def test_emt1():
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import Trajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0), (b, b, 0), (a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = Trajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f():
print(cu.get_distance(0, 1))
qn.attach(f)
qn.run(fmax=0.001)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
def relaxGPAW(structure, label, forcemax=0.1, niter_max=1, steps=10):
# Set calculator
calc = get_calculator()
calc.set(txt=label+'_true.txt')
# Set calculator
structure.set_calculator(calc)
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
if (structure.get_forces()**2).sum(axis = 1).max()**0.5 < forcemax:
return structure
traj = Trajectory(label+'_lcao.traj','w', structure)
while (structure.get_forces()**2).sum(axis = 1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure,
logfile=label+'.log')
vb = VariansBreak(structure, dyn, min_stdev = 0.01, N = 15)
dyn.attach(traj)
dyn.attach(vb)
dyn.run(fmax = forcemax, steps = steps)
niter += 1
E = structure.get_potential_energy()
F = structure.get_forces()
del calc
del dyn
return structure, E, F
def get_neb(in_file='input.traj'):
"""Performs a ASE NEB optimization with the ase-espresso
calculator with the keywords defined inside the atoms object information.
Parameters
----------
in_file : str
Name of the input file to load from the local directory.
"""
images = read(in_file, ':')
for atoms in images[1:-1]:
calc = espresso(**atoms.info)
atoms.set_calculator(calc)
neb = NEB(images)
opt = BFGS(neb, trajectory='output.traj', logfile=None)
opt.run(fmax=atoms.info.get('fmax'))
out_images = read('output.traj', ':')
# Save the calculator to the local disk for later use.
try:
calc.save_flev_output()
except (RuntimeError):
calc.save_output()
return atoms_to_encode(out_images)
def test_stress(atoms):
cell0 = atoms.get_cell()
atoms.set_cell(np.dot(
atoms.cell, [[1.02, 0, 0.03], [0, 0.99, -0.02], [0.1, -0.01, 1.03]]),
scale_atoms=True)
atoms *= (1, 2, 3)
cell0 *= np.array([1, 2, 3])[:, np.newaxis]
atoms.rattle()
# Verify analytical stress tensor against numerical value
s_analytical = atoms.get_stress()
s_numerical = atoms.calc.calculate_numerical_stress(atoms, 1e-5)
s_p_err = 100 * (s_numerical - s_analytical) / s_numerical
print("Analytical stress:\n", s_analytical)
print("Numerical stress:\n", s_numerical)
print("Percent error in stress:\n", s_p_err)
assert np.all(abs(s_p_err) < 1e-5)
# Minimize unit cell
opt = BFGS(UnitCellFilter(atoms))
opt.run(fmax=1e-3)
# Verify minimized unit cell using Niggli tensors
g_minimized = np.dot(atoms.cell, atoms.cell.T)
g_theory = np.dot(cell0, cell0.T)
g_p_err = 100 * (g_minimized - g_theory) / g_theory
print("Minimized Niggli tensor:\n", g_minimized)
print("Theoretical Niggli tensor:\n", g_theory)
print("Percent error in Niggli tensor:\n", g_p_err)
assert np.all(abs(g_p_err) < 1)
def test_relax_co_ase_interactive_bfgs(tmpdir):
tmpdir.chdir()
co = Atoms('CO', [[2.256 * Bohr, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = iEspresso(pw=24.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='relax',
ion_dynamics='ase3',
spinpol=False,
outdir='qe_ase_interactive_bfgs')
co.set_calculator(calc)
minimizer = BFGS(co, logfile='minimizer.log', trajectory='relaxed.traj')
minimizer.run(fmax=0.01)
ref_ene = -616.9017404193379
ref_pos = np.array([[1.19233393e+00, 0.0e+00, 0.00000000e+00],
[1.48996586e-03, 0.00000000e+00, 0.00000000e+00]])
ref_for = np.array([[0.00162288, 0.0, 0.0],
[-0.00162288, 0.0, 0.0]])
assert np.allclose(co.get_potential_energy(), ref_ene)
#assert np.allclose(co.positions, ref_pos)
#assert np.allclose(co.get_forces(), ref_for)
print(co.positions)
print(co.get_forces())
def run_server(launchclient=True):
atoms = getatoms()
with SocketIOCalculator(log=sys.stdout, port=port,
timeout=timeout) as calc:
if launchclient:
thread = launch_client_thread()
atoms.calc = calc
opt = BFGS(atoms)
opt.run()
if launchclient:
thread.join()
forces = atoms.get_forces()
energy = atoms.get_potential_energy()
atoms.calc = EMT()
ref_forces = atoms.get_forces()
ref_energy = atoms.get_potential_energy()
refatoms = run_normal()
ref_energy = refatoms.get_potential_energy()
eerr = abs(energy - ref_energy)
ferr = np.abs(forces - ref_forces).max()
perr = np.abs(refatoms.positions - atoms.positions).max()
print('errs e={} f={} pos={}'.format(eerr, ferr, perr))
assert eerr < 1e-11, eerr
assert ferr < 1e-11, ferr
assert perr < 1e-11, perr
def get_optimal_h(atoms, bottom, top, natoms, dyn = False):
# This find the optimal h - when the top is sliding:
if not dyn:
from scipy.optimize import fmin
pos_init = atoms.positions.copy()
zmax = np.amax(atoms.positions[bottom][:,2])
def get_epot(z):
new_pos = pos_init
for iat in range(len(atoms)):
if top[iat]:
new_pos[iat][2] = z + zmax
atoms.positions = new_pos
e = atoms.get_potential_energy()/natoms
print z, e
return e
hmin = fmin(get_epot, 3.34)
emin = get_epot(hmin)
atoms.positions = pos_init
print 'optimal height= %.2f and e=%.2f' %(hmin, emin)
return emin, hmin
else:
dyn = BFGS(atoms)
dyn.run(fmax=0.03)
e = atoms.get_potential_energy()/natoms
layers = find_layers(atoms.positions)[0]
hmin = layers[1] - layers[0]
return e, hmin
def scan_dihed_qforce(self,
all_config,
frag,
scan_dir,
mol,
n_run,
nsteps=1000):
md_energies = []
for i, coord in enumerate(frag.coords):
restraints = self.find_restraints(frag, frag.qm_coords[i], n_run)
atom = Atoms(frag.elements,
positions=coord,
calculator=QForce(frag.terms,
dihedral_restraints=restraints))
traj_name = f'{scan_dir}/{frag.id}_run{n_run+1}_{i:02d}.traj'
log_name = f'{scan_dir}/opt_{frag.id}_run{n_run+1}.log'
e_minimiz = BFGS(atom, trajectory=traj_name, logfile=log_name)
e_minimiz.run(fmax=0.01, steps=nsteps)
coords = atom.get_positions()
self.calc_fit_angles(frag, coords)
md_energies.append(atom.get_potential_energy())
