def test_pyscf():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='C', latticeconstant=3.5668)
print ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
#cell.gs=np.array([10,10,10])
cell.gs=np.array([20,20,20])
cell.verbose=7
cell.build(None,None)
print cell._atom
print "Cell nimgs =", cell.nimgs
print "Cell _basis =", cell._basis
print "Cell _pseudo =", cell._pseudo
print "Cell nelectron =", cell.nelectron
mf=pbcdft.RKS(cell)
mf.xc='lda,vwn'
mf.analytic_int=False
print mf.scf() # [10,10,10]: -44.8811199336
def test_cubic_diamond_C():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = Diamond(symbol='C', latticeconstant=3.5668)
print "Cell volume =", ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([10,10,10])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int = False
mf.xc = 'lda,vwn'
print mf.scf()
# Gamma point gs: 10x10x10: -11.220279983393
# gs: 14x14x14: -11.220122248175
# K pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
kmf.verbose = 7
print kmf.scf()
def test_cubic_diamond_C():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = Diamond(symbol='C', latticeconstant=3.5668)
print "Cell volume =", ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([10, 10, 10])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int = False
mf.xc = 'lda,vwn'
print mf.scf()
# Gamma point gs: 10x10x10: -11.220279983393
# gs: 14x14x14: -11.220122248175
# K pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
kmf.verbose = 7
print kmf.scf()
def make_dia_100_cell(size=(1, 1, 1), symbols=['Ni'], pbc=(1, 1, 1)):
direction_x = [1, 0, 0]
direction_y = [0, 1, 0]
direction_z = [0, 0, 1]
atoms = None
try:
atoms = Diamond(\
directions=[direction_x,direction_y,direction_z],
size=size,
symbol=symbols[0],
pbc=pbc)
except ValueError as e:
if str(
e
) == 'Cannot guess the diamond lattice constant of an element with crystal structure fcc.':
r = get_atomic_radius(symbol=symbols[0])
a0 = 3.567
atoms = Diamond(\
directions=[direction_x,direction_y,direction_z],
size=size,
symbol=symbols[0],
pbc=pbc,
latticeconstant=a0)
else:
raise ValueError("cannnot create the diamond cubic structure")
return atoms
def testForceAgainstDefaultNeighborList(self):
atoms = Diamond(symbol="C", pbc=False)
builtin = torchani.neurochem.Builtins()
calculator = torchani.ase.Calculator(builtin.species,
builtin.aev_computer,
builtin.models,
builtin.energy_shifter)
default_neighborlist_calculator = torchani.ase.Calculator(
builtin.species, builtin.aev_computer, builtin.models,
builtin.energy_shifter, True)
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 50 * units.kB, 0.002)
def test_energy(a=atoms):
a = a.copy()
a.set_calculator(calculator)
e1 = a.get_potential_energy()
a.set_calculator(default_neighborlist_calculator)
e2 = a.get_potential_energy()
self.assertLess(abs(e1 - e2), tol)
dyn.attach(test_energy, interval=1)
dyn.run(500)
def testEqualOneModelPTI(self):
calculator_pti = self.model_pti[0].ase()
calculator = self.model[0].ase()
atoms = Diamond(symbol="C", pbc=True)
atoms_pti = Diamond(symbol="C", pbc=True)
atoms.set_calculator(calculator)
atoms_pti.set_calculator(calculator_pti)
self.assertEqual(atoms.get_potential_energy(), atoms_pti.get_potential_energy())
def get_ase_diamond_cubic(atom='C'):
"""Get the ASE atoms for cubic (8-atom) diamond unit cell."""
from ase.lattice.cubic import Diamond
if atom == 'C':
ase_atom = Diamond(symbol='C', latticeconstant=3.5668*A2B)
else:
ase_atom = Diamond(symbol='Si', latticeconstant=5.431*A2B)
return ase_atom
def get_ase_diamond_cubic(atom='C'):
"""Get the ASE atoms for cubic (8-atom) diamond unit cell."""
from ase.lattice.cubic import Diamond
if atom == 'C':
ase_atom = Diamond(symbol='C', latticeconstant=3.5668*A2B)
elif atom == 'Si':
ase_atom = Diamond(symbol='Si', latticeconstant=5.431*A2B)
else:
raise NotImplementedError('No formula found for system ',
atom, '. Choose a different system? Or add it to the list!')
