def calculate(self, atoms, name):
args = self.args
if args.constrain_tags:
tags = [int(t) for t in args.constrain_tags.split(',')]
mask = [t in tags for t in atoms.get_tags()]
atoms.constraints = FixAtoms(mask=mask)
trajectory = PickleTrajectory(self.get_filename(name, 'traj'), 'w',
atoms)
if args.maximum_stress:
optimizer = LBFGS(UnitCellFilter(atoms), logfile=self.logfile)
fmax = args.maximum_stress
else:
optimizer = LBFGS(atoms, logfile=self.logfile)
fmax = args.maximum_force
optimizer.attach(trajectory)
optimizer.run(fmax=fmax)
data = RunCommand.calculate(self, atoms, name)
if hasattr(optimizer, 'force_calls'):
data['force calls'] = optimizer.force_calls
return data
def test_qchem_calculator():
import numpy as np
from ase.build import molecule
from ase.calculators.qchem import QChem
from ase.optimize import LBFGS
mol = molecule('C2H6')
calc = QChem(label='calc/ethane', method='B3LYP', basis='6-31+G*')
mol.set_calculator(calc)
# Check energy and forces
np.testing.assert_allclose(mol.get_potential_energy(),
-2172.379183703419,
atol=10.)
np.testing.assert_allclose(mol.get_forces(),
np.array(
[[0., 0.00240141, 0.04992568],
[-0., -0.00240141, -0.04992568],
[-0., 0.11626015, 0.07267481],
[-0.10132204, -0.05804009, 0.07538475],
[0.10132204, -0.05804009, 0.07538475],
[-0., -0.11626015, -0.07267481],
[-0.10132204, 0.05804009, -0.07538475],
[0.10132204, 0.05804009, -0.07538475]]),
atol=0.05)
opt = LBFGS(mol)
opt.run()
assert opt.converged()
def opt(self, rdkmol, dhls, logger='optlog.out'):
Na = rdkmol.GetNumAtoms()
X, S = __convert_rdkitmol_to_nparr__(rdkmol)
atm=Atoms(symbols=S, positions=X)
atm.set_calculator(ANIENS(self.ens)) #Set the ANI Ensemble as the calculator
phi_fix = []
for d in dhls:
phi_restraint=atm.get_dihedral(d)
phi_fix.append([phi_restraint, d])
c = FixInternals(dihedrals=phi_fix, epsilon=1.e-9)
atm.set_constraint(c)
dyn = LBFGS(atm, logfile=logger) #Choose optimization algorith
dyn.run(fmax=self.fmax, steps=1000) #optimize molecule to Gaussian's Opt=Tight fmax criteria, input in eV/A (I think)
e=atm.get_potential_energy()*hdt.evtokcal
s=atm.calc.stddev*hdt.evtokcal
phi_value = []
for d in dhls:
phi_value.append(atm.get_dihedral(d)*180./np.pi)
#X = mol.get_positions()
if self.printer:
print('Phi value (degrees), energy (kcal/mol), sigma= ', phi_value, "{0:.2f}".format(e), "{0:.2f}".format(s))
return phi_value, e, s, atm
def test_unitcellfilter(asap3):
cu = bulk('Cu') * (6, 6, 6)
cu.calc = asap3.EMT()
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
def optimize_rdkit_molecule(self, mrdk, cid, fmax=0.0001, steps=500, logger='opt.out'):
mol = __convert_rdkitmol_to_aseatoms__(mrdk,cid)
mol.set_calculator(ANI(False))
mol.calc.setnc(self.nc)
dyn = LBFGS(mol,logfile=logger)
#dyn = LBFGS(mol)
dyn.run(fmax=fmax,steps=steps)
stps = dyn.get_number_of_steps()
xyz = mol.get_positions()
for i,x in enumerate(xyz):
mrdk.GetConformer(cid).SetAtomPosition(i,x)
def test_optimizer(atoms):
pos = atoms.positions.copy()
atoms.calc = get_calc(label='opt', scf='qc')
opt_gauss = GaussianOptimizer(atoms)
opt_gauss.run(fmax='tight')
e_gaussopt = read('opt.log', index=-1).get_potential_energy()
atoms.positions[:] = pos
atoms.calc.set_label('sp')
opt_ase = LBFGS(atoms, trajectory='ase_opt.traj')
opt_ase.run(fmax=1e-2)
e_aseopt = atoms.get_potential_energy()