frag.coords[i] = coords
return np.array(md_energies)
def get_optimal_h(atoms, natoms, dyn = False, show = False):
# This find the optimal h - when the top is sliding:
if not dyn:
from scipy.optimize import fmin
pos_init = atoms.positions.copy()
def get_epot(z):
new_pos = pos_init
new_pos[:,2] = z
atoms.positions = new_pos
e = atoms.get_potential_energy()/natoms
#print z, e
return e
hmin = fmin(get_epot, 3.4, disp = 0)
emin = get_epot(hmin)
atoms.positions = pos_init
if show: print 'optimal height= %.2f and e=%.2f' %(hmin, emin)
return emin, hmin
else:
dyn = BFGS(atoms)
dyn.run(fmax=0.03)
e = atoms.get_potential_energy()/natoms
hmin = np.average(atoms.positions[:,2])
return e, hmin
def test_relax_co_ase_bfgs(tmpdir):
tmpdir.chdir()
co = Atoms('CO', [[2.256 * Bohr, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = Espresso(pw=24.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='scf',
ion_dynamics=None,
spinpol=False,
outdir='qe_ase_bfgs')
co.set_calculator(calc)
minimizer = BFGS(co, logfile='minimizer.log', trajectory='relaxed.traj')
minimizer.run(fmax=0.01)
print('ase(scf) bfgs:')
print('energy: ', co.get_potential_energy())
print('positions: ', co.positions)
print('forces: ', co.get_forces())
def do_constrained_optimization(self):
logfile = self.log_prefix + 'relax_' + str(self.a) + '.log'
trajectory = self.traj_prefix + 'relax_' + str(self.a) + '.traj'
if self.adaptive_threshold is None:
dyn = BFGS(self.atoms, logfile=logfile, trajectory=trajectory, maxstep=self.maxstep)
dyn.run(fmax=self.fmax * self.fixed_conv_ratio)
else:
dyn = scan_bfgs(self.atoms, logfile=logfile, trajectory=trajectory, maxstep=self.maxstep)
dyn.pass_constraint(self.scanned_constraint, totfmax=self.fmax)
dyn.run(fmax=self.adaptive_threshold)
pg = self.scanned_constraint.projected_force
self.atoms.set_constraint(self.only_other_constraints)
e = self.atoms.get_potential_energy()
f = self.atoms.get_forces()
fi_max = max([np.linalg.norm(f_1 + f_2) for f_1, f_2 in zip(f, self.scanned_constraint.projected_forces)])
self.atoms.set_constraint(self.constraintlist)
if self.a not in self.dopt:
self.dopt[self.a] = {}
self.dopt[self.a][fi_max] = {}
self.dopt[self.a][fi_max]['pf'] = pg
self.dopt[self.a][fi_max]['e'] = e
self.dopt[self.a][fi_max]['xyz'] = self.atoms.get_positions()
self.dopt[self.a][fi_max]['na_step'] = self.na_step
self.write_restart()
return e, pg, fi_max, f
def get_energies(autotst_object):
if isinstance(autotst_object, autotst.molecule.AutoTST_Molecule):
ase_object = autotst_object.ase_molecule
labels = []
if isinstance(autotst_object, autotst.reaction.AutoTST_Reaction):
ase_object = autotst_object.ts.ase_ts
labels = []
for atom in autotst_object.ts.rmg_ts.getLabeledAtoms().values():
labels.append(atom.sortingLabel)
if isinstance(autotst_object, autotst.reaction.AutoTST_TS):
ase_object = autotst_object.ase_ts
labels = []
for atom in autotst_object.ts.rmg_ts.getLabeledAtoms().values():
labels.append(atom.sortingLabel)
constrained_energy = ase_object.get_potential_energy()
ase_copy = ase_object.copy()
ase_copy.set_calculator(ase_object.get_calculator())
ase_copy.set_constraint(
FixBondLengths(list(itertools.combinations(labels, 2))))
opt = BFGS(ase_copy)
opt.run(fmax=0.01)
relaxed_energy = ase_copy.get_potential_energy()
return constrained_energy, relaxed_energy, ase_copy
def fixOverlap(clus_to_fix):
"""
Support function to fix any overlaps that may arise due to the mutations by radially moving the atoms that have overlap
"""
natoms = len(clus_to_fix)
CoM(clus_to_fix)
for i in range(natoms):
for j in range(i):
r1 = np.array(clus_to_fix[j].position)
r2 = np.array(clus_to_fix[i].position)
rij = r2 - r1
distance = np.sqrt(np.dot(rij, rij))
dmin = (covalent_radii[clus_to_fix[i].number] +
covalent_radii[clus_to_fix[j].number]) * 0.9
if distance < 0.9 * dmin:
a = np.dot(r2, r2)
b = np.dot(r1, r2)
c = np.dot(r1, r1) - dmin**2
alpha = 1.000001 * (b + np.sqrt(b * b - a * c)) / a
clus_to_fix[i].x *= alpha
clus_to_fix[i].y *= alpha
clus_to_fix[i].z *= alpha
clus_to_fix.center(vacuum=9)
clus_to_fix_sorted = sort(clus_to_fix)
clus_to_fix_sorted.pbc = (True, True, True)
clus_to_fix_sorted.calc = EMT()
dyn = BFGS(clus_to_fix_sorted, logfile=None)
dyn.run(fmax=0.05, steps=1000)
return clus_to_fix_sorted
def minimize(
atomno,
coord,
method="GFN2-xTB",
accuracy=1.0,
electronic_temperature=300.0,
max_iterations=250,
solvent="water",
cache_api=True,
constraints=None,
):
atoms = Atoms(numbers=atomno, positions=coord)
calc = XTB(
method=method,
accuracy=accuracy,
electronic_temperature=electronic_temperature,
max_iterations=max_iterations,
solvent=solvent,
cache_api=cache_api,
)
atoms.set_calculator(calc)
if constraints is not None:
for c in constraints:
atoms.set_constraint(c)
opt = BFGS(atoms)
opt.run(fmax=0.05)
return atoms.numbers, atoms.get_positions()
def test_relax():
"""
Test that a static relaxation that requires multiple neighbor list
rebuilds can be carried out successfully. This is verified by relaxing
an icosahedral cluster of atoms and checking that the relaxed energy
matches a known precomputed value for an example model.
"""
import numpy as np
from ase.cluster import Icosahedron
from pytest import importorskip
importorskip('kimpy')
from ase.calculators.kim import KIM
from ase.optimize import BFGS
energy_ref = -0.5420939378624228 # eV
# Create structure and calculator
atoms = Icosahedron("Ar", latticeconstant=3.0, noshells=2)
calc = KIM("ex_model_Ar_P_Morse_07C")
atoms.calc = calc
opt = BFGS(atoms, logfile=None)
opt.run(fmax=0.05)
assert np.isclose(atoms.get_potential_energy(), energy_ref)
def push_apart(atoms,
blmin,
variable_cell=False,
maxsteps=500,
logfile=None,
trajectory=None):
""" Push atoms apart so as to (try) satisfy the blmin dictionary
of minimal interatomic distances while not displacing the
atoms too much. The default SHPP calculator is used for
this purpose.