return ase_atom
def testWithNumericalForceWithPBCEnabled(self):
# Run a Langevin thermostat dynamic for 100 steps and after the dynamic
# check once that the numerical and analytical force agree to a given
# relative tolerance
atoms = Diamond(symbol="C", pbc=True)
calculator = self.model.ase()
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = atoms.get_forces()
fn = get_numeric_force(atoms, 0.001)
self.assertEqual(f, fn, rtol=0.1, atol=0.1)
def testWithNumericalForceWithPBCEnabled(self):
atoms = Diamond(symbol="C", pbc=True)
calculator = torchani.models.ANI1x().ase()
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = torch.from_numpy(atoms.get_forces())
fn = get_numeric_force(atoms, 0.001)
df = (f - fn).abs().max()
avgf = f.abs().mean()
if avgf > 0:
self.assertLess(df / avgf, 0.1)
def test_dsygv_dgelsd(self):
a = Diamond('C', size=[4,4,4])
b = a.copy()
b.positions += (np.random.random(b.positions.shape)-0.5)*0.1
i, j = neighbour_list("ij", b, 1.85)
dr_now = mic(b.positions[i] - b.positions[j], b.cell)
dr_old = mic(a.positions[i] - a.positions[j], a.cell)
dgrad1 = get_delta_plus_epsilon_dgesv(len(b), i, dr_now, dr_old)
dgrad2 = get_delta_plus_epsilon(len(b), i, dr_now, dr_old)
self.assertArrayAlmostEqual(dgrad1, dgrad2)
def build_surface(self, pot, size=(1, 1, 1)):
"""
Create an equivalent surface unit cell for the fracture system.
"""
if self.symbol == 'Si':
unit_slab = Diamond(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol=self.symbol,
pbc=True,
latticeconstant=self.a0)
elif self.symbol == 'Fe':
unit_slab = BodyCenteredCubic(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=self.a0)
# Does this work for more than 2 atoms?
unit_slab.info['adsorbate_info'] = None
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
surface = unit_slab.copy()
surface.center(vacuum=self.vacuum, axis=1)
surface.set_calculator(pot)
return surface
def dia_111(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
else:
a = B3(sym,
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx / (12 * nx), sy / (4 * nx), sz / (12 * nz)])
return a
def _testForce(self, pbc):
atoms = Diamond(symbol="C", pbc=pbc)
builtin = torchani.neurochem.Builtins()
calculator = torchani.ase.Calculator(
builtin.species, builtin.aev_computer,
builtin.models, builtin.energy_shifter)
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = torch.from_numpy(atoms.get_forces())
fn = get_numeric_force(atoms, 0.001)
df = (f - fn).abs().max()
avgf = f.abs().mean()
if avgf > 0:
self.assertLess(df / avgf, 0.1)
def test_hydrogenate(self):
a = Diamond('Si', size=[2, 2, 1])
b = hydrogenate(a, 2.85, 1.0, mask=[True, True, False], vacuum=5.0)
# Check if every atom is fourfold coordinated
syms = np.array(b.get_chemical_symbols())
c = np.bincount(neighbour_list('i', b, 2.4))
self.assertTrue((c[syms != 'H'] == 4).all())
def dia_111(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*nx), sz/(12*nz)])
return a
def __init__(self, a0, nlayers, *args, **kwargs):
self.atoms = Diamond(symbol="Sn",
latticeconstant=a0,
directions=[[1, -2, 0], [0, 0, -1], [2, 1, 0]],
size=(1, 1, nlayers),
pbc=(1, 1, 0),
miller=[None, None, [2, 1, 1]])
super().__init__(**{"a0": a0})
def main():
for x in fccs+bccs+hcps+diamonds+rocksalts+zincblendes+cscls:
f = x in fccs
b = x in bccs
h = x in hcps
d = x in diamonds
r = x in rocksalts
z = x in zincblendes
c = x in cscls
try:
if f: a = FaceCenteredCubic(x[0]).get_cell()[0][0]/2
elif b: a = BodyCenteredCubic(x[0]).get_cell()[0][0]/2
elif d: a = Diamond(x[0]).get_cell()[0][0]/2
elif h:
cell = HexagonalClosedPacked(x[0]).get_cell()
a,c = cell[0][0],cell[2][2]
elif r | z | c: a = dataLookup(x[0])
else: raise NotImplementedError
except ValueError:
a = sum([radDict[e] for e in elems])/len(elems)
print "Had to guess lattice constant of "+x[0]
if f: name,struc,pos,cell,n = '-fcc', 'fcc', [[0,0,0]], [[0,a,a],[a,0,a],[a,a,0]], 1
elif b: name,struc,pos,cell,n = '-bcc', 'bcc', [[0,0,0]], [[a,a,-a],[-a,a,a],[a,-a,a]],1
elif h: name,struc,pos,cell,n = '-hcp', 'hexagonal', [[0,0,0],[2./3,1./3,1./2]], [a,a,c,90,90,120], 2
elif d: name,struc,pos,cell,n = '-diamond', 'diamond', [[0,0,0],[0.25,0.25,0.25]], [[0,a,a],[a,0,a],[a,a,0]], 2
elif z: name,struc,pos,cell,n = '-zincblende','zincblende', [[0,0,0],[0.25,0.25,0.25]], [[0,a,a],[a,0,a],[a,a,0]], 1
elif r: name,struc,pos,cell,n = '-rocksalt', 'rocksalt', [[0,0,0],[0.5,0.5,0.5]], [[0,a,a],[a,0,a],[a,a,0]], 1
elif c: name,struc,pos,cell,n = '-cscl', 'cubic', [[0,0,0],[0.5,0.5,0.5]], [a,a,a,90,90,90], 1
mag = magLookup(x[0])
elems = parseChemicalFormula(x[0]).keys()*n
magmoms = [magmomInit if e in magElems else 0 for e in elems]
atoms = Atoms(elems,scaled_positions=pos,cell=cell,pbc=[1,1,1],magmoms=magmoms,calculator=EMT())
info = {'name': x[0]+name
,'relaxed': False
,'emt': atoms.get_potential_energy()/len(elems) #normalized to per-atom basis
,'comments': 'Autogenerated by createTrajs'
,'kind': 'bulk' # vs surface/molecules
### Stuff for bulk
,'structure': struc
### Stuff for surfaces
,'parent': None
,'sites': None
,'facet': None
,'xy': None
,'layers': None
,'constrained': None
,'symmetric': None
,'vacuum': None
,'adsorbates': None}
db.write(atoms,key_value_pairs=info)
def build_unit_slab(self, size=(1, 1, 1)):
"""
Initialize the unit slab for the given crack geometry.
