def make_hcp_0001_cell(size=(1, 1, 1), symbols=['Ni'], pbc=(1, 1, 1)):
direction_x = [2, -1, -1, 0]
direction_y = [0, 1, -1, 0]
direction_z = [0, 0, 0, 1]
directions = [direction_x, direction_y, direction_z]
atoms = None
try:
atoms = HexagonalClosedPacked(
directions=[direction_x, direction_y, direction_z],
size=size,
symbol=symbols[0],
pbc=pbc)
except ValueError as e:
if str(
e
) == 'Cannot guess the hcp lattice constant of an element with crystal structure fcc.':
r = get_atomic_radius(symbol=symbols[0])
_lattice_constants = {}
_lattice_constants['a'] = r
_lattice_constants['c/a'] = 1.663
atoms = HexagonalClosedPacked(\
directions=directions,
size=size,
symbol=symbols[0],
pbc=pbc,
latticeconstant=_lattice_constants)
else:
raise
return atoms
def EfccEhcpCalculator(self, EMT, PARAMETERS):
# Return 0 is used when the method is not desired to be used
# return 0
""" This method uses the EMT calculator to calculate and return the difference in energy between a system of
atoms placed in the HCP and FCC structure. """
# The atoms objects are created using the input size and element and the energy calculator
# is set to the EMT calculator
# The Lattice Constants, a,c, for the HCP lattice is here given by the nearest neighbor distance of
# the system in the FCC crystal structure, a = dnn, and the ideal relation between a and
# c: a/c = sqrt(8/3) => c = dnn / sqrt(8/3)
a = beta * PARAMETERS[self.Element][1] * Bohr
c = a * numpy.sqrt(8. / 3.)
# The HCP crystal is created, the size of the crystal is defined as 5,5,5, any smaller crystal will result in
# Neighborlist errors.
atoms1 = HexagonalClosedPacked(size=(5, 5, 5),
directions=[[2, -1, -1,
0], [0, 1, -1, 0],
[0, 0, 0, 1]],
symbol=self.Element,
latticeconstant={
'a': a,
'c': c
})
atoms1.set_calculator(EMT)
# The FCC crystal is created
atoms2 = FaceCenteredCubic(size=(self.Size, self.Size, self.Size),
symbol=self.Element)
atoms2.set_calculator(EMT)
# The energy difference pr atom is calculated and returned
return atoms1.get_potential_energy() / len(
atoms1) - atoms2.get_potential_energy() / len(atoms2)
def test_lattice_lindep():
from ase.lattice.cubic import FaceCenteredCubic
from ase.lattice.hexagonal import HexagonalClosedPacked
from ase.test import must_raise
with must_raise(ValueError):
# The Miller indices of the surfaces are linearly dependent
atoms = FaceCenteredCubic(symbol='Cu',
miller=[[1, 1, 0], [1, 1, 0], [0, 0, 1]])
# This one should be OK:
atoms = FaceCenteredCubic(symbol='Cu',
miller=[[1, 1, 0], [0, 1, 0], [0, 0, 1]])
print(atoms.get_cell())
with must_raise(ValueError):
# The directions spanning the unit cell are linearly dependent
atoms = FaceCenteredCubic(symbol='Cu',
directions=[[1, 1, 0], [1, 1, 0], [0, 0, 1]])
with must_raise(ValueError):
# The directions spanning the unit cell are linearly dependent
atoms = FaceCenteredCubic(symbol='Cu',
directions=[[1, 1, 0], [1, 0, 0], [0, 1, 0]])
# This one should be OK:
atoms = FaceCenteredCubic(symbol='Cu',
directions=[[1, 1, 0], [0, 1, 0], [0, 0, 1]])
print(atoms.get_cell())
with must_raise((ValueError, NotImplementedError)):
# The Miller indices of the surfaces are linearly dependent
atoms = HexagonalClosedPacked(symbol='Mg',
miller=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 1, -1, 0]])
