def calc_impurity_energy(self, structure, elements):
if structure not in ['oct38-center', 'oct38-face', 'oct38-edge']:
raise ValueError("Cannot calculate impurity energy for '%s'" %
(structure, ))
if len(elements) != 2:
raise ValueError("Tuple of elements must be of length two")
if self.debug:
print "Calculating impurity energy..."
print 40 * "*"
print "Structure: %s" % (structure, )
print "Elements: %s\n" % (elements, )
name, impurity = structure.split('-')
sym = reference_states[atomic_numbers[elements[1]]]['symmetry']
latticeconstant = self.get_lattice_constant_a(sym, (elements[1], ))
if name == 'oct38':
sites = {'center': 10, 'face': 9, 'edge': 0}
atoms = Octahedron(elements[1], 4, 1, latticeconstant)
atoms.set_calculator(self.get_calc())
dyn = BFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=0.001, steps=100)
assert dyn.converged()
s_clean = dyn.get_number_of_steps()
e_clean = atoms.get_potential_energy()
atoms[sites[impurity]].symbol = elements[0]
dyn.run(fmax=0.001, steps=100)
assert dyn.converged()
s_impurity = dyn.get_number_of_steps()
e_impurity = atoms.get_potential_energy()
self.values[('impurity_energy', structure,
elements)] = e_impurity - e_clean
if self.debug:
print "BFGS steps: %i %i" % (s_clean, s_impurity)
print "Impurity energy: %.5f - %.5f = %.5f eV" % (
e_impurity, e_clean, e_impurity - e_clean)
print 40 * "-" + "\n"
def test_fake_ase_opt():
atoms = Icosahedron("Ar", noshells=2, latticeconstant=3)
atoms.set_calculator(FakeASE(LennardJones()))
dyn = BFGS(atoms)
dyn.run(fmax=0.0005)
assert dyn.converged()
assert dyn.get_number_of_steps() == 14
assert np.linalg.norm(dyn.f0) == pytest.approx(0.0041872094)
def run_dftb(configuration, max_force, traj_name=None):
"""Run periodic DFTB+ on this configuration. Will set configuration.energy
and configuration.forces as their calculated values at the TB-DFT level
--------------------------------------------------------------------------
:param configuration: (gaptrain.configurations.Configuration)
:param max_force: (float) or None
:param traj_name: (str) or None
"""
from ase.optimize import BFGS
ase_atoms = configuration.ase_atoms()
dftb = DFTB(atoms=ase_atoms,
kpts=(1, 1, 1),
Hamiltonian_Charge=configuration.charge)
ase_atoms.set_calculator(dftb)
try:
configuration.energy = ase_atoms.get_potential_energy()
if max_force is not None:
minimisation = BFGS(ase_atoms, trajectory=traj_name)
minimisation.run(fmax=float(max_force))
configuration.n_opt_steps = minimisation.get_number_of_steps()
set_configuration_atoms_from_ase(configuration, ase_atoms)
except ValueError:
raise MethodFailed('DFTB+ failed to generate an energy')
configuration.forces = ase_atoms.get_forces()
configuration.partial_charges = ase_atoms.get_charges()
# Return self to allow for multiprocessing
return configuration
#combines all images into one file with energies written for each structure
inFile = open(os.path.join(path, 'structure%03d' % (i, ) + '.xyz'), 'r')
linesInFile = list()
for line in inFile:
linesInFile.append(line)
numOfLines = len(linesInFile)
outFile = open(outFileName, 'a')
outFile.write(linesInFile[0])
outFile.write(linesInFile[numOfLines - 1])
for i in range(1, numOfLines - 1):
outFile.write(linesInFile[i])
#writes the trajectory file in .xyz format
if os.path.exists("gradient"):
os.remove("gradient")
nsteps = dyn.get_number_of_steps()
for j in range(0, numOfImages):
traj = PickleTrajectory('neb-%01d.traj' % (j, ))
path1 = os.getcwd()
path1 = path1 + '/scratch%01d' % (j, )
if not os.path.exists(path1): os.makedirs(path1)
outFileName1 = 'trajectory%03d' % (j, ) + '.xyz'
fh = open("gradient", 'a')
fh.write("\n")
fh.write(str('********neb-%01d.traj' % (j, )))
fh.write(" Printing information for image %01d **********" %
((j + 1), ))
for i in range(0, nsteps + 1):
atoms = traj[i]
string1 = 'structure%03d' % (i, ) + '.xyz'
#combines all images into one file with energies written for each structure
inFile = open(os.path.join(path, 'structure%03d' % (i,) +'.xyz'), 'r')
linesInFile = list()
for line in inFile:
linesInFile.append(line)
numOfLines = len(linesInFile)
outFile = open(outFileName, 'a')
outFile.write(linesInFile[0])
outFile.write(linesInFile[numOfLines-1])
for i in range(1, numOfLines-1):
outFile.write(linesInFile[i])
#writes the trajectory file in .xyz format
if os.path.exists("gradient"):
os.remove("gradient")
nsteps = dyn.get_number_of_steps()
for j in range(0, numOfImages):
traj = PickleTrajectory('neb-%01d.traj' % (j,))
path1 = os.getcwd()
path1 = path1 + '/scratch%01d' % (j,)
if not os.path.exists(path1): os.makedirs(path1)
outFileName1 = 'trajectory%03d' % (j,) + '.xyz'
fh = open("gradient", 'a')
fh.write("\n")
fh.write(str('********neb-%01d.traj' % (j,)))
fh.write(" Printing information for image %01d **********" % ((j+1),))
for i in range(0, nsteps+1):
atoms = traj[i]
string1 = 'structure%03d' % (i,) +'.xyz'
outStruct1 = os.path.join(path1, string1)