assert e_gaussopt - e_aseopt == pytest.approx(0., abs=1e-3)
def test_pressure(atoms, cellfilter):
xcellfilter = cellfilter(atoms, scalar_pressure=10.0 * GPa)
# test all derivatives
f, fn = gradient_test(xcellfilter)
assert abs(f - fn).max() < 5e-6
opt = LBFGS(xcellfilter)
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
def optimize_molecule(self, X, S, fmax=0.1, steps=10000, logger='opt.out'):
mol = Atoms(symbols=S, positions=X)
mol.set_pbc((False, False, False))
mol.set_calculator(ANIENS(self.ens))
dyn = LBFGS(mol,logfile=logger)
#dyn = LBFGS(mol)
#dyn = QuasiNewton(mol,logfile=logger)
dyn.run(fmax=fmax,steps=steps)
stps = dyn.get_number_of_steps()
opt = True
if steps == stps:
opt = False
return np.array(mol.get_positions(),dtype=np.float32), opt
def relax_atoms(atoms,
tol=1e-3,
method='lbfgs_precon',
max_steps=1000,
traj_file=None,
**kwargs):
import model
atoms.set_calculator(model.calculator)
if hasattr(model, 'Optimizer'):
method = 'model_optimizer'
opt = model.Optimizer(atoms)
opt.run(tol, max_steps)
elif method.startswith('lbfgs') or method == 'fire' or method == 'cg_n':
if method == 'lbfgs_ASE':
from ase.optimize import LBFGS
opt = LBFGS(atoms, **kwargs)
elif method == 'cg_n':
from quippy import Minim
opt = Minim(atoms,
relax_positions=True,
relax_cell=False,
method='cg_n')
else:
from ase.optimize.precon.precon import Exp
from ase.optimize.precon.lbfgs import PreconLBFGS
precon = None
if method.endswith('precon'):
precon = Exp(3.0, recalc_mu=True)
if method.startswith('lbfgs'):
opt = PreconLBFGS(atoms, precon=precon, **kwargs)
else:
opt = FIRE(atoms, **kwargs)
if traj_file is not None and method != 'cg_n':
traj = open(traj_file, 'w')
def write_trajectory():
write(traj, atoms, format='extxyz')
opt.attach(write_trajectory)
opt.run(tol, max_steps)
try:
traj.close()
except:
pass
else:
raise ValueError('unknown method %s!' % method)
return atoms
def optimize(self, atoms, name):
args = self.args
if args.constrain_tags:
tags = [int(t) for t in args.constrain_tags.split(',')]
mask = [t in tags for t in atoms.get_tags()]
atoms.constraints = FixAtoms(mask=mask)
logfile = self.get_filename(name, 'log')
if args.maximum_stress:
optimizer = LBFGS(UnitCellFilter(atoms), logfile=logfile)
fmax = args.maximum_stress
else:
optimizer = LBFGS(atoms, logfile=logfile)
fmax = args.maximum_force
trajectory = Trajectory(self.get_filename(name, 'traj'), 'w', atoms)
optimizer.attach(trajectory)
optimizer.run(fmax=fmax)
def SurfaceEnergy(images, natoms, calc, fmax=0.01, debug=False):
"""Calculate the surface energy from a list of slab images.
Parameters
----------
images: List of slab images which the calculation is based on. The x and
y dimensions of the images unit cell must be conserved.
natoms: Number of atoms in a atomic layer in the slabs.
calc: Calculator object that can be attached to the images.
"""
ucell = images[0].get_cell()
layers = np.zeros(len(images))
energies = np.zeros(len(images))
if debug:
print "Layers Energy LBFGS steps"
for i, atoms in enumerate(images):
cell = atoms.get_cell()
if (ucell[0] != cell[0]).any() or (ucell[1] != cell[1]).any():
raise ValueError(
"The x and y dimensions of the unit cell must be conserved.")
atoms.set_calculator(calc)
dyn = LBFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=fmax, steps=1000)
assert dyn.converged(), "LBFGS not converged in 100 steps!"
