def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0/3.0) * 1.03
if ismaster:
# 50*50*50 would be big enough, but some vacancies are nice.
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
atoms = FaceCenteredCubic(symbol='Cu', size=(51,51,51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if isparallel:
atoms = atoms.repeat(cpuLayout)
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms)/2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0 / 3.0) * 1.03
if ismaster:
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
# 50*50*50 would be big enough, but some vacancies are nice.
atoms = FaceCenteredCubic(symbol='Cu', size=(51, 51, 51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms) / 2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
if isparallel:
# Move this contribution into position
uc = atoms.get_cell()
x = mpi.world.rank % cpuLayout[0]
y = (mpi.world.rank // cpuLayout[0]) % cpuLayout[1]
z = mpi.world.rank // (cpuLayout[0] * cpuLayout[1])
assert (0 <= x < cpuLayout[0])
assert (0 <= y < cpuLayout[1])
assert (0 <= z < cpuLayout[2])
offset = x * uc[0] + y * uc[1] + z * uc[2]
new_uc = cpuLayout[0] * uc[0] + cpuLayout[1] * uc[1] + cpuLayout[
2] * uc[2]
atoms.set_cell(new_uc, scale_atoms=False)
atoms.set_positions(atoms.get_positions() + offset)
# Distribute atoms. Maybe they are all on the wrong cpu, but that will
# be taken care of.
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0/3.0) * 1.03
if ismaster:
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
# 50*50*50 would be big enough, but some vacancies are nice.
atoms = FaceCenteredCubic(symbol='Cu', size=(51,51,51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms)/2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
if isparallel:
# Move this contribution into position
uc = atoms.get_cell()
x = mpi.world.rank % cpuLayout[0]
y = (mpi.world.rank // cpuLayout[0]) % cpuLayout[1]
z = mpi.world.rank // (cpuLayout[0] * cpuLayout[1])
assert(0 <= x < cpuLayout[0])
assert(0 <= y < cpuLayout[1])
assert(0 <= z < cpuLayout[2])
offset = x * uc[0] + y * uc[1] + z * uc[2]
new_uc = cpuLayout[0] * uc[0] + cpuLayout[1] * uc[1] + cpuLayout[2] * uc[2]
atoms.set_cell(new_uc, scale_atoms=False)
atoms.set_positions(atoms.get_positions() + offset)
# Distribute atoms. Maybe they are all on the wrong cpu, but that will
# be taken care of.
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
print " Periodic boundary conditions: %s" % (str(v),)
elif k == 'natoms':
print " Number of atoms: %i" % (v,)
elif hasattr(v, 'shape'):
print " %s: shape = %s, type = %s" % (k, str(v.shape), str(v.dtype))
else:
print " %s: %s" % (k, str(v))
# Read info from separate files.
for k, v in metadata['datatypes'].items():
if v and not k in small:
info = backend.read_info(frame, k)
if info and isinstance(info[0], tuple):
shape, dtype = info
else:
shape = info
dtype = 'unknown'
print " %s: shape = %s, type = %s" % (k, str(shape), dtype)
if __name__ == '__main__':
from ase.lattice.cubic import FaceCenteredCubic
from ase.io import read, write
atoms = FaceCenteredCubic(size=(5, 5, 5), symbol='Au')
write('test.bundle', atoms)
atoms2 = read('test.bundle')
assert (atoms.get_positions() == atoms2.get_positions()).all()
assert (atoms.get_atomic_numbers() == atoms2.get_atomic_numbers()).all()
def __init__(self,
symbol=None,
layers=None,
positions=None,
latticeconstant=None,
symmetry=None,
cell=None,
center=None,
multiplicity=1,
filename=None,
debug=0):
self.debug = debug
self.multiplicity = multiplicity
if filename is not None:
# We skip MonteCarloAtoms.__init__, do it manually.
self.mc_optim = np.zeros(101, np.intc)
self.mc_optim[0] = 10000 # MC optim invalid
self.read(filename)
return
#Find the atomic number
if symbol is not None:
if isinstance(symbol, str):
self.atomic_number = atomic_numbers[symbol]
else:
self.atomic_number = symbol
else:
raise Warning('You must specify a atomic symbol or number!')