Currently supports silicon and Fe.
"""
if self.symbol == 'Si':
unit_slab = Diamond(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol=self.symbol,
pbc=True,
latticeconstant=self.a0)
elif self.symbol == 'Fe':
unit_slab = BodyCenteredCubic(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=self.a0)
print 'Number atoms in unit slab', len(unit_slab)
unit_slab.info['adsorbate_info'] = None
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, self.param_file)
print pot_file
print self.mm_init_args
#pot = Potential(self.mm_init_args, param_filename = pot_file)
#pot = Potential("IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312" , param_filename = "/Users/lambert/pymodules/imeall/imeall/potentials/PotBH.xml")
#unit_slab.set_calculator(pot)
return unit_slab
def __init__(self, a0, nlayers, *args, **kwargs):
self.atoms = Diamond(symbol="Sn",
latticeconstant=a0,
directions=[[1, -1, 0], [0, 0, -1], [1, 1, 0]],
size=(1, 1, nlayers),
pbc=(1, 1, 0),
miller=[None, None, [1, 1, 0]])
# self.atoms = ase.build.cut(self.atoms, a=(1, 0, 0), b=(0, 1, 0), c=None, clength=None, origo=(0, 0, 0), nlayers=nlayers, extend=1.0, tolerance=0.01, maxatoms=None)
super().__init__(**{"a0": a0})
def test_calculator():
"""
Take ASE structure, PySCF object,
and run through ASE calculator interface.
This allows other ASE methods to be used with PySCF;
here we try to compute an equation of state.
"""
ase_atom=Diamond(symbol='C', latticeconstant=3.5668)
# Set up a cell; everything except atom; the ASE calculator will
# set the atom variable
cell = pbcgto.Cell()
cell.h=ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs=np.array([8,8,8])
cell.verbose = 0
# Set up the kind of calculation to be done
# Additional variables for mf_class are passed through mf_dict
mf_class=pbcdft.RKS
mf_dict = { 'xc' : 'lda,vwn' }
# Once this is setup, ASE is used for everything from this point on
ase_atom.set_calculator(pyscf_ase.PySCF(molcell=cell, mf_class=mf_class, mf_dict=mf_dict))
print "ASE energy", ase_atom.get_potential_energy()
print "ASE energy (should avoid re-evaluation)", ase_atom.get_potential_energy()
# Compute equation of state
ase_cell=ase_atom.cell
volumes = []
energies = []
for x in np.linspace(0.95, 1.2, 5):
ase_atom.set_cell(ase_cell * x, scale_atoms = True)
print "[x: %f, E: %f]" % (x, ase_atom.get_potential_energy())
volumes.append(ase_atom.get_volume())
energies.append(ase_atom.get_potential_energy())
eos = EquationOfState(volumes, energies)
v0, e0, B = eos.fit()
print(B / kJ * 1.0e24, 'GPa')
eos.plot('eos.png')
def test_klda8_cubic_gamma(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
cell = build_cell(ase_atom, 8)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#kmf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -44.892502703975893, 8)
def dia_100_2x1(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
else:
a = B3(sym,
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(8*nx), sz/(8*nz)])
bulk = a.copy()
for i in a:
if i.z < sz/(4*nz) or i.z > sz-sz/(4*nz):
if i.x < sx/2:
i.x = i.x+0.5
else:
i.x = i.x-0.5
return bulk, a
def test_klda8_cubic_kpt_222(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
cell = build_cell(ase_atom, 8)
abs_kpts = cell.get_abs_kpts(scaled_kpts)
mf = pbcdft.KRKS(cell, abs_kpts)
#mf.analytic_int = False
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -45.425834895129569, 8)
def test_sqlite():
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
assert a == op1a
a, ra = CP(op2)(a, 2.0)
assert a == op2a
assert(np.abs(ra - op2ra).max() < 1e-5)
def test_sqlite(self):
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2,2,2])
a = CP(self.op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(self.op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2,2,2])
a = CP(self.op1)(a, 1.0)
self.assertAtomsAlmostEqual(a, op1a)
a, ra = CP(self.op2)(a, 2.0)
self.assertAtomsAlmostEqual(a, op2a)
self.assertArrayAlmostEqual(ra, op2ra)
def MD():
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
orig_stdout = sys.stdout
f = open('out.txt', 'w')
sys.stdout = f
#f = open('out_' + str(temp) + '.txt', 'w')
#sys.stdout = f
Tmin = 1000
Tmax = 15000
a0 = 5.43
N = 1
atoms = Diamond(symbol='Si', latticeconstant=a0)
atoms *= (N, N, N)
atoms.set_calculator(model.calculator)
MaxwellBoltzmannDistribution(atoms, Tmin * units.kB) ###is this allowed?