layers[i] = len(atoms) / natoms
energies[i] = atoms.get_potential_energy()
if debug:
print "%4i%12.3f%10i" % (layers[i], energies[i],
dyn.get_number_of_steps())
p = polyfit(layers.reshape((-1, 1)), energies, 1)
surface_energy = p.c[0] / (2 * natoms)
assert surface_energy > 0.0
return surface_energy
def make_methylamine():
# Construct Methylamine.
atoms = Atoms('NH2CH3')
# Define connectivity.
atoms_bonds = [ [0,1], [0,2], [0,3], [3,4], [3,5], [3,6] ]
# Displace atoms so that they aren't on top of each other.
atoms.rattle(0.001)
# Construct VSEPR calculator.
calculator = VSEPR(atoms, atoms_bonds)
atoms.set_calculator(calculator)
atoms.center()
# Run optimization.
opt = LBFGS(atoms, logfile='/dev/null')
opt.run()
return atoms
def optimize_rdkit_molecule(self, mrdk, cid, fmax=0.1, steps=10000, logger='opt.out'):
mol = __convert_rdkitmol_to_aseatoms__(mrdk,cid)
mol.set_pbc((False, False, False))
mol.set_calculator(ANIENS(self.ens))
dyn = LBFGS(mol,logfile=logger)
#dyn = LBFGS(mol)
#dyn = QuasiNewton(mol,logfile=logger)
dyn.run(fmax=fmax,steps=steps)
stps = dyn.get_number_of_steps()
opt = True
if steps == stps:
opt = False
xyz = mol.get_positions()
for i,x in enumerate(xyz):
mrdk.GetConformer(cid).SetAtomPosition(i,x)
return opt
def SurfaceEnergy(images, natoms, calc, fmax=0.01, debug=False):
"""Calculate the surface energy from a list of slab images.
Parameters
----------
images: List of slab images which the calculation is based on. The x and
y dimensions of the images unit cell must be conserved.
natoms: Number of atoms in a atomic layer in the slabs.
calc: Calculator object that can be attached to the images.
"""
ucell = images[0].get_cell()
layers = np.zeros(len(images))
energies = np.zeros(len(images))
if debug:
print "Layers Energy LBFGS steps"
for i, atoms in enumerate(images):
cell = atoms.get_cell()
if (ucell[0] != cell[0]).any() or (ucell[1] != cell[1]).any():
raise ValueError("The x and y dimensions of the unit cell must be conserved.")
atoms.set_calculator(calc)
dyn = LBFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=fmax, steps=1000)
assert dyn.converged(), "LBFGS not converged in 100 steps!"
layers[i] = len(atoms) / natoms
energies[i] = atoms.get_potential_energy()
if debug:
print "%4i%12.3f%10i" % (layers[i], energies[i], dyn.get_number_of_steps())
p = polyfit(layers.reshape((-1,1)), energies, 1)
surface_energy = p.c[0] / (2 * natoms)
assert surface_energy > 0.0
return surface_energy
def relax_bare_cluster(cluster, relax_fmax=0.05):
c0 = cluster.copy()
orig_index = c0.get_array("orig_index")
fix_list = np.loadtxt("cp2k_fix_list.txt", dtype="int") - 1
fix_orig_index = [orig_index[i] for i in fix_list]
hydrogens = np.where(c0.get_atomic_numbers() == 1)[0]
del c0[hydrogens]
new_fix_list = [i for i, j in enumerate(c0.get_array("orig_index")) if j in fix_orig_index]
pot = calc
c0.set_calculator(pot)
c0.get_potential_energy()
c0.set_array("fixdip", np.array([True if i in new_fix_list else False for i in range(len(c0))]))
c0.set_array("dipoles", np.zeros((len(c0), 3))) # pot.atoms.arrays['dipoles'])
# c0.arrays['dipoles'][new_fix_list, :] = 0.0
const = FixAtoms(indices=new_fix_list)
c0.set_constraint(const)
opt = LBFGS(c0)
opt.run(fmax=relax_fmax)
return c0
def test_Ar_minimize():
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
from ase.optimize import LBFGS
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815886953914,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def add_ligand(atoms, ligand, site, position=None):
atoms.set_tags(0)
ligand = ligand.copy()
# Extract nanoparticle.
np_idx = [ i for i in xrange(len(atoms)) if atoms[i].number > 20 ]
nanoparticle = atoms[np_idx]