#Find the crystal structure
if symmetry is not None:
if symmetry.lower() in ['bcc', 'fcc', 'hcp']:
self.symmetry = symmetry.lower()
else:
raise Warning('The %s symmetry does not exist!' %
symmetry.lower())
else:
self.symmetry = reference_states[
self.atomic_number]['symmetry'].lower()
if self.debug:
print 'Crystal structure:', self.symmetry
#Find the lattice constant
if latticeconstant is None:
if self.symmetry == 'fcc':
self.lattice_constant = reference_states[
self.atomic_number]['a']
else:
raise Warning(('Cannot find the lattice constant ' +
'for a %s structure!' % self.symmetry))
else:
self.lattice_constant = latticeconstant
if self.debug:
print 'Lattice constant(s):', self.lattice_constant
#Make the cluster of atoms
if layers is not None and positions is None:
layers = list(layers)
#Make base crystal based on the found symmetry
if self.symmetry == 'fcc':
if len(layers) != data.lattice[self.symmetry]['surface_count']:
raise Warning(
'Something is wrong with the defined number of layers!'
)
xc = int(np.ceil(layers[1] / 2.0)) + 1
yc = int(np.ceil(layers[3] / 2.0)) + 1
zc = int(np.ceil(layers[5] / 2.0)) + 1
xs = xc + int(np.ceil(layers[0] / 2.0)) + 1
ys = yc + int(np.ceil(layers[2] / 2.0)) + 1
zs = zc + int(np.ceil(layers[4] / 2.0)) + 1
center = np.array((xc, yc, zc)) * self.lattice_constant
size = (xs, ys, zs)
if self.debug:
print 'Base crystal size:', size
print 'Center cell position:', center
atoms = FaceCenteredCubic(
symbol=symbol,
size=size,
latticeconstant=self.lattice_constant,
align=False)
else:
raise Warning(
('The %s crystal structure is not' + ' supported yet.') %
self.symmetry)
positions = atoms.get_positions()
numbers = atoms.get_atomic_numbers()
cell = atoms.get_cell()
elif positions is not None:
numbers = [self.atomic_number] * len(positions)
else:
numbers = None
#Load the constructed atoms object into this object
self.set_center(center)
MonteCarloAtoms.__init__(self,
numbers=numbers,
positions=positions,
cell=cell,
pbc=False)
#Construct the particle with the assigned surfasces
if layers is not None:
self.set_layers(layers)
atoms2 = atoms.copy()
atoms = MonteCarloAtoms(atoms)
print "Number of atoms:", len(atoms)
# Replace 10% of the atoms with element2
newz = where(greater(random.random((len(atoms), )), 0.9), element2number,
elementnumber)
atoms.set_atomic_numbers(newz)
atoms2.set_atomic_numbers(newz)
atoms.set_calculator(MonteCarloEMT())
atoms2.set_calculator(EMT())
atoms.get_potential_energy()
for e in ((element, elementnumber), (element2, element2number)):
print("Number of %s atoms (Z=%d): %d" %
(e[0], e[1], sum(equal(atoms.get_atomic_numbers(), e[1]))))
print
print "Testing perturbations of single atoms"
magnarr = array((0.0, 0.01, 0.1, 1.0, 3.0, 10.0))
numarr = array((1, 3, 10, len(atoms) / 2, -3))
pick1 = argsort(random.random((len(magnarr), )))
for magn in take(magnarr, pick1):
pick2 = argsort(random.random((len(numarr), )))
for number in take(numarr, pick2):
# Pick number random atoms.
if number < 0:
# Find N neighboring atoms and perturb them
number = -number
nblist = atoms.get_calculator().get_neighborlist()
b = ss[4]
assert a.index == b.index
assert a.atoms is b.atoms
a2 = Atoms(ss)
ReportTest("number of atoms in copy of subset", len(a2), 6, 0)
a = Filter(atoms, indices=(5, 6, 7, 8))
ReportTest("Number of atoms in subset", len(a), 4, 0)
a.set_atomic_numbers(47 * ones(4, int32))
ReportTest("subset: z[0]", a.get_atomic_numbers()[0], 47, 0)
ReportTest("subset: z[1]", a.get_atomic_numbers()[1], 47, 0)
ReportTest("subset: z[2]", a.get_atomic_numbers()[2], 47, 0)
ReportTest("subset: z[3]", a.get_atomic_numbers()[3], 47, 0)
z = atoms.get_atomic_numbers()
ReportTest("full: z[0]", z[0], 29, 0)
ReportTest("full: z[4]", z[4], 29, 0)
ReportTest("full: z[5]", z[5], 47, 0)
ReportTest("full: z[8]", z[8], 47, 0)
ReportTest("full: z[9]", z[9], 29, 0)
ReportTest("full: z[100]", z[100], 29, 0)
r = a.get_positions()
r[2] = array([10.0, 20.0, 30.0])
a.set_positions(r)
r = atoms.get_positions()
ReportTest("full: r[7,0]", r[7, 0], 10.0, 0)
ReportTest("full: r[7,1]", r[7, 1], 20.0, 0)
ReportTest("full: r[7,2]", r[7, 2], 30.0, 0)
def __init__(self, symbol=None, layers=None, positions=None,
latticeconstant=None, symmetry=None, cell=None,
center=None, multiplicity=1, filename=None, debug=0):
self.debug = debug
self.multiplicity = multiplicity
if filename is not None:
# We skip MonteCarloAtoms.__init__, do it manually.
self.mc_optim = np.zeros(101, np.intc)
self.mc_optim[0] = 10000 # MC optim invalid
self.read(filename)
return
#Find the atomic number
if symbol is not None:
if isinstance(symbol, str):
self.atomic_number = atomic_numbers[symbol]
else:
self.atomic_number = symbol
else:
raise Warning('You must specify a atomic symbol or number!')
#Find the crystal structure
if symmetry is not None:
if symmetry.lower() in ['bcc', 'fcc', 'hcp']:
self.symmetry = symmetry.lower()
else:
raise Warning('The %s symmetry does not exist!' % symmetry.lower())
else:
self.symmetry = reference_states[self.atomic_number]['symmetry'].lower()
if self.debug:
print 'Crystal structure:', self.symmetry
#Find the lattice constant
if latticeconstant is None:
if self.symmetry == 'fcc':
self.lattice_constant = reference_states[self.atomic_number]['a']
else:
raise Warning(('Cannot find the lattice constant ' +
'for a %s structure!' % self.symmetry))
else:
self.lattice_constant = latticeconstant
if self.debug:
print 'Lattice constant(s):', self.lattice_constant
#Make the cluster of atoms
if layers is not None and positions is None:
layers = list(layers)
#Make base crystal based on the found symmetry
if self.symmetry == 'fcc':
if len(layers) != data.lattice[self.symmetry]['surface_count']:
raise Warning('Something is wrong with the defined number of layers!')
xc = int(np.ceil(layers[1] / 2.0)) + 1
yc = int(np.ceil(layers[3] / 2.0)) + 1
zc = int(np.ceil(layers[5] / 2.0)) + 1
xs = xc + int(np.ceil(layers[0] / 2.0)) + 1
ys = yc + int(np.ceil(layers[2] / 2.0)) + 1
zs = zc + int(np.ceil(layers[4] / 2.0)) + 1
center = np.array((xc, yc, zc)) * self.lattice_constant
size = (xs, ys, zs)
if self.debug:
print 'Base crystal size:', size
print 'Center cell position:', center
atoms = FaceCenteredCubic(symbol=symbol,
size=size,
latticeconstant=self.lattice_constant,
align=False)
else:
raise Warning(('The %s crystal structure is not' +
' supported yet.') % self.symmetry)
positions = atoms.get_positions()
numbers = atoms.get_atomic_numbers()
cell = atoms.get_cell()
elif positions is not None:
numbers = [self.atomic_number] * len(positions)
else:
numbers = None
#Load the constructed atoms object into this object
self.set_center(center)
MonteCarloAtoms.__init__(self, numbers=numbers, positions=positions,
cell=cell, pbc=False)
#Construct the particle with the assigned surfasces
if layers is not None:
self.set_layers(layers)
for latconst, maxrdf, nbins, withemt in testtypes:
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
symbol="Cu", size=(10,10,10),
latticeconstant=latconst, debug=0)
natoms = len(atoms)
ReportTest("Number of atoms", natoms, 4000, 0)
if withemt:
atoms.set_calculator(EMT())
print atoms.get_potential_energy()
result = _asap.RawRDF(atoms, maxrdf, nbins, zeros(len(atoms), int32), 1,
ListOfElements(atoms))
z = atoms.get_atomic_numbers()[0]
globalrdf, rdfdict, countdict = result
print globalrdf
ReportTest("Local and global RDF are identical",
min( globalrdf == rdfdict[0][(z,z)]), 1, 0)
ReportTest("Atoms are counted correctly", countdict[0][z], natoms, 0)
shellpop = [12, 6, 24, 12, 24, -1]
shell = [sqrt(i+1.0)/sqrt(2.0) for i in range(6)]
print shell
print shellpop
n = 0