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms)
def printenergy(a=atoms):
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print(ekin)
traj = Trajectory('Si.traj', 'w', atoms)
for temp in np.linspace(Tmin, Tmax, 5):
dyn = Langevin(atoms, 5 * units.fs, units.kB * temp, 0.002)
dyn.attach(traj.write, interval=1)
dyn.attach(printenergy, interval=1)
dyn.run(100)
sys.stdout = orig_stdout
f.close()
def test_cubic_diamond_He():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='He', latticeconstant=3.5)
print ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell.T
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
cell.gs = np.array([15,15,15])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic: -18.2278622592408
mf = pbcdft.RKS(cell)
mf.analytic_int=True
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic (analytic): -18.2278622592283
# = -4.556965564807075 / cell
# K pt calc
scaled_kpts=ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
print kmf.scf()
def test_cubic_diamond_He():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='He', latticeconstant=3.5)
print ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
cell.gs = np.array([15,15,15])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic: -18.2278622592408
mf = pbcdft.RKS(cell)
mf.analytic_int=True
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic (analytic): -18.2278622592283
# = -4.556965564807075 / cell
# K pt calc
scaled_kpts=ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
print kmf.scf()
def test_klda8_cubic_kpt_222(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.h = ase_atom.cell
cell.gs = np.array([8]*3)
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
kpts = cell.make_kpts((2,2,2))
mf = pbcdft.KUKS(cell, kpts)
mf.xc = 'lda,vwn'
e1 = mf.scf()
self.assertAlmostEqual(e1, -45.42583489512954, 8)
self.assertAlmostEqual(mf._ecoul, 3.2519161200384685, 8)
self.assertAlmostEqual(mf._exc, -13.937886385300949, 8)
def build_surface(self,pot, size=(1,1,1)):
"""
Create an equivalent surface unit cell for the fracture system.
"""
if self.symbol=='Si':
unit_slab = Diamond(directions = [self.crack_direction, self.cleavage_plane, self.crack_front],
size = size, symbol=self.symbol, pbc=True, latticeconstant= self.a0)
elif self.symbol=='Fe':
unit_slab = BodyCenteredCubic(directions=[self.crack_direction, self.cleavage_plane, self.crack_front],
size=size, symbol='Fe', pbc=(1,1,1),
latticeconstant=self.a0)
# Does this work for more than 2 atoms?
unit_slab.info['adsorbate_info'] = None
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1]-unit_slab.positions[0, 1])/2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
surface = unit_slab.copy()
surface.center(vacuum=self.vacuum, axis=1)
surface.set_calculator(pot)
return surface
def test_sqlite(testdir):
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
assert a == op1a
a, ra = CP(op2)(a, 2.0)
assert a == op2a
assert(np.abs(ra - op2ra).max() < 1e-5)
def test_sqlite(self):
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(self.op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(self.op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(self.op1)(a, 1.0)
self.assertEqual(a, op1a)
a, ra = CP(self.op2)(a, 2.0)
self.assertEqual(a, op2a)
self.assert_(np.abs(ra - op2ra).max() < 1e-5)
def build_unit_slab(self, size=(1,1,1)):
"""
Initialize the unit slab for the given crack geometry.
Currently supports silicon and Fe.