# Pick a binding site and shift ligand above it.
com = nanoparticle.get_center_of_mass()
v = atoms[site].position - com
v /= numpy.linalg.norm(v)
ligand.center()
displacement_length = 1.1 * ligand_size(ligand)
if position is None:
ligand.positions += atoms.positions[site] + displacement_length*v
else:
ligand.positions += position + displacement_length*v
ligand.set_tags(1)
# Create combined system.
atoms += ligand
# Construct VSEPR calculator with N-Au interaction.
ligand_mask = [tag == 1 for tag in atoms.get_tags()]
ligand_bonds = connect_bonds(atoms, mask=ligand_mask)
calculator = VSEPR(atoms,
ligand_bonds + [[site,len(atoms)-len(ligand)]],
nonbonded=connect_nonbonded(atoms,
connect_angles(ligand_bonds),
r_cut=displacement_length*2))
atoms.set_calculator(calculator)
atoms.set_constraint(FixAtoms(indices=range(len(atoms)-len(ligand))))
# Run optimization.
opt = LBFGS(atoms, memory=10, maxstep=0.2)
opt.run(fmax=1e-2)
def optimize(self, atoms, name):
args = self.args
if args.constrain_tags:
tags = [int(t) for t in args.constrain_tags.split(',')]
mask = [t in tags for t in atoms.get_tags()]
atoms.constraints = FixAtoms(mask=mask)
trajectory = Trajectory(self.get_filename(name, 'traj'), 'w', atoms)
if args.maximum_stress:
optimizer = LBFGS(UnitCellFilter(atoms), logfile=self.logfile)
fmax = args.maximum_stress
else:
optimizer = LBFGS(atoms, logfile=self.logfile)
fmax = args.maximum_force
optimizer.attach(trajectory)
optimizer.run(fmax=fmax)
data = {}
if hasattr(optimizer, 'force_calls'):
data['force_calls'] = optimizer.force_calls
return data
def test_Ar_minimize(factory, ar_nc, params):
with factory.calc(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815886953914,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def test_unitcellfilter(asap3):
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=1) * (6, 6, 6)
cu.calc = asap3.EMT()
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import bulk
cu = bulk('Cu', 'hcp', a=a / sqrt(2))
cu.cell[1, 0] -= 0.05
cu *= (6, 6, 3)
cu.calc = asap3.EMT()
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
def test_unitcellfilter():
from math import sqrt
from ase import Atoms
from ase.optimize import LBFGS
from ase.constraints import UnitCellFilter
from ase.io import Trajectory
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b),
(b, b, 0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import bulk
cu = bulk('Cu', 'hcp', a=a / sqrt(2))
cu.cell[1, 0] -= 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
def relax(self):
from ase.optimize import LBFGS
cached = sys.__stdout__
try:
optimizer = LBFGS(self.ucf)
optimizer.logfile = None
optimised = optimizer.run(fmax=0.05, steps=100)
except Exception:
optimised = False
self.doc["optimised"] = bool(optimised)
self.doc["positions_abs"] = self.atoms.get_positions().tolist()
self.doc["lattice_cart"] = self.atoms.get_cell().tolist()
self.doc["lattice_abc"] = cart2abc(self.doc["lattice_cart"])
self.doc["positions_frac"] = cart2frac(self.doc["lattice_cart"],
self.doc["positions_abs"])
self.doc["enthalpy_per_atom"] = float(self.calc.results["energy"] /
len(self.doc["atom_types"]))
self.doc["enthalpy"] = float(self.calc.results["energy"])
self.queue.put(self.doc)
sys.stdout = cached
!wget https://www.quantum-espresso.org/upf_files/Cl.pbesol-n-kjpaw_psl.1.0.0.UPF
#----
from ase.build import bulk
from ase.calculators.espresso import Espresso
from ase.constraints import UnitCellFilter