# This one should be OK
#
# It is not! The miller argument is broken in hexagonal crystals!
#
# atoms = HexagonalClosedPacked(symbol='Mg',
# miller=[[1, -1, 0, 0],
# [1, 0, -1, 0],
# [0, 0, 0, 1]])
# print(atoms.get_cell())
with must_raise(ValueError):
# The directions spanning the unit cell are linearly dependent
atoms = HexagonalClosedPacked(symbol='Mg',
directions=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 1, -1, 0]])
# This one should be OK
atoms = HexagonalClosedPacked(symbol='Mg',
directions=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 0, 0, 1]])
print(atoms.get_cell())
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 test_CuZr(self):
# This is a test for the potential published in:
# Mendelev, Sordelet, Kramer, J. Appl. Phys. 102, 043501 (2007)
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
calc = EAM('CuZr_mm.eam.fs', kind='eam/fs')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
a_Cu = a.cell.diagonal().mean() / 2
#print('a_Cu (3.639) = ', a_Cu)
self.assertAlmostEqual(a_Cu, 3.639, 3)
a = HexagonalClosedPacked('Zr', size=[2, 2, 2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
a, b, c = a.cell / 2
#print('a_Zr (3.220) = ', norm(a), norm(b))
#print('c_Zr (5.215) = ', norm(c))
self.assertAlmostEqual(norm(a), 3.220, 3)
self.assertAlmostEqual(norm(b), 3.220, 3)
self.assertAlmostEqual(norm(c), 5.215, 3)
# CuZr3
a = L1_2(['Cu', 'Zr'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 4.324, 3)
# Cu3Zr
a = L1_2(['Zr', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 3.936, 3)
# CuZr
a = B2(['Zr', 'Cu'], size=[2, 2, 2], latticeconstant=3.3)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 3.237, 3)
for b in bccs:
try: a = BodyCenteredCubic(b[0]).get_cell()[0][0]/2
except ValueError: a = radDict[b[0]]; print "Should look up lattice constant of "+b[0]
name = root+b[0]+'-bcc.traj'
mag = magLookup(b[0])
info = {'name':b[0]+'-bcc','bravais':'cubic','mag':mag,'comments':'Autogenerated by createTrajs'}
if name not in ds:
io.write(name,Atoms(b[0],scaled_positions=[[0,0,0]],cell=[[a,a,-a],[-a,a,a],[a,-a,a]],pbc=[1,1,1]
,magmoms=[3 if e in magElems else 0 for e in b[0]],info=info))
#####################################################################
#####################################################################
for h in hcps:
try:
cell = HexagonalClosedPacked(h[0]).get_cell()
a,c = cell[0][0],cell[2][2]
except ValueError:
a = radDict[h[0]]
c = a*1.7
name = root+h[0]+'-hcp.traj'
mag = magLookup(h[0])
info = {'name':h[0]+'-hcp','bravais':'hexagonal','mag':mag,'comments':'Autogenerated by createTrajs'}
if name not in ds:
io.write(name,Atoms([h[0]]*2,scaled_positions=[[0,0,0],[2./3,1./3,1./2]],cell=[a,a,c,90,90,120],pbc=[1,1,1]
magmoms=[3 if e in magElems else 0 for e in h[0]],info=info))
#####################################################################
#####################################################################
for d in diamonds:
try: a = Diamond(d[0]).get_cell()[0][0]*(2**(-0.5))
directions=[[1, 1, 0], [1, 1, 0], [0, 0, 1]])
with must_raise(ValueError):
# The directions spanning the unit cell are linearly dependent
atoms = FaceCenteredCubic(symbol='Cu',
directions=[[1, 1, 0], [1, 0, 0], [0, 1, 0]])
# This one should be OK:
atoms = FaceCenteredCubic(symbol='Cu',
directions=[[1, 1, 0], [0, 1, 0], [0, 0, 1]])
print(atoms.get_cell())
with must_raise((ValueError, NotImplementedError)):
# The Miller indices of the surfaces are linearly dependent
atoms = HexagonalClosedPacked(symbol='Mg',
miller=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 1, -1, 0]])
# This one should be OK
#
# It is not! The miller argument is broken in hexagonal crystals!
#
# atoms = HexagonalClosedPacked(symbol='Mg',
# miller=[[1, -1, 0, 0],
# [1, 0, -1, 0],
# [0, 0, 0, 1]])
# print(atoms.get_cell())
with must_raise(ValueError):
# The directions spanning the unit cell are linearly dependent
atoms = HexagonalClosedPacked(symbol='Mg',
from ase.lattice.hexagonal import HexagonalClosedPacked
from vasp import Vasp
import matplotlib.pyplot as plt
atoms = HexagonalClosedPacked(symbol='Ru',
latticeconstant={'a': 2.7,
'c/a': 1.584})
a_list = [2.5, 2.6, 2.7, 2.8, 2.9]
covera_list = [1.4, 1.5, 1.6, 1.7, 1.8]
for a in a_list:
energies = []
for covera in covera_list:
atoms = HexagonalClosedPacked(symbol='Ru',
latticeconstant={'a': a,
'c/a': covera})
wd = 'bulk/Ru/{0:1.2f}-{1:1.2f}'.format(a, covera)
calc = Vasp(wd,
xc='PBE',
# the c-axis is longer than the a-axis, so we use
# fewer kpoints.
kpts=[6, 6, 4],
encut=350,
atoms=atoms)
energies.append(atoms.get_potential_energy())
if not None in energies:
plt.plot(covera_list, energies, label=r'a={0} $\AA$'.format(a))
plt.xlabel('$c/a$')
plt.ylabel('Energy (eV)')
plt.legend()
plt.savefig('images/Ru-covera-scan.png')
def get_structure(self, name, elements, a=None, c=None, l=None):
# Check number of elements
if name[:3] in ['fcc', 'hcp']:
if len(elements) != 1:
raise ValueError("Tuple of elements must be of length one")
if name[:3] in ['l12', 'l10'] or name[:2] == 'B2':
if len(elements) != 2:
raise ValueError("Tuple of elements must be of length two")
# Get lattice constants
if a is None:
if name[:2] == 'B2':
a = self.get_lattice_constant_a(name[:2], elements)
elif name[:3] in ['fcc', 'hcp', 'bcc', 'l12', 'l10']:
a = self.get_lattice_constant_a(name[:3], elements)
if c is None:
if name[:3] in ['hcp', 'l10']:
c = self.get_lattice_constant_c(name[:3], elements)
# Get size
if name in ['fcc', 'hcp', 'bcc', 'l12', 'l10', 'B2']:
size = self.properties[name + '_size']
elif name in ['fcc100', 'fcc111', 'hcp0001']:
size = self.properties[name + '_size'][:2] + (l, )
# Make structure
if name == 'fcc':
atoms = FaceCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'hcp':
atoms = HexagonalClosedPacked(symbol=elements[0],
size=size,
directions=[[2, -1, -1, 0],
[0, 1, -1, 0],
[0, 0, 0, 1]],
latticeconstant=(a, c))
elif name == 'bcc':
atoms = BodyCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'B2':
atoms = B2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l12':
atoms = L1_2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l10':
atoms = L1_0(symbol=elements, size=size, latticeconstant=(a, c))
elif name == 'fcc100':
atoms = fcc100(symbol=elements[0], size=size, a=a, vacuum=10.0)
elif name == 'fcc111':
atoms = fcc111(symbol=elements[0],
size=size,
a=a,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp0001':
atoms = hcp0001(symbol=elements[0],
size=size,
a=a,
c=c,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp1010A':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'hcp1010B':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'l12100':
n = (l + 1) / 2
atoms = L1_2(symbol=elements, size=(8, 8, n), latticeconstant=a)
atoms.set_pbc([True, True, False])
# Remove layers
atoms = atoms[atoms.get_positions()[:, 2] > 0.1 * a]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
elif name == 'l12111':
if l % 3 == 0:
n = l / 3
c = 0
else:
n = l / 3 + 1
c = 3 - l % 3
atoms = L1_2(
symbol=elements,
size=(8, 4, n),
#directions=[[1,-1,0],[1,0,-1],[1,1,1]], latticeconstant=a)
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]],
latticeconstant=a)
atoms.set_pbc([True, True, False])
# Wrap positions
scpos = atoms.get_scaled_positions()
scpos[scpos > (1.0 - 1e-12)] = 0.0
atoms.set_scaled_positions(scpos)
# Remove layers
if c > 0:
atoms = atoms[atoms.get_positions()[:, 2] > (c - 0.5) * a /
np.sqrt(3.0)]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
else:
raise ValueError("Structure '%s' not supported" % (name, ))
return atoms
def test_hcp():
atoms = HexagonalClosedPacked(symbol='Mg',
directions=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 0, 0, 1]])
print(atoms.get_cell())
def test_hcp_cell_linearly_dependent():
with pytest.raises(ValueError):
# The directions spanning the unit cell are linearly dependent
HexagonalClosedPacked(symbol='Mg',
directions=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 1, -1, 0]])
def test_hcp_miller_lienarly_dependent():
with pytest.raises((ValueError, NotImplementedError)):
# The Miller indices of the surfaces are linearly dependent
HexagonalClosedPacked(symbol='Mg',
miller=[[1, -1, 0, 0], [1, 0, -1, 0],
[0, 1, -1, 0]])