"""
if self.symbol=='Si':
unit_slab = Diamond(directions = [self.crack_direction, self.cleavage_plane, self.crack_front],
size = size, symbol=self.symbol, pbc=True, latticeconstant= self.a0)
elif self.symbol=='Fe':
unit_slab = BodyCenteredCubic(directions=[self.crack_direction, self.cleavage_plane, self.crack_front],
size=size, symbol='Fe', pbc=(1,1,1),
latticeconstant=self.a0)
print 'Number atoms in unit slab', len(unit_slab)
unit_slab.info['adsorbate_info'] = None
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1]-unit_slab.positions[0, 1])/2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, self.param_file)
print pot_file
print self.mm_init_args
#pot = Potential(self.mm_init_args, param_filename = pot_file)
#pot = Potential("IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312" , param_filename = "/Users/lambert/pymodules/imeall/imeall/potentials/PotBH.xml")
#unit_slab.set_calculator(pot)
return unit_slab
here we try to compute an equation of state. """ import numpy as np from pyscf.pbc.tools import pyscf_ase import pyscf.pbc.gto as pbcgto import pyscf.pbc.dft as pbcdft import ase import ase.lattice from ase.lattice.cubic import Diamond from ase.units import kJ from ase.utils.eos import EquationOfState ase_atom=Diamond(symbol='C', latticeconstant=3.5668) # Set up a cell; everything except atom; the ASE calculator will # set the atom variable cell = pbcgto.Cell() cell.a=ase_atom.cell cell.basis = 'gth-szv' cell.pseudo = 'gth-pade' cell.verbose = 0 # Set up the kind of calculation to be done # Additional variables for mf_class are passed through mf_dict # E.g. gamma-point SCF calculation can be set to mf_class = pbcdft.RKS # SCF with k-point sampling can be set to mf_class = lambda cell: pbcdft.KRKS(cell, kpts=cell.make_kpts([2,2,2]))
output_file = 'crack.xyz' # File to which structure will be written
set_fortran_indexing(False)
si_bulk = bulk('Si', 'diamond', a=5.431, cubic=True)
mm_pot = Potential("IP SW")
si_bulk.set_calculator(mm_pot)
c = mm_pot.get_elastic_constants(si_bulk)
E = youngs_modulus(c, cleavage_plane)
nu = poisson_ratio(c, cleavage_plane, crack_direction)
unit_slab = Diamond(directions=[crack_direction,
cleavage_plane,
crack_front],
size=(1, 1, 1),
symbol='Si',
pbc=True,
latticeconstant=5.431)
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
surface = unit_slab.copy()
surface.center(vacuum, axis=1)
surface.set_calculator(mm_pot)
""" Take ASE Diamond structure, input into PySCF and run """ import numpy as np import pyscf.pbc.gto as pbcgto import pyscf.pbc.dft as pbcdft from pyscf.pbc.tools import pyscf_ase import ase import ase.lattice from ase.lattice.cubic import Diamond ase_atom=Diamond(symbol='C', latticeconstant=3.5668) print(ase_atom.get_volume()) cell = pbcgto.Cell() cell.verbose = 5 cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom) cell.a=ase_atom.cell cell.basis = 'gth-szv' cell.pseudo = 'gth-pade' cell.build() mf=pbcdft.RKS(cell) mf.xc='lda,vwn' print(mf.kernel()) # [10,10,10]: -44.8811199336
def __init__(self, a0, nlayers, *args, **kwargs):
self.atoms = Diamond(symbol="Sn", latticeconstant=a0, pbc=(1, 1, 1))
super().__init__()
def dia_111_pandey(sym, a0, nx=nx, ny=nx, nz=nz):
"""2x1 Pandey reconstructed (111) surface."""
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*ny), sz/(6*nz)])
a.set_scaled_positions(a.get_scaled_positions()%1.0)
bulk = a.copy()
bondlen = a0*sqrt(3)/4
x, y, z = a.positions.T
mask = np.abs(z-z.max()) < 0.1*a0
top1, top2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.max()) < bondlen, np.logical_not(mask))
topA, topB = np.arange(len(a))[mask].reshape(-1, 2).T
y[topA] += bondlen/3
y[topB] -= bondlen/3
y[top1] += bondlen
x[top1] += a.cell[0,0]/(2*nx)
x[top2] += a.cell[0,0]/(2*nx)
mask = np.abs(z-z.min()) < 0.1*a0
bot1, bot2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.min()) < bondlen, np.logical_not(mask))
botA, botB = np.arange(len(a))[mask].reshape(-1, 2).T
y[botA] += bondlen/3
y[botB] -= bondlen/3
y[bot2] -= bondlen
x[bot2] += a.cell[0,0]/(2*nx)
x[bot1] += a.cell[0,0]/(2*nx)
a.set_scaled_positions(a.get_scaled_positions()%1.0)
return bulk, a
def setUp(self):
self.pot = quippy.Potential('IP SW', param_str="""