from ase.optimize import LBFGS
import ase.io
pseudopotentials = {'Na': 'Na.pbesol-spn-kjpaw_psl.1.0.0.UPF',
'Cl': 'Cl.pbesol-n-kjpaw_psl.1.0.0.UPF'}
rocksalt = bulk('NaCl', crystalstructure='rocksalt', a=6.0)
calc = Espresso(pseudopotentials=pseudopotentials,pseudo_dir = './',
tstress=True, tprnfor=True, kpts=(3, 3, 3))
rocksalt.set_calculator(calc)
ucf = UnitCellFilter(rocksalt)
opt = LBFGS(ucf)
opt.run(fmax=0.005)
# cubic lattic constant
print((8*rocksalt.get_volume()/len(rocksalt))**(1.0/3.0))
#----
# %cd /content
!mkdir Cu
# %cd Cu
#----
!wget https://www.quantum-espresso.org/upf_files/Cu.pz-d-rrkjus.UPF
#----
from ase import Atoms
from ase.build import bulk
from ase.calculators.espresso import Espresso
atoms = bulk("Cu")
pseudopotentials = {'Cu':'Cu.pz-d-rrkjus.UPF'}
input_data = {
(-r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0),
(-r * cos(a), 0, r * sin(a)), (-r, 0, 0)])
dimer.positions[3:, 0] += 2.8
dimer.constraints = FixBondLengths([
((selection[i] + 3) % 6, (selection[i - 1] + 3) % 6) for i in range(3)
])
dimer.calc = EIQMMM(selection,
GPAW(txt=name + '.txt', h=0.16),
TIP4P(),
interaction,
vacuum=4,
embedding=Embedding(rc=0.2, rc2=20, width=1),
output=name + '.out')
opt = LBFGS(dimer, trajectory=name + '.traj')
opt.run(0.02)
monomer = dimer[selection]
monomer.center(vacuum=4)
monomer.calc = GPAW(txt=name + 'M.txt', h=0.16)
opt = PreconLBFGS(monomer, precon=Exp(A=3), trajectory=name + 'M.traj')
opt.run(0.02)
e0 = monomer.get_potential_energy()
be = dimer.get_potential_energy() - e0
d = dimer.get_distance(0, 3)
print(name, be, d)
if name == '012':
assert abs(be - -0.288) < 0.002
assert abs(d - 2.76) < 0.02
else:
assert abs(be - -0.316) < 0.002
atoms=read('../'+fo2+'.xsf')
mask = [atom.position[2] < 17 for atom in atoms]
fixlayers = FixAtoms(mask=mask)
atoms.set_constraint(fixlayers)
atoms.set_pbc([1,1,1])
# 2. Benchmark.
###############################################################################
# 2.C Optimize using LBFGS.
initial_lbfgs = atoms.copy()
initial_lbfgs.set_calculator(calc)
lbfgs_opt = LBFGS(initial_lbfgs, trajectory=fo2+'_lbfgs.traj')
itime=time.default_timer()
lbfgs_opt.run(fmax=0.01)
logging.warning('lbfgs = %s', time.default_timer()-itime)
# 2.D Optimize using FIRE.
initial_fire = atoms.copy()
initial_fire.set_calculator(calc)
fire_opt = FIRE(initial_fire, trajectory=fo2+'_fire.traj')
itime=time.default_timer()
fire_opt.run(fmax=0.01)
logging.warning('fires = %s', time.default_timer()-itime)
# 2.A. Optimize structure using MLMin (CatLearn).
initial_mlmin = atoms.copy()
initial_mlmin.set_calculator(calc)
mlmin_opt = MLMin(initial_mlmin, trajectory=fo2+'_catlearn.traj')
itime=time.default_timer()
ediffg = float(line.split('=')[1])
ediffg = ediffg * -1.0
return nsw, pstress, tebeg, potim, ediffg
if __name__ == '__main__':
'''
stress format: XX XY XZ YY YZ ZZ
units: kB
'''
calc = GAP(rcut=6.0)
nsw, pstress, _, _, ediffg = read_incar()
my_atoms = read('POSCAR', format='vasp')
my_atoms.set_calculator(calc)
dyn = LBFGS(my_atoms, trajectory='ase.traj')
dyn.run(fmax=ediffg, steps=nsw)
atoms_lat = my_atoms.cell
atoms_pos = my_atoms.positions
atoms_force = my_atoms.get_forces()
atoms_stress = my_atoms.get_stress()
atoms_num = my_atoms.get_atomic_numbers()
atoms_symbols = my_atoms.get_chemical_symbols()
atoms_formula = my_atoms.get_chemical_formula()
atoms_ene = my_atoms.get_potential_energy()
atoms_vol = my_atoms.get_volume()
element, ele = get_ele_dict(atoms_symbols)
