj".format(py_fname)
log_fname = "{}.log".format(py_fname)
optimizer = FIRE(neb, trajectory=traj_fname, logfile=log_fname)
optimizer.run(fmax=0.04)
neb_result = list(iread(traj_fname))
for i in neb_result:
#print(i.get_potential_energy())
pass
neb_result = NEBTools(neb_result)
neb_result.plot_bands(True, True, label=py_fname)
print(neb_result.get_barrier(), neb_result.get_fmax())
from ann import ATOMModel, Ann
from ase.io import read
from ase.optimize.fire import FIRE
p1 = read('au55.xyz', index=0, format='xyz')
model = ATOMModel(restore='atom_model', n=55)
p1.set_calculator(Ann(atoms=p1, ann_model=model))
opt = FIRE(atoms=p1,
maxmove=1.0,
dt=0.2,
dtmax=1.0,
logfile='geo_opt.dat',
trajectory='geo_opt.traj')
opt.run(fmax=0.05, steps=1000)
from ase.build import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE as QuasiNewton
# Optimise molecule.
initial = molecule('C2H6')
initial.calc = EMT()
relax = QuasiNewton(initial)
relax.run(fmax=0.05)
# Create final state.
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
# Generate blank images.
images = [initial]
for i in range(9):
images.append(initial.copy())
for image in images:
image.calc = EMT()
images.append(final)
# Run IDPP interpolation.
neb = NEB(images)
neb.interpolate('idpp')
# Run NEB calculation.
at.set_calculator(SubdirCalculator(quip_pot, opt.chdir, opt.calc_args))
if rank == 0:
print 'Starting NEB run with %d images' % len(neb.images)
if not os.path.exists('%s-initial.xyz' % basename):
neb.write('%s-initial.xyz' % basename)
if opt.eval:
# actually evaluate end forces as well
neb.get_forces(all=True)
neb.write('%s-eval.xyz' % basename)
elif not opt.dry_run:
# Optimize:
if opt.optimizer == 'FIRE':
from ase.optimize.fire import FIRE
optimizer = FIRE(neb)
elif opt.optimizer == 'MDMin':
from ase.optimize import MDMin
optimizer = MDMin(neb)
else:
p.error('Unknown optimizer %s' % opt.optimizer)
if opt.write_traj is not None:
def write_traj():
global neb
n = 0
while os.path.exists('%s-band-%d.xyz' % (basename, n)):
n += 1
neb.write('%s-band-%d.xyz' % (basename, n))
'J': 0
},
'Ir': {
'L': 2,
'U': 3.75,
'J': 1.0
},
'O': {
'L': -1,
'U': 0,
'J': 0
}
},
lmaxmix=4)
p1.set_calculator(calc)
pstress = p1.get_cell() * 0.0
pstress[2][0] = 3.0
p1box = mushybox(p1, express=pstress)
# for ase.3.15 and later
dyn = FIRE(p1box, maxmove=0.1, dt=0.1, dtmax=0.1, force_consistent=False)
#dyn = MDMin(p1box, dt=0.1, force_consistent = False)
# for ase.3.12 and earlier
#dyn = FIRE(p1box,maxmove = 0.1, dt = 0.1, dtmax = 0.1)
#dyn = MDMin(p1box, dt=0.1)
dyn.run(fmax=0.01, steps=100)
write("CONTCAR", p, format='vasp')
from ase.build import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE
# Optimise molecule
initial = molecule('C2H6')
initial.set_calculator(EMT())
relax = FIRE(initial)
relax.run(fmax=0.05)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
# Generate blank images
images = [initial]
for i in range(9):
images.append(initial.copy())
images.append(final)
for image in images:
image.set_calculator(EMT())
# Run IDPP interpolation
neb = NEB(images)
neb.interpolate('idpp')
# Run NEB calculation
def __init__(self, atoms, maxmove=None, trustradius=0.2, **kwargs):
maxmove = maxmove or trustradius / 10
FIRE.__init__(self, atoms, maxmove=maxmove, **kwargs)
self.trustradius = trustradius
# Reference for the trustradius
self.start_geo = atoms.get_positions()
from ase.optimize.fire import FIRE as QuasiNewton
from ase.io import read
# Read the previous configurations
initial = read('N2.traj')
final = read('2N.traj')
# Make 9 images (note the use of copy)
configs = [initial.copy() for i in range(8)] + [final]
# As before, fix the Cu atoms
constraint = FixAtoms(mask=[atom.symbol != 'N' for atom in initial])
for config in configs:
config.set_calculator(EMT())
config.set_constraint(constraint)
# Make the NEB object, interpolate to guess the intermediate steps
band = NEB(configs)
band.interpolate()
relax = QuasiNewton(band)
# Do the calculation
relax.run()
# Compare intermediate steps to initial energy
e0 = initial.get_potential_energy()
for config in configs:
d = config[-2].position - config[-1].position
print(np.linalg.norm(d), config.get_potential_energy() - e0)
from __future__ import division
import numpy as np
from ase.cluster import Icosahedron
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE
from ase.lattice.compounds import L1_2
from ase.ga.utilities import get_rdf
eps = 1e-5
atoms = Icosahedron('Cu', 3)
atoms.numbers[[0, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30]] = 79
atoms.set_calculator(EMT())
opt = FIRE(atoms, logfile=None)
opt.run(fmax=0.05)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(atoms, rmax, nbins, elements=c,
