def relax_structure(system,
potential,
potential_filename=None,
relax_positions=True,
relax_cell=True):
"""
Run a geometry optimisation on the structure to find the energy minimum.
Parameters
----------
system : ase.Atoms
A system of atoms to run the minimisation on. The structure is
altered in-place.
potential : Potential or str
A quippy Potential object with the desired potential, or a
potential_str to initialise a new potential.
Returns
-------
minimised_structure : Atoms
The geometry optimised structure.
"""
info("Inside minimiser.")
qsystem = Atoms(system)
if not isinstance(potential, Potential):
if potential_filename:
potential = Potential(potential, param_filename=potential_filename)
else:
potential = Potential(potential)
qsystem.set_calculator(potential)
minimiser = Minim(qsystem,
relax_positions=relax_positions,
relax_cell=relax_cell)
with Capturing(debug_on_exit=True):
minimiser.run()
system.set_cell(qsystem.cell)
system.set_positions(qsystem.positions)
system.energy = qsystem.get_potential_energy()
info("Minimiser done.")
return system
def h2_formation_energy(pot):
"""
Given a potential calculate the H2 formation energy and
equilibrium bond spacing.
Args:
pot(:quippy:class:`Potential`) potential object.
Returns:
float: Hydrogen molecule formation energy.
"""
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
h2.set_calculator(pot)
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
return E_h2
block=block,
corner=corner,
shape=shape,
exe = vasp,
ediffg = -0.05,
nelmin = 6,
nelmdl = -15,
kpar = 32,
parmode='cobalt',
xc='PBE',
lreal=False, ibrion=13, nsw=40,
algo='VeryFast', npar=8,
lplane=False, lwave=False, lcharg=False, nsim=1,
voskown=1, ismear=1, sigma=0.01, iwavpr=11, isym=2, nelm=100)
sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True)
bulk.set_calculator(sock_calc)
opt = LBFGS(bulk)
opt.run(fmax=0.05, steps=100)
sock_e = bulk.get_potential_energy()
sock_f = bulk.get_forces()
sock_s = bulk.get_stress()
print 'energy', sock_e
print 'forces', sock_f
print 'stress', sock_s
sock_calc.shutdown()
ibrion=13,
nsw=40,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
nsim=1,
voskown=1,
ismear=1,
sigma=0.01,
iwavpr=11,
isym=2,
nelm=100)
sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True)
bulk.set_calculator(sock_calc)
opt = LBFGS(bulk)
opt.run(fmax=0.05, steps=100)
sock_e = bulk.get_potential_energy()
sock_f = bulk.get_forces()
sock_s = bulk.get_stress()
print 'energy', sock_e
print 'forces', sock_f
print 'stress', sock_s
sock_calc.shutdown()
def calc_bulk_dissolution(args):
"""Calculate the bulk dissolution energy for hydrogen
in a tetrahedral position in bcc iron.
Args:
args(list): determine applied strain to unit cell.
"""
POT_DIR = os.path.join(app.root_path, 'potentials')
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
alat = 2.83
gb = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(6, 6, 6),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=alat)
cell = gb.get_cell()
print 'Fe Cell', cell
e1 = np.array([1, 0, 0])
e2 = np.array([0, 1, 0])
e3 = np.array([0, 0, 1])
if args.hydrostatic != 0.0:
strain_tensor = np.eye(3) + args.hydrostatic * np.eye(3)
cell = cell * strain_tensor
gb.set_cell(cell, scale_atoms=True)
print 'Hydrostatic strain', args.hydrostatic
print 'strain tensor', strain_tensor
print gb.get_cell()
elif args.stretch != 0.0:
strain_tensor = np.tensordot(e2, e2, axes=0)
strain_tensor = np.eye(3) + args.stretch * strain_tensor
cell = strain_tensor * cell
print 'Stretch strain'
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
elif args.shear != 0.0:
strain_tensor = np.tensordot(e1, e2, axes=0)
strain_tensor = np.eye(3) + args.shear * strain_tensor
cell = strain_tensor.dot(cell)
print 'Shear Strain', strain_tensor
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
gb.write('sheared.xyz')
else:
print 'No strain applied.'
tetra_pos = alat * np.array([0.25, 0.0, 0.5])
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
gb = Atoms(gb)
gb_h = gb.copy()
gb_h.add_atoms(tetra_pos, 1)
#caclulators
gb.set_calculator(pot)
h2.set_calculator(pot)
gb_h.set_calculator(pot)
gb_h.write('hydrogen_bcc.xyz')
#Calc Hydrogen molecule energy
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
h2.write('h2mol.xyz')
#strain_mask = [1,1,1,0,0,0]
strain_mask = [0, 0, 0, 0, 0, 0]
ucf = UnitCellFilter(gb_h, strain_mask)
#opt = BFGS(gb_h)
opt = FIRE(ucf)
opt.run(fmax=0.0001)
E_gb = gb.get_potential_energy()
E_gbh = gb_h.get_potential_energy()
E_dis = E_gbh - E_gb - 0.5 * E_h2
print 'E_gb', E_gb
print 'E_gbh', E_gbh
print 'H2 Formation Energy', E_h2
print 'Dissolution Energy', E_dis
h2 = Atoms(h2)
gb = Atoms(gb)
gb_h = gb.copy()
gb_h.add_atoms(tetra_pos, 1)
#caclulators
gb.set_calculator(pot)
h2.set_calculator(pot)
gb_h.set_calculator(pot)
gb_h.write('hydrogen_bcc.xyz')
#Calc Hydrogen molecule energy
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
strain_mask = [1, 1, 1, 0, 0, 0]
ucf = UnitCellFilter(gb_h, strain_mask)
#opt = BFGS(gb_h)
opt = FIRE(ucf)
opt.run(fmax=0.0001)
E_gb = gb.get_potential_energy()
E_gbh = gb_h.get_potential_energy()
E_dis = E_gbh - E_gb - 0.5 * E_h2
print 'E_gb', E_gb
print 'E_gbh', E_gbh
print 'H2 Formation Energy', E_h2
print 'Dissolution Energy', E_dis