atoms: an Atoms object
blmin: dictionary with the minimal interatomic distance
for each (sorted) pair of atomic numbers
variable_cell: whether to allow the cell vectors to vary
maxsteps: maximum number of optimizer steps
trajectory: (filename of the) trajectory to attach to the optimizer
logfile: (filename of the) logfile for the optimizer
"""
if variable_cell:
blminmax = max([blmin[k] for k in blmin if k[0] == k[1]])
cell = atoms.get_cell()
for i in range(3):
cell[i] *= max(1, blminmax / np.linalg.norm(cell[i]))
atoms.set_cell(cell, scale_atoms=True)
calc = SHPP(atoms, blmin)
atoms.set_calculator(calc)
dyn = BFGS(atoms, maxstep=0.05, logfile=logfile, trajectory=trajectory)
dyn.run(fmax=0.05, steps=maxsteps)
return atoms
def test_au111(wrap):
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.set_calculator(calc)
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%d.traj' % wrap)
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
assert abs(slab.get_distance(-2, -1, mic=1) - d2) < 1e-9
def calc(id):
db = connect(db_name)
atoms_orig = db.get_atoms(id=id)
kvp = db.get(id=id).key_value_pairs
atoms = atoms_orig.copy()
# Do linear interpolation of the cell size
a_au = 4.0782
a_cu = 3.6149
symbs = atoms.get_chemical_symbols()
count = {"Au": 0, "Cu": 0}
for s in symbs:
count[s] += 1
c_au = float(count["Au"]) / len(atoms)
a = a_au * c_au + a_cu * (1.0 - c_au)
a_orig = 3.9
cell = atoms.get_cell()
atoms.set_cell(cell * a / a_orig, scale_atoms=True)
calc = EMT()
atoms.set_calculator(calc)
relaxer = BFGS(atoms)
relaxer.run(fmax=0.025)
res = minimize(relax_cell, a, args=(atoms, cell))
print(res["x"])
relaxer = BFGS(atoms)
relaxer.run(fmax=0.025)
energy = atoms.get_potential_energy()
del db[id]
calc = SinglePointCalculator(atoms_orig, energy=energy)
atoms_orig.set_calculator(calc)
kvp["converged"] = True
db.write(atoms_orig, key_value_pairs=kvp)
def run_cp2k(template_file):
from ase.calculators.cp2k import CP2K, parse_input
from ase.build import molecule
from ase.optimize import BFGS
with open('cp2k_mm_energy.inp', 'r') as f:
content = f.read()
calc = CP2K()
#print("input parameters")
#print(calc.inp)
print(calc)
print("input parameters")
#print(calc.todict())
print("parsing input")
parsed = parse_input(content)
print(parsed)
print(parsed.name)
print(parsed.params)
print(parsed.keywords)
print(parsed.subsections)
exit(0)
atoms = molecule('H2O', calculator=calc)
atoms.center(vacuum=2.0)
gopt = BFGS(atoms, logfile=None)
gopt.run(fmax=1e-6)
print(atoms.get_potential_energy())
return
def relax_VarianceBreak(structure, calc, label='', niter_max=10, forcemax=0.1):
'''
Relax a structure and saves the trajectory based in the index i
Parameters
----------
structure : ase Atoms object to be relaxed
Returns
-------
'''
# Set calculator
structure.set_calculator(calc)
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
if (structure.get_forces()**2).sum(axis = 1).max()**0.5 < forcemax:
return structure
while (structure.get_forces()**2).sum(axis = 1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure,
logfile=label+'.log')
vb = VariansBreak(structure, dyn, min_stdev = 0.01, N = 15)
dyn.attach(vb)
dyn.run(fmax = forcemax, steps = 200)
niter += 1
return structure
def optimize_molecule(nuclear_charges, coordinates):
# LOAD AND SET MODEL
parameters = {}
parameters["offset"] = -97084.83100465109
parameters["sigma"] = 10.0
alphas = np.load(FILENAME_ALPHAS)
X = np.load(FILENAME_REPRESENTATIONS)
Q = np.load(FILENAME_CHARGES)
calculator = QMLCalculator(parameters, X, Q, alphas)
molecule = ase.Atoms(nuclear_charges, coordinates)
molecule.set_calculator(calculator)
energy = molecule.get_potential_energy()
forces = molecule.get_forces()
dyn = BFGS(molecule)
dyn.run(fmax=0.5)
dump_xyz(molecule, "tmp_opt.xyz")
return
def run_one_in_plane_distance(self,
cell_length_x=2.0,
cell_length_y=2.0,
direction=(0, 0, 1),
smax=0.003):
# Rotate the atoms object such that the z-direction points along target_z_direction
self.atoms = align_direction_with_z(self.atoms, direction=direction)
lengths_angles = self.atoms.get_cell_lengths_and_angles()
ratio_x = cell_length_x / lengths_angles[0]
ratio_y = cell_length_y / lengths_angles[1]
cell = self.atoms.get_cell()
cell[0, :] *= ratio_x
cell[1, :] *= ratio_y
self.atoms.set_cell(cell.T, scale_atoms=True)
strfilter = StrainFilter(self.atoms, mask=[0, 0, 1, 1, 1, 1])
relaxer = BFGS(self.atoms)
V = self.atoms.get_volume()
relaxer.run(fmax=smax * V)
# Store the results to ase db
db = connect(self.db_name)
kvp = {
"cell_length_x": cell_length_x,
"cell_length_y": cell_length_y,
"direction_x": direction[0],
"direction_y": direction[1],
"direction_z": direction[2]
}
db.write(self.atoms, key_value_pairs=kvp)
def run_NEB():
if method == 'dyn':
neb = DyNEB(images, fmax=fmax, dynamic_relaxation=True)
neb.interpolate()
elif method == 'dyn_scale':
neb = DyNEB(images,
fmax=fmax,
dynamic_relaxation=True,
scale_fmax=6.)
neb.interpolate()
else:
# Default NEB
neb = DyNEB(images, dynamic_relaxation=False)
neb.interpolate()
# Optimize and check number of calculations.
# We use a hack with a global counter to count the force evaluations:
force_evaluations[0] = 0
opt = BFGS(neb)
opt.run(fmax=fmax)
force_calls.append(force_evaluations[0])
# Get potential energy of transition state.
Emax.append(
np.sort([image.get_potential_energy()
for image in images[1:-1]])[-1])
def Surface001(self, EMT, PARAMETERS):
""" The Method calculates and returns the surface energy for the given element along the [0,0,1] direction in
the FCC crystal structure. """
# The size of the crystals are set:
S001 = 3, 3, 5
# The surfaces (slabs) are created (pbc=(1,1,0) creates periodic boudry conditions
# in two of three directions and thus leaves the last direction as two surfaces.
Surface001 = FaceCenteredCubic(size=S001,
symbol=self.Element,
pbc=(1, 1, 0))
Surface001.set_calculator(EMT)
# A structural relaxsation is run for the surface crystal in order to secure
# the correct structure of the crystal.
dyn001 = BFGS(Surface001, logfile=None)
dyn001.run(fmax=0.01)
# The referance bulk crystals are created
Bulk001 = FaceCenteredCubic(size=S001, symbol=self.Element)
# The calculator is assigned
Bulk001.set_calculator(EMT)
# The surface area is calculated
# The cross product between the x and y axis in the crystal is determined
Cross001 = numpy.cross(Bulk001.get_cell()[:, 0],
Bulk001.get_cell()[:, 1])
# The area of the surface is determined from the formular A = |X x Y|.
area001 = numpy.sqrt(numpy.dot(Cross001, Cross001))
# The surface energy is calculated and returned (two surfaces are present in
# SurfaceRelaxed)
return ((Surface001.get_potential_energy() -
Bulk001.get_potential_energy()) / 2 / area001)
def create_lst_images(freactant, fproduct, nimages=11, mic=False):
"""create images with original LST algorithm without NEB force projection as in IDPP
Parameters
----------
freactant : path to initial atoms
fproduct : path to final atoms
nimages : the number of images to be interpolated including two endpoints
mic : apply mic or not (PBC)
"""
from ase.neb import IDPP
from ase.optimize import BFGS
from ase.build import minimize_rotation_and_translation
# create linearly interpolated images
images = _create_images(freactant, fproduct, nimages)
neb = NEB(images, remove_rotation_and_translation=True)
neb.interpolate()
# refine images with LST algorithm
d1 = images[0].get_all_distances(mic=mic)
d2 = images[-1].get_all_distances(mic=mic)
d = (d2 - d1) / (nimages - 1)
for i, image in enumerate(images):
image.set_calculator(IDPP(d1 + i * d, mic=mic))
qn = BFGS(image)
qn.run(fmax=0.1)
# apply optimal translation and rotation
for i in range(nimages - 1):
minimize_rotation_and_translation(images[i], images[i + 1])
return images
def relaxGPAW(structure, label, calc, forcemax=0.1, niter_max=1, steps=10):
calc.set(txt=label + '_init.txt')
# Set calculator
structure.set_calculator(calc)
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
if (structure.get_forces()**2).sum(axis=1).max()**0.5 < forcemax:
return structure
#print('relaxgpaw start',flush=True)
traj = Trajectory(label + '_lcao.traj', 'w', structure)
while (structure.get_forces()**
2).sum(axis=1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure, logfile=label + '.log')
vb = VariansBreak(structure, dyn, min_stdev=0.01, N=15)
dyn.attach(traj)
dyn.attach(vb)
dyn.run(fmax=forcemax, steps=steps)
niter += 1
#print('relaxgpaw over',flush=True)
return structure
def test_dftb_relax_dimer():
import os
from ase import Atoms
from ase.test import require
from ase.test.testsuite import datafiles_directory
from ase.calculators.dftb import Dftb
from ase.optimize import BFGS
require('dftb')
os.environ['DFTB_PREFIX'] = datafiles_directory
calc = Dftb(
label='dftb',
Hamiltonian_SCC='No',
Hamiltonian_PolynomialRepulsive='SetForAll {Yes}',
)
atoms = Atoms('Si2',
positions=[[5., 5., 5.], [7., 5., 5.]],
cell=[12.] * 3,
pbc=False)
atoms.set_calculator(calc)
dyn = BFGS(atoms, logfile='-')
dyn.run(fmax=0.1)
e = atoms.get_potential_energy()
assert abs(e - -64.830901) < 1., e
def compute_energy(self, particle, relax_atoms=False):
"""Compute the energy using EMT.