a = Triclinic(directions=[[2, 1, 0], [-2, 3, 0], [0, 1, 4]],
size=(3, 3, 3),
symbol="Cu",
latticeconstant=(3.61, a0, a0, 60, 45, 45))
testFCC(a, 32 * 3 * 3 * 3, "Triclinic/FCC 3")
a = BaseCenteredMonoclinic(directions=[[2, 1, 0], [-2, 3, 0], [0, 1, 4]],
size=(3, 3, 3),
symbol="Cu",
latticeconstant=(3.61, 3.61, a0, 45))
testFCC(a, 64 * 3 * 3 * 3, "Monoclinic/FCC")
a0 = 3.15 * sqrt(3) / 2
a = Triclinic(directions=[[2, 1, 0], [-2, 3, 0], [0, 1, 4]],
size=(3, 3, 3),
symbol="Mo",
latticeconstant=(3.15, 3.15, a0, 54.736, 54.736, 90))
testBCC(a, 32 * 3 * 3 * 3, "Triclinic/BCC")
a = HexagonalClosedPacked(directions=[[2, -1, -1, 0], [0, 1, -1, 0],
[0, 0, 0, 1]],
size=(10, 5, 5),
symbol="Cu",
latticeconstant={
'a': 3.61 / sqrt(2),
'c/a': 2 * sqrt(2) / sqrt(3)
})
testHCP(a, 1000, "HCP 1")
ReportTest.Summary()
from ase.lattice.hexagonal import HexagonalClosedPacked
from vasp import Vasp
import matplotlib.pyplot as plt
atoms = HexagonalClosedPacked(symbol='Ru',
latticeconstant={
'a': 2.7,
'c/a': 1.584
})
a_list = [2.5, 2.6, 2.7, 2.8, 2.9]
covera_list = [1.4, 1.5, 1.6, 1.7, 1.8]
for a in a_list:
energies = []
for covera in covera_list:
atoms = HexagonalClosedPacked(symbol='Ru',
latticeconstant={
'a': a,
'c/a': covera
})
wd = 'bulk/Ru/{0:1.2f}-{1:1.2f}'.format(a, covera)
calc = Vasp(
wd,
xc='PBE',
# the c-axis is longer than the a-axis, so we use
# fewer kpoints.
kpts=[6, 6, 4],
encut=350,
atoms=atoms)
energies.append(atoms.get_potential_energy())
if not None in energies:
plt.plot(covera_list, energies, label=r'a={0} $\AA$'.format(a))
plt.xlabel('$c/a$')
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 = dataLookup(x[0]) / 2
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 misc.magElems else 0 for e in elems]
atoms = Atoms(elems,
scaled_positions=pos,
cell=cell,
pbc=[1, 1, 1],
magmoms=magmoms)
info = {'name': x[0] + name, 'structure': struc}
db.write(atoms, key_value_pairs=info)
# properties with a given model
#
# INPUTS:
# model.calculator -- an ase.calculator.Calculator instance
# this script can assume the calculator is checkpointed.
#
# OUTPUTS:
# properties -- dictionary of key/value pairs corresponding
# to physical quantities computed by this test
# standard ASE structure generation routines
from ase.lattice.hexagonal import HexagonalClosedPacked
from math import sqrt
import lattice_tetragonal
# the current model
import model
c_over_a = 1.8
a0 = (16.0*2*2/sqrt(3.0)/c_over_a)**(1.0/3.0)# initial guess at lattice constant, cell will be relaxed below
# set up the a
bulk = HexagonalClosedPacked(symbol='Si', latticeconstant=(a0,a0*c_over_a))
(E_vs_V) = lattice_tetragonal.do_lattice(bulk, elastic=False, tol=1.0e-2)
# dictionary of computed properties - this is output of this test, to
# be compared with other models
properties = {'hcp_E_vs_V': E_vs_V }
if __name__ == '__main__':
from asap3 import EMT, units, EMThcpParameters
from ase.lattice.cubic import FaceCenteredCubic
from ase.lattice.hexagonal import HexagonalClosedPacked
print "Calculating cubic constants for Cu"
atoms = FaceCenteredCubic(size=(5, 5, 5),
symbol='Cu',
latticeconstant=3.59495722231)
atoms.set_calculator(EMT())
e = ElasticConstants(atoms, 'cubic')
print np.array(e) / units.GPa
print "Pretending that Cu is hexagonal"
e = ElasticConstants(atoms, 'hexagonal', sanity=False)
print np.array(e) / units.GPa
print "Calculating elastic constants for Ru"
atoms = HexagonalClosedPacked(size=(5, 5, 5),
symbol='Ru',
directions=[[1, -2, 1, 0], [1, 0, -1, 0],
[0, 0, 0, 1]])
atoms.set_calculator(EMT(EMThcpParameters()))
e = ElasticConstants(atoms, 'hexagonal', minimize=True)
print np.array(e) / units.GPa
print "The EMT values are not even close to experimental values!"
print "Pretending Ru is cubic"
e = ElasticConstants(atoms, 'cubic')
print np.array(e) / units.GPa