<SW_params n_types="2" label="PRB_31_plus_H">
<comment> Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements </comment>
<per_type_data type="1" atomic_num="1" />
<per_type_data type="2" atomic_num="14" />
<per_pair_data atnum_i="1" atnum_j="1" AA="0.0" BB="0.0"
p="0" q="0" a="1.0" sigma="1.0" eps="0.0" />
<per_pair_data atnum_i="1" atnum_j="14" AA="8.581214" BB="0.0327827"
p="4" q="0" a="1.25" sigma="2.537884" eps="2.1672" />
<per_pair_data atnum_i="14" atnum_j="14" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.0951" eps="2.1675" />
<!-- triplet terms: atnum_c is the center atom, neighbours j and k -->
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
</SW_params>
""")
self.fmax = 1e-4
self.at0 = Diamond('Si', latticeconstant=5.43)
self.at0.set_calculator(self.pot)
# relax initial positions and unit cell
FIRE(StrainFilter(self.at0, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=self.fmax)
self.C_ref = np.array([[ 151.4276439 , 76.57244456, 76.57244456, 0. , 0. , 0. ],
[ 76.57244456, 151.4276439 , 76.57244456, 0. , 0. , 0. ],
[ 76.57244456, 76.57244456, 151.4276439 , 0. , 0. , 0. ],
[ 0. , 0. , 0. , 109.85498798, 0. , 0. ],
[ 0. , 0. , 0. , 0. , 109.85498798, 0. ],
[ 0. , 0. , 0. , 0. , 0. , 109.85498798]])
self.C_err_ref = np.array([[ 1.73091718, 1.63682097, 1.63682097, 0. , 0. , 0. ],
[ 1.63682097, 1.73091718, 1.63682097, 0. , 0. , 0. ],
[ 1.63682097, 1.63682097, 1.73091718, 0. , 0. , 0. ],
[ 0. , 0. , 0. , 1.65751232, 0. , 0. ],
[ 0. , 0. , 0. , 0. , 1.65751232, 0. ],
[ 0. , 0. , 0. , 0. , 0. , 1.65751232]])
self.C_ref_relaxed = np.array([[ 151.28712587, 76.5394162 , 76.5394162 , 0. ,
0. , 0. ],
[ 76.5394162 , 151.28712587, 76.5394162 , 0. ,
0. , 0. ],
[ 76.5394162 , 76.5394162 , 151.28712587, 0. ,
0. , 0. ],
[ 0. , 0. , 0. , 56.32421772,
0. , 0. ],
[ 0. , 0. , 0. , 0. ,
56.32421772, 0. ],
[ 0. , 0. , 0. , 0. ,
0. , 56.32421772]])
self.C_err_ref_relaxed = np.array([[ 1.17748661, 1.33333615, 1.33333615, 0. , 0. ,
0. ],
[ 1.33333615, 1.17748661, 1.33333615, 0. , 0. ,
0. ],
[ 1.33333615, 1.33333615, 1.17748661, 0. , 0. ,
0. ],
[ 0. , 0. , 0. , 0.18959684, 0. ,
0. ],
[ 0. , 0. , 0. , 0. , 0.18959684,
0. ],
[ 0. , 0. , 0. , 0. , 0. ,
0.18959684]])
from mdcore import *
from mdcore.tests import test_forces, test_virial
# import ase_ext_io as io
###
sx = 2
dx = 1e-6
dev_thres = 1e-4
###
tests = [
( r6, dict(el1='Si', el2='Si', A=1.0, r0=1.0, cutoff=5.0),
[ ( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ) ] ),
( Brenner, Erhart_PRB_71_035211_SiC,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]) ),
( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ),
( "dia-Si-C", B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]) ) ] ),
( BrennerScr, Erhart_PRB_71_035211_SiC__Scr,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]) ),
( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ),
( "dia-Si-C", B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]) ) ] ),
( Brenner, Henriksson_PRB_79_114107_FeC,
[ dict( name='dia-C', struct=Diamond('C', size=[sx,sx,sx]) ),
dict( name='bcc-Fe',
struct=BodyCenteredCubic('Fe', size=[sx,sx,sx]) ),
dict( name='fcc-Fe',
""" Take ASE Diamond structure, input into PySCF and run """ import numpy as np import pyscf.pbc.gto as pbcgto import pyscf.pbc.dft as pbcdft from pyscf.pbc.tools import pyscf_ase import ase import ase.lattice from ase.lattice.cubic import Diamond ase_atom = Diamond(symbol='C', latticeconstant=3.5668) print(ase_atom.get_volume()) cell = pbcgto.Cell() cell.verbose = 5 cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom) cell.a = ase_atom.cell cell.basis = 'gth-szv' cell.pseudo = 'gth-pade' cell.build() mf = pbcdft.RKS(cell) mf.xc = 'lda,vwn' print(mf.kernel()) # [10,10,10]: -44.8811199336
E = youngs_modulus(C, params.cleavage_plane)
print('Young\'s modulus %.1f GPa' % (E / units.GPa))
nu = poisson_ratio(C, params.cleavage_plane, params.crack_direction)
print('Poisson ratio % .3f\n' % nu)
# **** Setup crack slab unit cell ******
directions = [params.crack_direction,
params.cleavage_plane,
params.crack_front]
print_crack_system(directions)
# now, we build system aligned with requested crystallographic orientation
unit_slab = Diamond(directions=directions,
size=(1, 1, 1),