BFGS is used for relaxation. By default, the atoms are NOT relaxed, i.e. the
geometry remains unchanged unless this is explicitly stated.
Parameters:
particle : Nanoparticle
relax_atoms : bool
"""
cell_width = 1e3
cell_height = 1e3
cell_length = 1e3
atoms = particle.get_ase_atoms(exclude_x=True)
if not relax_atoms:
atoms = atoms.copy()
atoms.set_cell(np.array([[cell_width, 0, 0], [0, cell_length, 0], [0, 0, cell_height]]))
atoms.set_calculator(EMT())
dyn = BFGS(atoms)
dyn.run(fmax=self.fmax, steps=self.steps)
energy = atoms.get_potential_energy()
particle.set_energy(self.energy_key, energy)
def optimize(self):
self.calc = EMT()
dyn = BFGS(self)
dyn.run(fmax=0.05)
self.optimized = ZMatrix()
for _atom in dyn.atoms:
self.optimized += _atom
def main():
'''Main driver routine.'''
initial = read('NH3_initial.traj')
final = read('NH3_final.traj')
images = [initial]
images += [initial.copy() for ii in range(NIMAGES)]
images += [final]
neb = NEB(images)
neb.interpolate()
opt = BFGS(neb, trajectory='i2f.traj')
calcs = [
Dftb(label='NH3_inversion',
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance='1.00E-06',
Hamiltonian_MaxAngularMomentum_N='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"') for ii in range(NIMAGES)
]
for ii, calc in enumerate(calcs):
images[ii + 1].set_calculator(calc)
opt.run(fmax=1.00E-02)
def test(size, R, nk):
atoms_flat = get_square_uCell(size)
view(atoms_flat)
# CALCULATOR FLAT
calc_f = Hotbit(SCC=False, kpts=(nk,nk,1), \
txt= path + 'test_consistency/optimization_flat.cal')
atoms_flat.set_calculator(calc_f)
opt_f = BFGS(atoms_flat)
opt_f.run(fmax = 0.05)
e_flat = atoms_flat.get_potential_energy()
atoms_c = atoms_flat.copy()
L = atoms_c.get_cell().diagonal()
atoms_c.set_cell(L)
angle = L[1]/R
atoms_c.rotate('y', np.pi/2)
atoms_c.translate((-atoms_c[0].x, 0, 0) )
for a in atoms_c:
r0 = a.position
phi = r0[1]/L[1]*angle
a.position[0] = R*np.cos(phi)
a.position[1] = R*np.sin(phi)
atoms_c = Atoms(atoms = atoms_c, container = 'Wedge')
atoms_c.set_container(angle = angle, height = L[0], physical = False, pbcz = True)
if R < 100:
view(atoms_c.extended_copy((8,1,3)))
# CALCULATOR Cyl
calc_c = Hotbit(SCC=False, kpts=(nk,1, nk), physical_k = False, \
txt= path + 'test_consistency/optimization_cyl.cal')
atoms_c.set_calculator(calc_c)
opt_c = BFGS(atoms_c)
opt_c.run(fmax = 0.05)
e_cyl = atoms_c.get_potential_energy()
print 'R = %.2f' %R
print 'energy flat = %.6f' %e_flat
print 'energy cylinder = %.6f' %e_cyl
print 'energy dif (e_cylinder - eflat)/nAtoms = %.6f \n' %(-(e_flat - e_cyl)/len(atoms_flat))
return e_flat, e_cyl, len(atoms_flat)
def ase_minimization(indiv, Optimizer):
"""Function to use built in ASE minimizers to minimize atomic positions in structure.
Input:
indiv = Individual class object to be optimized
Optimizer = Optimizer class object with needed parameters
Output:
indiv = Optimized Individual class object.
"""
if 'MU' in Optimizer.debug:
debug = True
else:
debug = False
cwd1=os.getcwd()
olammpsmin = Optimizer.lammps_min
if Optimizer.lammps_min:
Optimizer.lammps_min = None
calc2 = setup_calculator(Optimizer)
# if 'mass' in indiv[0].get_calculator():
# mass2 = ['1 '+ str(Optimizer.atomlist[0][2])]
# if len(Optimizer.atomlist) > 1:
# for i in range(len(Optimizer.atomlist)-1):
# mass2.append(str(i+2) + ' ' + str(Optimizer.atomlist[i+1][2]))
# calc2=LAMMPS(parameters={ 'pair_style' : Optimizer.pair_style, 'pair_coeff' : Optimizer.pair_coeff , 'mass' : mass2 },files=[ Optimizer.pot_file ])
# else:
# calc2=LAMMPS(parameters={ 'pair_style' : Optimizer.pair_style, 'pair_coeff' : Optimizer.pair_coeff},files=[ Optimizer.pot_file ])
if Optimizer.structure==Defect:
nat=indiv[0].get_number_of_atoms
sol=Atoms()
sol.extend(indiv[0])
sol.extend(indiv.bulko)
sol.set_calculator(calc2)
sol.set_cell(indiv.bulko.get_cell())
sol.set_pbc(True)
dyn=BFGS(sol)
dyn.run(fmax=0.001, steps=2500)
positions=sol[0:nat].get_positions()
indiv[0].set_positions(positions)
else:
atomsdup=indiv[0].copy()
atomsdup.set_calculator(calc2)
dyn=BFGS(indiv[0])
dyn.run(fmax=0.001, steps=2500)
positions=atomsdup.get_positions()
indiv[0].set_positions(positions)
os.chdir(cwd1)
calc2.clean()
Optimizer.lammps_min = olammpsmin
Optimizer.output.write('ASE Minimization mutation performed on individual = '+repr(indiv.index)+'\n')
muttype='ASEM'
if indiv.energy==0:
indiv.history_index=indiv.history_index+'m'+muttype
else:
indiv.history_index=repr(indiv.index)+'m'+muttype
return indiv
def test_geopt():
calc = CP2K(label='test_geopt')
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
dyn = BFGS(h2)
dyn.run(fmax=0.05)
dist = h2.get_distance(0, 1)
diff = abs((dist - 1.36733746519) / dist)
assert(diff < 1e-10)
print('passed test "geopt"')
def run(sigma, atoms):
calc = CP2K(label = 'molecules/co-relax/sigma{0}'.format(sigma),
xc='PBE')
atoms.set_calculator(calc)
gopt = BFGS(atoms, logfile=None)
gopt.run(fmax=1e-2)
e = atoms.get_potential_energy()
pos = atoms.get_positions()
d = ((pos[0] - pos[1])**2).sum()**0.5
print('{0:1.2f} {1:1.4f} {2:1.4f}'.format(sigma, e, d))
def idpp_interpolate(self, traj='idpp.traj', log='idpp.log', fmax=0.1,
optimizer=BFGS):
d1 = self.images[0].get_all_distances()
d2 = self.images[-1].get_all_distances()
d = (d2 - d1) / (self.nimages - 1)
old = []
for i, image in enumerate(self.images):
old.append(image.calc)
image.calc = IDPP(d1 + i * d)
opt = BFGS(self, trajectory=traj, logfile=log)
opt.run(fmax=0.1)
for image, calc in zip(self.images, old):
image.calc = calc
def ase_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA')
Al.set_calculator(calc)
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile='relaxation.log')
qn.run(fmax=0.1, steps=5)
print 'Stress:\n', calc.read_stress()
print 'Al post ASE volume relaxation\n', calc.get_atoms().get_cell()
return Al
def run_neb_calculation(cpu):
images = [PickleTrajectory('H.traj')[-1]]
for i in range(nimages):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images, parallel=True, world=cpu)
neb.interpolate()
images[cpu.rank + 1].set_calculator(Calculator())
dyn = BFGS(neb)
dyn.run(fmax=fmax)
if cpu.rank == 1:
results.append(images[2].get_potential_energy())
def ase_vol_relax():
Al = bulk("Al", "fcc", a=4.5, cubic=True)
calc = Vasp(xc="LDA")
Al.set_calculator(calc)
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile="relaxation.log")
qn.run(fmax=0.1, steps=5)
print("Stress:\n", calc.read_stress())
print("Al post ASE volume relaxation\n", calc.get_atoms().get_cell())
return Al
def test_pwscf_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_pwx():
skip("no pw.x found, skipping test")
else:
pseudo_dir = pj(testdir, prefix, 'pseudo')
print common.backtick("mkdir -pv {p}; cp files/qe_pseudos/*.gz {p}/; \
gunzip {p}/*".format(p=pseudo_dir))
at = get_atoms_with_calc_pwscf(pseudo_dir)
print "scf"
# trigger calculation here
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_pw_scf(at.calc.label + '.out')
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa)
# files/ase/pw.scf.out.start is a norm-conserving LDA struct,
# calculated with pz-vbc.UPF, so the PBE vc-relax will make the cell
# a bit bigger
print "vc-relax"
from ase.optimize import BFGS
from ase.constraints import UnitCellFilter
opt = BFGS(UnitCellFilter(at))
cell = parse.arr2d_from_txt("""
-1.97281509 0. 1.97281509
0. 1.97281509 1.97281509
-1.97281509 1.97281509 0.""")