write_contcar(element, ele, atoms_lat, atoms_pos)
write_outcar(element, ele, atoms_vol, atoms_lat, atoms_pos, \
atoms_ene, atoms_force, atoms_stress * 10.0, pstress)
# Construct pyNeuroChem class
nc = pync.molecule(cnstfile, saefile, nnfdir, 0)
files = [f for f in os.listdir(idir) if f.split(".")[1] == "ipt"]
for i, f in enumerate(files):
data = hdn.read_rcdb_coordsandnm(idir + f)
X = data['coordinates']
S = data['species']
mol = Atoms(positions=X, symbols=S)
mol.set_calculator(ANI(False))
mol.calc.setnc(nc)
dyn = LBFGS(mol, logfile='optimization.log')
dyn.run(fmax=0.00001, steps=1000)
X = mol.get_positions()
Nc = int(f.split(".")[0].split("-")[1])
Fp = f.split("-")[0]
smiles = get_smiles(idir + f)
print(i, 'of', len(files), ':', f, dyn.get_number_of_steps(), Nc)
hdn.write_rcdb_input(X,
S,
Nc,
sdir,
Fp,
50,
'wb97x/6-31g*',
from ase.io import Trajectory
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
#!/usr/bin/env python3
from ase import Atom, Atoms
from ase.build import bulk, fcc100, add_adsorbate, add_vacuum
from ase.calculators.vasp import Vasp
from ase.calculators.kim.kim import KIM
from ase.calculators.qmmm import ForceQMMM, RescaledCalculator
from ase.constraints import StrainFilter
from ase.optimize import LBFGS
from ase.visualize import view
atoms = bulk("Pd", "fcc", a=3.5, cubic=True)
atoms.calc = KIM("MEAM_LAMMPS_JeongParkDo_2018_PdMo__MO_356501945107_000")
opt = LBFGS(StrainFilter(atoms), logfile=None)
opt.run(0.03, steps=30)
length = atoms.cell.cellpar()[0]
atoms = fcc100("Pd", (2,2,5), a=length, vacuum=10, periodic=True)
add_adsorbate(atoms, Atoms([Atom("Mo")]), 1.2)
qm_mask = [len(atoms)-1, len(atoms)-2]
qm_calc = Vasp(directory="./qmmm")
mm_calc = KIM("MEAM_LAMMPS_JeongParkDo_2018_PdMo__MO_356501945107_000")
mm_calc = RescaledCalculator(mm_calc, 1, 1, 1, 1)
qmmm = ForceQMMM(atoms, qm_mask, qm_calc, mm_calc, buffer_width=3)
qmmm.initialize_qm_buffer_mask(atoms)
atoms.pbc=True
atoms.calc = qmmm
print(atoms.get_forces())
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
calc = LAMMPS(specorder=['Ar'], **params)
ar_nc.set_calculator(calc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815886953914,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dir = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnntsgdb11_02/'
#bz = read('C_100.xyz')
#bz = read('/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_testdata/specialtest/test.xyz')
bz = read(dir + 'molecule-0.xyz')
#L = 16.0
#bz.set_cell(([[L,0,0],[0,L,0],[0,0,L]]))
#bz.set_pbc((True, True, True))
bz.set_calculator(ANI(False))
bz.calc.setnc(nc)
start_time = time.time()
dyn = LBFGS(bz)
dyn.run(fmax=0.0001)
print('[ANI Total time:', time.time() - start_time, 'seconds]')
# Write visualization of molecule
#f = open("optmol_begin.xyz",'w')
#f.write('\n' + str(len(bz)) + '\n')
#for i in bz:
# f.write(str(i.symbol) + ' ' + str(i.x) + ' ' + str(i.y) + ' ' + str(i.z) + '\n')
#f.close()
# Temperature
T = 300.0
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 5 fs, the temperature T and the friction
# coefficient to 0.02 atomic units.
import numpy as np
from ase.build import molecule
from ase.calculators.qchem import QChem
from ase.optimize import LBFGS
mol = molecule('C2H6')
calc = QChem(label='calc/ethane', method='B3LYP', basis='6-31+G*')
mol.set_calculator(calc)
# Check energy and forces
np.testing.assert_allclose(mol.get_potential_energy(),
-2172.379183703419,
atol=10.)