symbol='Si',
pbc=True,
latticeconstant=a0)
if (hasattr(params, 'check_rotated_elastic_constants') and
# Check that elastic constants of the rotated system
# lead to same Young's modulus and Poisson ratio
params.check_rotated_elastic_constants):
unit_slab.set_calculator(params.calc)
C_r1 = measure_triclinic_elastic_constants(unit_slab,
optimizer=FIRE,
fmax=params.bulk_fmax)
R = np.array([ np.array(x)/np.linalg.norm(x) for x in directions ])
import numpy as np
import ase.io, sys
# set of utility routines specific this this model/testing framework
from utilities import relax_atoms, relax_atoms_cell
# the current model
import model
a0 = 5.44 # initial guess at lattice constant, cell will be relaxed below
fmax = 0.01 # maximum force following relaxtion [eV/A]
if not hasattr(model, 'bulk_reference'):
# set up the a
bulk = Diamond(symbol='Si', latticeconstant=a0)
# specify that we will use model.calculator to compute forces, energies and stresses
bulk.set_calculator(model.calculator)
# use one of the routines from utilities module to relax the initial
# unit cell and atomic positions
bulk = relax_atoms_cell(bulk, tol=fmax, traj_file=None)
else:
bulk = model.bulk_reference.copy()
bulk.set_calculator(model.calculator)
a0 = bulk.cell[0, 0] # get lattice constant from relaxed bulk
print "got a0 ", a0
bulk = Diamond(symbol="Si",
latticeconstant=a0,
def test_pbc(self):
a = Diamond('Si', latticeconstant=5.432, size=[2,2,2])
sx, sy, sz = a.get_cell().diagonal()
a.set_calculator(Tersoff())
e1 = a.get_potential_energy()
a.set_pbc([True,True,False])
e2 = a.get_potential_energy()
a.set_pbc(True)
a.set_cell([sx,sy,2*sz])
e3 = a.get_potential_energy()
self.assertEqual(e2, e3)
# This should give the unrelaxed surface energy
esurf = (e2-e1)/(2*sx*sy) * Jm2
self.assertTrue(abs(esurf-2.309) < 0.001)
def test_pbc(self):
a = Diamond('Si', latticeconstant=5.432, size=[2,2,2])
sx, sy, sz = a.get_cell().diagonal()
a.set_calculator(Tersoff())
e1 = a.get_potential_energy()
a.set_pbc([True,True,False])
e2 = a.get_potential_energy()
a.set_pbc(True)
a.set_cell([sx,sy,2*sz])
e3 = a.get_potential_energy()
self.assertEqual(e2, e3)
# This should give the unrelaxed surface energy
esurf = (e2-e1)/(2*sx*sy) * Jm2
self.assertTrue(abs(esurf-2.309) < 0.001)
class TestFitElasticConstants(matscipytest.MatSciPyTestCase):
"""
Tests of elastic constant calculation.
We test with a cubic Silicon lattice, since this also has most of the
symmetries of the lower-symmetry crystal families
"""
def setUp(self):
self.pot = quippy.Potential('IP SW', param_str="""
<SW_params n_types="2" label="PRB_31_plus_H">
<comment> Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements </comment>
<per_type_data type="1" atomic_num="1" />
<per_type_data type="2" atomic_num="14" />
<per_pair_data atnum_i="1" atnum_j="1" AA="0.0" BB="0.0"
p="0" q="0" a="1.0" sigma="1.0" eps="0.0" />
<per_pair_data atnum_i="1" atnum_j="14" AA="8.581214" BB="0.0327827"
p="4" q="0" a="1.25" sigma="2.537884" eps="2.1672" />
<per_pair_data atnum_i="14" atnum_j="14" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.0951" eps="2.1675" />
<!-- triplet terms: atnum_c is the center atom, neighbours j and k -->
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
</SW_params>
""")
self.fmax = 1e-4
self.at0 = Diamond('Si', latticeconstant=5.43)
self.at0.set_calculator(self.pot)
# relax initial positions and unit cell
FIRE(StrainFilter(self.at0, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=self.fmax)
self.C_ref = np.array([[ 151.4276439 , 76.57244456, 76.57244456, 0. , 0. , 0. ],
[ 76.57244456, 151.4276439 , 76.57244456, 0. , 0. , 0. ],
[ 76.57244456, 76.57244456, 151.4276439 , 0. , 0. , 0. ],
[ 0. , 0. , 0. , 109.85498798, 0. , 0. ],
[ 0. , 0. , 0. , 0. , 109.85498798, 0. ],
[ 0. , 0. , 0. , 0. , 0. , 109.85498798]])
self.C_err_ref = np.array([[ 1.73091718, 1.63682097, 1.63682097, 0. , 0. , 0. ],
[ 1.63682097, 1.73091718, 1.63682097, 0. , 0. , 0. ],
[ 1.63682097, 1.63682097, 1.73091718, 0. , 0. , 0. ],
[ 0. , 0. , 0. , 1.65751232, 0. , 0. ],
[ 0. , 0. , 0. , 0. , 1.65751232, 0. ],
[ 0. , 0. , 0. , 0. , 0. , 1.65751232]])
self.C_ref_relaxed = np.array([[ 151.28712587, 76.5394162 , 76.5394162 , 0. ,
0. , 0. ],
[ 76.5394162 , 151.28712587, 76.5394162 , 0. ,
0. , 0. ],
[ 76.5394162 , 76.5394162 , 151.28712587, 0. ,
0. , 0. ],
[ 0. , 0. , 0. , 56.32421772,
0. , 0. ],
[ 0. , 0. , 0. , 0. ,
56.32421772, 0. ],
[ 0. , 0. , 0. , 0. ,
0. , 56.32421772]])
self.C_err_ref_relaxed = np.array([[ 1.17748661, 1.33333615, 1.33333615, 0. , 0. ,
0. ],
[ 1.33333615, 1.17748661, 1.33333615, 0. , 0. ,
0. ],
[ 1.33333615, 1.33333615, 1.17748661, 0. , 0. ,
0. ],
[ 0. , 0. , 0. , 0.18959684, 0. ,
0. ],
[ 0. , 0. , 0. , 0. , 0.18959684,
0. ],
[ 0. , 0. , 0. , 0. , 0. ,
0.18959684]])
def test_measure_triclinic_unrelaxed(self):
# compare to brute force method without relaxation
C = measure_triclinic_elastic_constants(self.at0, delta=1e-2, optimizer=None)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref, tol=0.2)
def test_measure_triclinic_relaxed(self):
# compare to brute force method with relaxation
C = measure_triclinic_elastic_constants(self.at0, delta=1e-2, optimizer=FIRE,
fmax=self.fmax)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref_relaxed, tol=0.2)
def testcubic_unrelaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'cubic', verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref, tol=1e-2)
if abs(C_err).max() > 0.:
self.assertArrayAlmostEqual(C_err/units.GPa, self.C_err_ref, tol=1e-2)
def testcubic_relaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'cubic',
optimizer=FIRE, fmax=self.fmax,
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref_relaxed, tol=1e-2)
if abs(C_err).max() > 0.:
self.assertArrayAlmostEqual(C_err/units.GPa, self.C_err_ref_relaxed, tol=1e-2)
def testorthorhombic_unrelaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'orthorhombic',
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref, tol=0.1)
def testorthorhombic_relaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'orthorhombic',
optimizer=FIRE, fmax=self.fmax,
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref_relaxed, tol=0.1)
def testmonoclinic_unrelaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'monoclinic',
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref, tol=0.2)
def testmonoclinic_relaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'monoclinic',
optimizer=FIRE, fmax=self.fmax,
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref_relaxed, tol=0.2)
def testtriclinic_unrelaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'triclinic',
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref, tol=0.2)
def testtriclinic_relaxed(self):
C, C_err = fit_elastic_constants(self.at0, 'triclinic',
optimizer=FIRE, fmax=self.fmax,
verbose=False, graphics=False)
self.assertArrayAlmostEqual(C/units.GPa, self.C_ref_relaxed, tol=0.2)
def diamond_110_110(el, a0, n, crack_surface=[1,1,0],
crack_front=[1,-1,0],
skin_x=0.5, skin_y=1.0,
central_x=-1.0, central_y=-1.0,
vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
a = Diamond(el,
latticeconstant = a0,
size = [nx, ny, nz],
directions = [third_dir, crack_surface, crack_front]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(4*ny), sz/(4*nz)])
a.set_scaled_positions(a.get_scaled_positions())
skin_x = skin_x*sx/nx
skin_y = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < skin_x, r[:, 0] > sx-skin_x),
r[:, 1] < skin_y),
r[:, 1] > sy-skin_y),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < sx/2-central_x, r[:, 0] > sx/2+central_x),
r[:, 1] < sy/2-central_y),
r[:, 1] > sy/2+central_y),
g,
2*np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
def diamond_110_001(el, a0, n, crack_surface=[1,1,0], crack_front=[0,0,1],
skin_x=1.0, skin_y=1.0, vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
directions = [ third_dir, crack_surface, crack_front ]
if np.linalg.det(directions) < 0:
third_dir = -third_dir
directions = [ third_dir, crack_surface, crack_front ]
a = Diamond(el, latticeconstant = a0, size = [ nx,ny,nz ],
directions = directions)
sx, sy, sz = a.get_cell().diagonal()
a.translate([a0/100,a0/100,a0/100])
a.set_scaled_positions(a.get_scaled_positions())
a.center()
lx = skin_x*sx/nx
ly = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < lx, r[:, 0] > sx-lx),
r[:, 1] < ly),
r[:, 1] > sy-ly),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