assert np.allclose(cell, at.get_cell())
opt.run(fmax=0.05) # run only 2 steps
cell = parse.arr2d_from_txt("""
-2.01837531 0. 2.01837531
0. 2.01837531 2.01837531
-2.01837531 2.01837531 0""")
assert np.allclose(cell, at.get_cell())
# at least 1 backup files must exist: pw.*.0 is the SCF run, backed up
# in the first iter of the vc-relax
assert os.path.exists(at.calc.infile + '.0')
def relaxBend(bend, left_idxs, right_idxs, edge, bond, mdrelax):
constraints = []
constraints.append(FixAtoms(indices = left_idxs))
constraints.append(FixAtoms(indices = right_idxs))
#twist = twistConst_Rod(bend, 1, edge, bond ,F = 20)
#twist.set_angle(np.pi/3 + 2./180*np.pi)
#constraints.append(twist)
add_pot = LJ_potential_smooth(bend, bond)
constraints.append(add_pot)
calc = LAMMPS(parameters=get_lammps_params())
bend.set_calculator(calc)
# END CALCULATOR
# RELAX
bend.set_constraint(constraints)
dyn = BFGS(bend, trajectory = mdrelax)
dyn.run(fmax=0.05)
def test_lammps_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_lmp():
skip("no lammps found, skipping test")
else:
at = get_atoms_with_calc_lammps()
at.rattle(stdev=0.001, seed=int(time.time()))
common.makedirs(at.calc.directory)
print common.backtick("cp -v utils/lammps/AlN.tersoff {p}/".format(
p=at.calc.directory))
print "scf"
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_lammps_md_txt(at.calc.label + '.out')[0]
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa,
atol=1e-10)
print "relax"
from ase.optimize import BFGS
opt = BFGS(at, maxstep=0.04)
opt.run(fmax=0.001, steps=10)
coords_frac = parse.arr2d_from_txt("""
3.3333341909920072e-01 6.6666683819841532e-01 4.4325467247779138e-03
6.6666681184103216e-01 3.3333362368205072e-01 5.0443254824788963e-01
3.3333341909918301e-01 6.6666683819838046e-01 3.8356759709402671e-01
6.6666681184101539e-01 3.3333362368201563e-01 8.8356759861713752e-01
""")
assert np.allclose(coords_frac, at.get_scaled_positions(), atol=1e-2)
# at least 1 backup files must exist
assert os.path.exists(at.calc.infile + '.0')
assert os.path.exists(at.calc.outfile + '.0')
assert os.path.exists(at.calc.dumpfile + '.0')
assert os.path.exists(at.calc.structfile + '.0')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_GOPT')
atoms = molecule('H2', calculator=calc)
atoms.center(vacuum=2.0)
# Run Geo-Opt
gopt = BFGS(atoms, logfile=None)
gopt.run(fmax=1e-6)
# check distance
dist = atoms.get_distance(0, 1)
dist_ref = 0.7245595
assert (dist - dist_ref) / dist_ref < 1e-7
# check energy
energy_ref = -30.7025616943
energy = atoms.get_potential_energy()
assert (energy - energy_ref) / energy_ref < 1e-10
print('passed test "H2_GEO_OPT"')
def run_ase_min(totalsol, fmax=0.01, mxstep=1000, fitscheme='totalenfit', STR=''):
try:
dyn=BFGS(totalsol)
dyn.run(fmax=fmax, steps=mxstep)
except OverflowError:
STR+='--- Error: Infinite Energy Calculated - Implement Random shake---\n'
totalsol.rattle(stdev=0.3)
dyn=BFGS(totalsol)
dyn.run(fmax=fmax, steps=mxstep)
except numpy.linalg.linalg.LinAlgError:
STR+='--- Error: Singular Matrix - Implement Random shake ---\n'
totalsol.rattle(stdev=0.2)
dyn=BFGS(totalsol)
dyn.run(fmax=fmax, steps=mxstep)
# Get Energy of Minimized Structure
en=totalsol.get_potential_energy()
if fitscheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(totalsol.get_stress())
else:
pressure=0
volume = totalsol.get_volume()
energy=en
return totalsol, energy, pressure, volume, STR
def find_adhesion_potential(params):
bond = params['bond']
a = np.sqrt(3)*bond # 2.462
h = params['h']
CperArea= (a**2*np.sqrt(3)/4)**(-1)
atoms = make_graphene_slab(a,h,width,length,N, (True, True, False))[3]
# FIX
constraints = []
top = get_mask(atoms.positions.copy(), 'top', 1, h)
bottom = np.logical_not(top)
fix_bot = FixAtoms(mask = bottom)
constraints.append(fix_bot)
# END FIX
# DEF CALC AND RELAX
parameters = {'pair_style':'airebo 3.0',
'pair_coeff':['* * CH.airebo C'],
'mass' :['* 12.01'],
'units' :'metal',
'boundary' :'p p f'}
calc = LAMMPS(parameters=parameters) #, files=['lammps.data'])
atoms.set_calculator(calc)
dyn = BFGS(atoms)
dyn.run(fmax=0.05)
# SLAB IS RELAXED
atoms.set_constraint(constraints)
zmax = np.amax(atoms.positions[bottom][:,2])
natoms = 0
for i in range(len(top)):
if top[i]: natoms += 1
def get_epot(z):
new_pos = atoms.positions.copy()
for iat in range(len(atoms)):
if top[iat]:
new_pos[iat][2] = z
atoms.positions = new_pos
return atoms.get_potential_energy()/natoms
def lj(z):
ecc = 0.002843732471143
sigmacc = 3.4
return 2./5*np.pi*CperArea*ecc*(2*(sigmacc**6/z**5)**2 - 5*(sigmacc**3/z**2)**2), \
8.*ecc*CperArea*np.pi*(sigmacc**12/z**11 - sigmacc**6/z**5)
# Start to move the top layer in z direction
zrange = np.linspace(h - .7, h + 8, 100)
adh_pot = np.zeros((len(zrange), 2))
for i, z in enumerate(zrange):
adh_pot[i] = [z, get_epot(zmax + z)]
adh_pot[:,1] = adh_pot[:,1] - np.min(adh_pot[:,1])
hmin = adh_pot[np.where(adh_pot[:,1] == np.min(adh_pot[:,1]))[0][0], 0]
np.savetxt('adh_potential.gz', adh_pot, fmt='%.12f')
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(adh_pot[:,0], adh_pot[:,1], label = 'lamps')
ax.plot(zrange, lj(zrange)[0] - np.min(lj(zrange)[0]), label = 'lj')
ax.plot(zrange, lj(zrange)[1], label = 'lj')
ax.scatter(hmin, 0)
ax.set_title('Adhesion energy')
ax.set_xlabel('height, Angst')
ax.set_ylabel('Pot. E, eV')
plt.legend(frameon = False)
plt.savefig('Adhesion_energy.svg')
plt.show()
for i in range(3):
ranks = range(i * n, (i + 1) * n)
image = initial.copy()
if rank in ranks:
calc = GPAW(h=0.3,
kpts=(2, 2, 1),
txt='neb%d.txt' % j,
communicator=ranks)
image.set_calculator(calc)
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images, parallel=True)
neb.interpolate()
qn = BFGS(neb, logfile='qn.log')
traj = PickleTrajectory('neb%d.traj' % j, 'w', images[j],
master=(rank % n == 0))
qn.attach(traj)
qn.run(fmax=0.05)
F = np.array(F)
# plt.plot(D, E)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
dimer.constraints = FixInternals(
bonds=[(r, (0, 2)), (r, (1, 2)),
(r, (3, 5)), (r, (4, 5))],
angles=[(a, (0, 2, 1)), (a, (3, 5, 4))])
opt = BFGS(dimer,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.006
assert abs(a0 - aexp) < 2
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
nsteps = '0',
nstfout = '1',
nstlog = '1',
nstenergy = '1',