np.testing.assert_allclose(mol.get_forces(),
np.array([[0., 0.00240141, 0.04992568],
[-0., -0.00240141, -0.04992568],
[-0., 0.11626015, 0.07267481],
[-0.10132204, -0.05804009, 0.07538475],
[0.10132204, -0.05804009, 0.07538475],
[-0., -0.11626015, -0.07267481],
[-0.10132204, 0.05804009, -0.07538475],
[0.10132204, 0.05804009, -0.07538475]]),
atol=0.05)
opt = LBFGS(mol)
opt.run()
assert opt.converged()
from ase_interface import aniensloader
import ase
import time
from ase import units
from ase.io import read, write
from ase.optimize import BFGS, LBFGS
# Read molecule from xyz
mol = read('data/water.xyz')
# Current ANI model options are:
# '../ani_models/ani-1ccx_8x.info' Coupled cluster transfer learned model
# '../ani_models/ani-1x_8x.info' Full ANI-1x wb97x/6-31g* dataset model
mol.set_calculator(ANIENS(aniensloader('../ani_models/ani-1ccx_8x.info', 0)))
# Calculate energy
ei = mol.get_potential_energy()
print("Initial Energy: ", ei)
# Optimize molecule
print("Optimizing...")
start_time = time.time()
dyn = LBFGS(mol)
dyn.run(fmax=0.001)
print('[ANI Optimization - Total time:', time.time() - start_time, 'seconds]')
# Calculate energy
ef = mol.get_potential_energy()
print("Final Energy: ", ef)
calc = fp_GD_Calculator()
# atoms.set_calculator(calc)
atoms.calc = calc
############################## Relaxation type ##############################
'''
Ref :
https://wiki.fysik.dtu.dk/ase/ase/optimize.html#module-optimize
https://wiki.fysik.dtu.dk/ase/ase/constraints.html
'''
af = atoms
# af = StrainFilter(atoms)
# af = UnitCellFilter(atoms)
print(af.get_forces())
############################## Relaxation method ##############################
# opt = BFGS(af, maxstep = 1.e-3, trajectory = trajfile)
# opt = FIRE(af, maxstep = 1.e-3, trajectory = trajfile)
opt = LBFGS(af, maxstep = 1.e-1, trajectory = trajfile, memory = 10, use_line_search = True)
# opt = LBFGS(af, maxstep = 1.e-3, trajectory = trajfile, memory = 10, use_line_search = False)
# opt = SciPyFminCG(af, trajectory = trajfile)
# opt = SciPyFminBFGS(af, trajectory = trajfile)
opt.run(fmax = 1.e-10)
traj = Trajectory(trajfile)
ase.io.write('opt.vasp', traj[-1], direct = True, long_format=True, vasp5 = True)
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from ase.optimize import LBFGS
import numpy as np
calc = EMT()
symbol = 'Cu'
syms = ((True, True, True),
(False, False, False),
(True, True, False),
(True, False, False))
for symmetry in syms:
print "Periodicity:", symmetry
for n in (4,6):
atoms = FaceCenteredCubic(symbol=symbol, size=(4, 8, n), pbc=symmetry)
atoms.set_calculator(calc)
dyn = LBFGS(atoms, trajectory=None, logfile=None)
dyn.run(fmax=0.05)
e = atoms.get_potential_energy()
print "Layers, energy: %2i %8.3f" % (n, e)
print "TEST PASSED."
file_name = file_name_py.replace('.py', '')
file_traj = file_name + '.traj'
start_file = '../In2O3_110_clean.traj'
mode = 'a'
try:
sys = Trajectory(file_traj, 'r')[-1]
except (IOError, RuntimeError):
print "Importing trajectory file from: %s" % start_file
sys = read(start_file)
sys.center(vacuum=5.0, axis=2)
else:
print "Importing trajectory file from: %s" % file_traj
set_calc_In2O3(sys)
print "Constraints:"
print " c1: Fix bottom two layers."
avg_z = np.mean([atom.z for atom in sys])
c1 = FixAtoms(mask=[atom.z < avg_z for atom in sys])
sys.set_constraint(c1)
if testRun == True:
run_testRun(sys)
else:
geo_traj = Trajectory(file_traj, mode, sys)
dyn = LBFGS(sys, trajectory=geo_traj)
dyn.run(fmax=0.05)
energy = sys.get_potential_energy()
print "Energy: %f" % energy
print "Completed %s" % file_name_py
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu',
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)