s = a0.get_scaled_positions() s[:, 0] *= 0.995 a0.set_scaled_positions(s) # perturb the cell a0.cell[...] += np.random.uniform(-1e-2, 1e-2, size=9).reshape((3, 3)) atoms = a0.copy() atoms.set_calculator(LennardJones()) ucf = UnitCellFilter(atoms, scalar_pressure=10.0 * GPa) # test all deritatives f, fn = gradient_test(ucf) assert abs(f - fn).max() < 1e-6 opt = FIRE(ucf) opt.run(1e-3) # check pressure is within 0.1 GPa of target sigma = atoms.get_stress() / GPa pressure = -(sigma[0] + sigma[1] + sigma[2]) / 3.0 assert abs(pressure - 10.0) < 0.1 atoms = a0.copy() atoms.set_calculator(LennardJones()) ecf = ExpCellFilter(atoms, scalar_pressure=10.0 * GPa) # test all deritatives f, fn = gradient_test(ecf) assert abs(f - fn).max() < 1e-6
for i in range(100):
while True:
sg = randint(16, 191)
crystal = molecular_crystal(sg, ['H2O'], [4], 1.0) #, lattice=para)
if crystal.valid:
struc = Atoms(
crystal.spg_struct[2],
cell=crystal.spg_struct[0],
scaled_positions=crystal.spg_struct[1],
)
break
#struc = struc.repeat((2,2,2))
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, mol=True)
struc.set_calculator(lammps)
box = mushybox(struc)
dyn = FIRE(box)
dyn.run(fmax=0.01, steps=200)
dyn = BFGS(box)
dyn.run(fmax=0.01, steps=200)
Eng = struc.get_potential_energy() * 96 / len(struc) * 3
Vol = struc.get_volume() / len(struc) * 3
stress = np.max(struc.get_stress())
struc = sort(struc)
try:
spg = get_symmetry_dataset(struc, symprec=1e-1)['number']
except:
spg = 1
struc.write(out_folder + '/' + str(i) + ".vasp", format='vasp', vasp5=True)
logging.info(
'{:4d} Spg: {:4d} Eng: {:8.4f} Vol: {:8.4f} Stress: {:5.2f}'.format(
i, spg, Eng, Vol, stress))
import numpy as np
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize.fire import FIRE as QuasiNewton
initial = read('N2.traj')
final = read('2N.traj')
configs = [initial.copy() for i in range(8)] + [final]
constraint = FixAtoms(mask=[atom.symbol != 'N' for atom in initial])
for config in configs:
config.set_calculator(EMT())
config.set_constraint(constraint)
band = NEB(configs)
band.interpolate()
# Create a quickmin object:
relax = QuasiNewton(band)
relax.run(steps=20)
e0 = initial.get_potential_energy()
for config in configs:
d = config[-2].position - config[-1].position
print np.linalg.norm(d), config.get_potential_energy() - e0
from ase.build import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE
from mlpot.mlneb import run_mla_neb
from mlpot.calculators.gprcalculator import GPRCalculator
from mlpot.kernels import RBFKernel
# Optimise molecule
initial = molecule('C2H6')
initial.set_calculator(EMT())
relax = FIRE(initial)
relax.run(fmax=0.05)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
# Generate blank images
images = [initial]
for i in range(9):
images.append(initial.copy())
images.append(final)
for image in images:
image.set_calculator(EMT())
# Run IDPP interpolation
neb = NEB(images)
from __future__ import division
import numpy as np
from ase.cluster import Icosahedron
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE
from ase.lattice.compounds import L1_2
from ase.ga.utilities import get_rdf
eps = 1e-5
atoms = Icosahedron('Cu', 3)
atoms.numbers[[0, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30]] = 79
atoms.set_calculator(EMT())
opt = FIRE(atoms, logfile=None)
opt.run(fmax=0.05)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(
from ase.structure import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE as QuasiNewton
from ase.visualize import view
#Optimise molecule
initial = molecule('C2H6')
initial.set_calculator(EMT())
relax = QuasiNewton(initial)
relax.run(fmax=0.05)
view(initial)
#Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
#Generate blank images
images = [initial]
for i in range(9):
images.append(initial.copy())
for image in images:
image.set_calculator(EMT())
images.append(final)
#Run IDPP interpolation
neb = NEB(images)
neb.interpolate()
import numpy as np
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize.fire import FIRE as QuasiNewton
initial = read('N2.traj')
final = read('2N.traj')
configs = [initial.copy() for i in range(8)] + [final]
constraint = FixAtoms(mask=[atom.symbol != 'N' for atom in initial])
for config in configs:
config.set_calculator(EMT())
config.set_constraint(constraint)
band = NEB(configs)
band.interpolate()
# Create a quickmin object:
relax = QuasiNewton(band)
relax.run(steps=20)
e0 = initial.get_potential_energy()
for config in configs:
d = config[-2].position - config[-1].position
print np.linalg.norm(d), config.get_potential_energy() - e0
#print(mol.get_chemical_symbols())
# Set NC
aens = ensemblemolecule(cnstfile, saefile, nnfdir, Nn, 5)
# Set ANI calculator
mol.set_calculator(ANIENS(aens, sdmx=20000000.0))
print(mol.get_potential_energy())
print(np.where(mol.get_forces() > 200.0))
print("size: ", len(mol.get_chemical_symbols()))
# Optimize molecule
start_time = time.time()
dyn = QuasiNewton(mol)
dyn.run(fmax=C)
print('[ANI Total time:', time.time() - start_time, 'seconds]')
#print(hdt.evtokcal*mol.get_potential_energy())
#print(hdt.evtokcal*mol.get_forces())
# Save optimized mol
spc = mol.get_chemical_symbols()
pos = mol.get_positions(wrap=False).reshape(1, len(spc), 3)
hdt.writexyzfile(optfile, pos, spc)
# Open MD output
mdcrd = open(xyzfile, 'w')