nstlist = '1',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM.generate_topology_and_g96file()
CALC_MM.generate_gromacs_run_file()
CALC_QMMM = AseQmmmManyqm(nqm_regions = 3,
qm_calculators = [CALC_QM1, CALC_QM2, CALC_QM3],
mm_calculator = CALC_MM,
link_info = 'byQM')
# link_info = 'byFILE')
SYSTEM = read_gromos('gromacs_qm.g96')
SYSTEM.set_calculator(CALC_QMMM)
DYN = BFGS(SYSTEM)
DYN.run(fmax = 0.05)
print('exiting fine')
LOG_FILE.close()
comp = InteratomicDistanceComparator(n_top=n_to_optimize, pair_cor_cum_diff=0.015, pair_cor_max=0.7, dE=0.02, mic=False)
pairing = CutAndSplicePairing(slab, n_to_optimize, blmin)
mutations = OperationSelector(
[1.0, 1.0, 1.0],
[MirrorMutation(blmin, n_to_optimize), RattleMutation(blmin, n_to_optimize), PermutationMutation(n_to_optimize)],
)
# Relax all unrelaxed structures (e.g. the starting population)
while da.get_number_of_unrelaxed_candidates() > 0:
a = da.get_an_unrelaxed_candidate()
a.set_calculator(EMT())
print("Relaxing starting candidate {0}".format(a.info["confid"]))
dyn = BFGS(a, trajectory=None, logfile=None)
dyn.run(fmax=0.05, steps=100)
a.set_raw_score(-a.get_potential_energy())
da.add_relaxed_step(a)
# create the population
population = Population(data_connection=da, population_size=population_size, comparator=comp)
# test n_to_test new candidates
for i in xrange(n_to_test):
print("Now starting configuration number {0}".format(i))
a1, a2 = population.get_two_candidates()
a3, desc = pairing.get_new_individual([a1, a2])
if a3 == None:
continue
da.add_unrelaxed_candidate(a3, description=desc)
#constraint = FixAtoms(mask=[0,1,0,1,0]) # fix OO #Works without patch
for image in images:
image.set_calculator(Turbomole()) #BUG No.2: (Over-)writes coord file
image.set_constraint(constraint)
# Write all commands for the define command in a string
define_str = '\n\na coord\n\n*\nno\nb all 3-21g hondo\n*\neht\n\n-1\nno\ns\n*\n\ndft\non\nfunc pwlda\n\n\nscf\niter\n300\n\n*'
# Run define
p = Popen('define', stdout=PIPE, stdin=PIPE, stderr=STDOUT)
stdout = p.communicate(input=define_str)
# Relax initial and final states:
if 1:
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.10)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.10)
# Interpolate positions between initial and final states:
neb.interpolate()
if 1:
for image in images:
print image.get_distance(1, 2), image.get_potential_energy()
dyn = BFGS(neb, trajectory='turbomole_h3o2m.traj')
dyn.run(fmax=0.10)
for image in images:
print image.get_distance(1, 2), image.get_potential_energy()
nimages = 3
print [a.get_potential_energy() for a in PickleTrajectory('H.traj')]
images = [PickleTrajectory('H.traj')[-1]]
for i in range(nimages):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images)
neb.interpolate()
for image in images[1:]:
image.set_calculator(Calculator())
dyn = BFGS(neb, trajectory='mep.traj')
dyn.run(fmax=fmax)
for a in neb.images:
print a.positions[-1], a.get_potential_energy()
results = [images[2].get_potential_energy()]
def run_neb_calculation(cpu):
images = [PickleTrajectory('H.traj')[-1]]
for i in range(nimages):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images, parallel=True, world=cpu)
neb.interpolate()
images[cpu.rank + 1].set_calculator(Calculator())
# Make a mask of zeros and ones that select fixed atoms (the
# two bottom layers):
mask = initial.positions[:, 2] - min(initial.positions[:, 2]) < 1.5 * h
constraint = FixAtoms(mask=mask)
print mask
for image in images:
# Let all images use an EMT calculator:
image.set_calculator(EMT())
image.set_constraint(constraint)
# Relax the initial and final states:
QuasiNewton(initial).run(fmax=0.05)
QuasiNewton(final).run(fmax=0.05)
# Create a Nudged Elastic Band:
neb = NEB(images)
# Make a starting guess for the minimum energy path (a straight line
# from the initial to the final state):
neb.interpolate()
# Relax the NEB path:
minimizer = BFGS(neb)
minimizer.run(fmax=0.05)
# Write the path to a trajectory:
view(images) # 126 meV
write('jump1.traj', images)
from ase.structure import molecule
from ase.optimize import BFGS
from gpaw import GPAW
from gpaw.mixer import MixerDif
for name in ['H2', 'N2', 'O2', 'NO']:
mol = molecule(name)
mol.center(vacuum=5.0)
calc = GPAW(xc='PBE',
h=0.2,
txt=name + '.txt')
if name == 'NO':
mol.translate((0, 0.1, 0))
calc.set(mixer=MixerDif(0.05,5))
mol.set_calculator(calc)
opt = BFGS(mol, logfile=name + '.log', trajectory=name + '.traj')
opt.run(fmax=0.05)
calc.write(name)
def shearDyn(params_set, pot_key, save = False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric= params_set['dt'], params_set['fric']
tau = params_set['tau']
vmax = params_set['vmax']
vMAX = params_set['vMAX']
thres_Z = params_set['thresZ']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
atoms, L, W, length_int, b_idxs = \
create_stucture(ratio, width, edge, key = 'top', a = bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_twistRod', width, \
length_int, vmax * 1000, int(T), taito)
#view(atoms)
# FIXES
constraints, add_pot, twist, rend_b, rend_t = \
get_constraints(atoms, edge, bond, b_idxs, \
key = 'twist_p', pot = pot_key)
# END FIXES
if relaxed:
atoms = PickleTrajectory(mdrelax, 'r')[-1]
else:
trans = trans_atomsKC(atoms.positions[rend_b], edge, bond)
atoms.translate(trans)
#plot_posits(atoms, edge, bond)
# CALCULATOR LAMMPS
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_pot)
dyn = BFGS(atoms, trajectory = mdrelax)
dyn.run(fmax=0.05)
dist = np.linalg.norm(atoms.positions[rend_b] - atoms.positions[rend_t])
twist.set_dist(dist)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
y0 = atoms.positions[rend_b, 1]
kink_formed = False
kink_vanished = False
i = 0
print 'width = %i, length = %i, v=%.6f' %(width, length_int, vmax)
M_therm = int(tau / dt)
dyn.run(M_therm)
M = int(2 * L / (np.pi * dt * vmax))
M_min = int(2 * L / (np.pi * dt * vMAX))
dtheta = np.pi / 2 / M
dtheta_max = np.pi / 2 / M_min
interval = int( M / 1000 )
theta, time, m = 0., 0., 0
i_kink = 0
while 0. <= theta:
if not kink_formed:
if theta < np.pi/4:
theta += dtheta_max
else:
theta += dtheta
twist.set_angle(theta)
else:
if i_kink / 10 < m:
theta -= dtheta
twist.set_angle(theta)
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
deltaY = atoms.positions[rend_b, 1] - y0
hmax = np.max(atoms.positions[:,2]) #substract the height of the plane?
R = get_R(L, deltaY)
data = [time, deltaY, R, theta, hmax, epot, ekin, epot + ekin]
if save:
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1 or k == 2:
stringi += '%.4f ' %d
else:
stringi += '%.12f ' %d
write_line_own(mdlogfile, stringi + '\n', 'a')
if thres_Z < hmax and not kink_formed:
idxs = np.where(thres_Z < atoms.positions[:,2])
write_line_own(mdlogfile, '# Kink! at idxs %s' %str(idxs) + '\n', 'a')
print ' kink formed! ' + str(i / interval)
kink_formed = True
i_kink = i
if hmax < 3.6 and kink_formed and not kink_vanished:
write_line_own(mdlogfile, '# Kink vanished! \n', 'a')
print ' kink vanished '
kink_vanished = True
print i/interval, theta / (2*np.pi) * 360, R
if kink_formed: m += 1
i += 1
time += dt
make_simul_param_file(simulfile, W, L, width, length_int, dtheta/dt, dtheta, T, \
dt, fric, thres_Z, interval, deltaY, theta, i, edge)
return folder
ref = np.array([[-1.26446863e-01, 4.09628186e-01, -0.00000000e+00],
[4.27934442e-01, 2.50425467e-02, -5.14220671e-05],
[-2.99225008e-01, -4.31533987e-01, -5.14220671e-05]])
error = np.sqrt(np.sum((forces_an - ref)**2))
print('forces_an')
print(forces_an)
print('diff from reference:')
print(error)
assert(error < tol)
# optimize geometry
dyn = BFGS(atoms)
dyn.run(fmax=0.01)
positions = atoms.get_positions()
ref = np.array([[ 9.61364579e-01, 2.81689367e-02, -1.58730770e-06],
[ -3.10444398e-01, 9.10289261e-01, -5.66399075e-06],
[ -1.56957763e-02, -2.26044053e-02, -2.34155615e-06]])
error = np.sqrt(np.sum((positions - ref)**2))
print('positions')
print(positions)
print('diff from reference:')
print(error)
assert(error < tol)
constraint = FixAtoms(indices=[1, 3]) # fix OO
for image in images:
image.set_calculator(EMT())
image.set_constraint(constraint)
for image in images: # O-H(shared) distance
print(image.get_distance(1, 2), image.get_potential_energy())
# Relax initial and final states:
if 1:
# XXX: Warning:
# One would have to optimize more tightly in order to get
# symmetric anion from both images[0] and [1], but
# if one optimizes tightly one gets rotated(H2O) ... OH- instead
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.01)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.01)
# Interpolate positions between initial and final states:
neb.interpolate()
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
dyn = BFGS(neb, trajectory='emt_h3o2m.traj')
dyn.run(fmax=0.05)
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
import os
from ase.io import read
from ase.neb import NEB
from ase.calculators.turbomole import Turbomole
from ase.optimize import BFGS
initial = read('initial.coord')
final = read('final.coord')
os.system('rm -f coord; cp initial.coord coord')
# Make a band consisting of 5 configs:
configs = [initial]
configs += [initial.copy() for i in range(3)]
configs += [final]
band = NEB(configs, climb=True)
# Interpolate linearly the positions of the not-endpoint-configs:
band.interpolate()
#Set calculators
for config in configs:
config.set_calculator(Turbomole())
# Optimize the Path:
relax = BFGS(band, trajectory='neb.traj')
relax.run(fmax=0.05)
def run_moldy(N, save = False):
#
params = {'bond':bond, 'a':a, 'h':h}
# DEFINE FILES
mdfile, mdlogfile, mdrelax = get_fileName(N, 'tear_E_rebo+KC_v', taito, v, edge)
# GRAPHENE SLAB
atoms = make_graphene_slab(a,h,width,length,N, \
edge_type = edge, h_pass = True, \
stacking = 'abc')[3]
view(atoms)
#exit()
params['ncores'] = ncores
params['positions'] = atoms.positions.copy()
params['pbc'] = atoms.get_pbc()
params['cell'] = atoms.get_cell().diagonal()
params['ia_dist'] = 10
params['chemical_symbols'] \
= atoms.get_chemical_symbols()
# FIX
constraints = []
print 'hii'
left = get_ind(atoms.positions.copy(), 'left', 2, bond)
top = get_ind(atoms.positions.copy(), 'top', fixtop - 1, left)
rend_t = get_ind(atoms.positions.copy(), 'rend', atoms.get_chemical_symbols(), 1, edge)
rend = get_ind(atoms.positions.copy(), 'rend', atoms.get_chemical_symbols(), fixtop, edge)
print rend
print 'hoo'
exit()
fix_left = FixAtoms(indices = left)
fix_top = FixAtoms(indices = top)
add_kc = KC_potential_p(params)
for ind in rend:
fix_deform = FixedPlane(ind, (0., 0., 1.))
constraints.append(fix_deform)
for ind in rend_t:
fix_deform = FixedPlane(ind, (0., 0., 1.))
constraints.append(fix_deform)
constraints.append(fix_left)
constraints.append(fix_top)
constraints.append(add_kc)
# END FIX
# CALCULATOR LAMMPS
parameters = {'pair_style':'rebo',
'pair_coeff':['* * CH.airebo C H'],
'mass' :['1 12.0', '2 1.0'],
'units' :'metal',
'boundary' :'f p f'}
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
# END CALCULATOR
#view(atoms)
# TRAJECTORY
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_kc)
dyn = BFGS(atoms, trajectory = mdrelax)
dyn.run(fmax=0.05)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
n = 0
header = '#t [fs], d [Angstrom], epot_tot [eV], ekin_tot [eV], etot_tot [eV] \n'
log_f = open(mdlogfile, 'w')
log_f.write(header)
log_f.close()
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
print 'Start the dynamics for N = %i' %N
for i in range(0, M):
if T == 0:
for ind in rend:
atoms[ind].position[2] -= dz
elif T != 0:
if tau < i*dt:
hw = i*dz
for ind in rend:
atoms[ind].position[2] -= dz
dyn.run(1)
if i%interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
if T != 0:
if tau < i*dt: hw = i*dz - tau*v
else: hw = 0
else: hw = i*dz
data = [i*dt, hw, epot, ekin, epot + ekin]
if save:
log_f = open(mdlogfile, 'a')
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1:
stringi += '%.6f ' %d
else:
stringi += '%.12f ' %d
log_f.write(stringi + '\n')
log_f.close()
n += 1
if save and T != 0 and i*dt == tau:
log_f = open(mdlogfile, 'a')
log_f.write('# Thermalization complete. ' + '\n')
log_f.close()
if 1e2 <= M:
if i%(int(M/100)) == 0: print 'ready = %.1f' %(i/(int(M/100))) + '%'
def test_emt1(testdir):
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
def f():
print(cu.get_distance(0, 1))
qn = BFGS(cu)
with Trajectory('cu2ag.traj', 'w', cu) as t:
qn.attach(t.write)
qn.attach(f)
qn.run(fmax=0.001)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
def eval_energy(input):
"""Function to evaluate energy of an individual
Inputs:
input = [Optimizer class object with parameters, Individual class structure to be evaluated]
Outputs:
energy, bul, individ, signal
energy = energy of Individual evaluated
bul = bulk structure of Individual if simulation structure is Defect
individ = Individual class structure evaluated
signal = string of information about evaluation
"""
if input[0]==None:
energy=0
bul=0
individ=0
rank = MPI.COMM_WORLD.Get_rank()
signal='Evaluated none individual on '+repr(rank)+'\n'
else:
[Optimizer, individ]=input
if Optimizer.calc_method=='MAST':
energy = individ.energy
bul = individ.energy
signal = 'Recieved MAST structure\n'
else:
if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank()
if not Optimizer.genealogy:
STR='----Individual ' + str(individ.index)+ ' Optimization----\n'
else:
STR='----Individual ' + str(individ.history_index)+ ' Optimization----\n'
indiv=individ[0]
if 'EE' in Optimizer.debug:
debug = True
else:
debug = False
if debug:
write_xyz(Optimizer.debugfile,indiv,'Recieved by eval_energy')
Optimizer.debugfile.flush()
if Optimizer.structure=='Defect':
indi=indiv.copy()
if Optimizer.alloy==True:
bulk=individ.bulki
else:
bulk=individ.bulko
nat=indi.get_number_of_atoms()
csize=bulk.get_cell()
totalsol=Atoms(cell=csize, pbc=True)
totalsol.extend(indi)
totalsol.extend(bulk)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Defect configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
elif Optimizer.structure=='Surface':
totalsol=Atoms()
totalsol.extend(indiv)
nat=indiv.get_number_of_atoms()
totalsol.extend(individ.bulki)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Surface-Bulk configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
cell=numpy.maximum.reduce(indiv.get_cell())
totalsol.set_cell([cell[0],cell[1],500])
totalsol.set_pbc([True,True,False])
if Optimizer.constrain_position:
ts = totalsol.copy()
indc,indb,vacant,swap,stro = find_defects(ts,Optimizer.solidbulk,0)
sbulk = Optimizer.solidbulk.copy()
bcom = sbulk.get_center_of_mass()
#totalsol.translate(-bulkcom)
#indc.translate(-bulkcom)
#totalsol.append(Atom(position=[0,0,0]))
# for one in indc:
# index = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
# if totalsol.get_distance(-1,index) > Optimizer.sf:
# r = random.random()
# totalsol.set_distance(-1,index,Optimizer.sf*r,fix=0)
# totalsol.pop()
# totalsol.translate(bulkcom)
com = indc.get_center_of_mass()
dist = (sum((bcom[i] - com[i])**2 for i in range(3)))**0.5
if dist > Optimizer.sf:
STR+='Shifting structure to within region\n'
r = random.random()*Optimizer.sf
comv = numpy.linalg.norm(com)
ncom = [one*r/comv for one in com]
trans = [ncom[i]-com[i] for i in range(3)]
indices = []
for one in indc:
id = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
totalsol[id].position += trans
# Check for atoms that are too close
min_len=0.7
#pdb.set_trace()
if not Optimizer.fixed_region:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After minlength check')
Optimizer.debugfile.flush()
else:
for i in range(len(indiv)):
for j in range(len(indiv)):
if i != j:
d=indiv.get_distance(i,j)
if d < min_len:
indiv.set_distance(i,j,min_len,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
if debug:
write_xyz(Optimizer.debugfile,indiv,'After minlength check')
Optimizer.debugfile.flush()
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
pms=copy.deepcopy(calc.parameters)
try:
pms['mass'][len(pms['mass'])-1] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
except KeyError:
pms['pair_coeff'][0] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
calc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir)
lmin = copy.copy(Optimizer.lammps_min)
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc=Optimizer.calc
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
else:
indiv.set_calculator(calc)
indiv.set_pbc(True) #Current bug in ASE optimizer-Lammps prevents pbc=false
if Optimizer.structure=='Cluster':
indiv.set_cell([500,500,500])
indiv.translate([250,250,250])
cwd=os.getcwd()
# Perform Energy Minimization
if not Optimizer.parallel:
Optimizer.output.flush()
if Optimizer.ase_min == True:
try:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
dyn=BFGS(totalsol)
else:
dyn=BFGS(indiv)
dyn.run(fmax=Optimizer.ase_min_fmax, steps=Optimizer.ase_min_maxsteps)
except OverflowError:
STR+='--- Error: Infinite Energy Calculated - Implement Random ---\n'
box=Atoms()
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
except numpy.linalg.linalg.LinAlgError:
STR+='--- Error: Singular Matrix - Implement Random ---\n'
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
# Get Energy of Minimized Structure
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
en=totalsol.get_potential_energy()
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(totalsol.get_stress())
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
STR+='Number of positions = '+repr(len(bul)+len(individ[0]))+'\n'
individ[0].set_cell(csize)
indiv=individ[0]
else:
en=indiv.get_potential_energy()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=indiv.get_isotropic_pressure(indiv.get_stress())
cell_max=numpy.maximum.reduce(indiv.get_positions())
cell_min=numpy.minimum.reduce(indiv.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=indiv.get_number_of_atoms()
ena=en/na
energy=ena
individ[0]=indiv
bul=0
else:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
if Optimizer.calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
try:
totcop=totalsol.copy()
if debug: write_xyz(Optimizer.debugfile,totcop,'Individual sent to lammps')
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if Optimizer.fixed_region:
if debug:
print 'Energy of fixed region calc = ', OUT['thermo'][-1]['pe']
totalsol.set_calculator(Optimizer.static_calc)
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if debug:
print 'Energy of static calc = ', OUT['thermo'][-1]['pe']
en=OUT['thermo'][-1]['pe']
stress=numpy.array([OUT['thermo'][-1][i] for i in ('pxx','pyy','pzz','pyz','pxz','pxy')])*(-1e-4*GPa)
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After Lammps Minimization')
Optimizer.debugfile.flush()
except Exception, e:
os.chdir(cwd)
STR+='WARNING: Exception during energy eval:\n'+repr(e)+'\n'
f=open('problem-structures.xyz','a')
write_xyz(f,totcop,data='Starting structure hindex='+individ.history_index)
write_xyz(f,totalsol,data='Lammps Min structure')
en=10
stress=0
f.close()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(stress)
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=totalsol.get_isotropic_pressure(stress)
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
if Optimizer.structure=='Defect':
if Optimizer.fixed_region==True or Optimizer.finddefects==False:
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if 'FI' in Optimizer.debug:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=Optimizer.debugfile)
else:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False)
individ[0]=outt[0]
bul=outt[1]
individ.vacancies = outt[2]
individ.swaps = outt[3]
STR += outt[4]
indiv=individ[0]
else:
top,bul=find_top_layer(totalsol,Optimizer.surftopthick)
indiv=top.copy()
individ[0]=top.copy()
else: