def test_coordination_shells():
from random import random
from numpy import array
from numpy.random import randint, random
from pylada.crystal import supercell, Structure
lattice = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]) \
.add_atom(0, 0, 0, "Si") \
.add_atom(0.25, 0.25, 0.25, "Ge")
for atom in lattice:
check(lattice, atom)
structure = supercell(lattice, [[1, 1, 0], [-5, 2, 0], [0, 0, 1]])
for index in randint(len(structure), size=4):
check(structure, structure[index])
for atom in lattice:
atom.pos += random(3) * 1e-4 - 5e-5
for atom in lattice:
check(lattice, atom, 1e-2)
for atom in structure:
atom.pos += random(3) * 1e-4 - 5e-5
for index in randint(len(structure), size=4):
check(structure, structure[index], 1e-2)
check_against_neighbors(structure, 1e-8)
lattice = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]) \
.add_atom(0, 0, 0, "Si")
check_against_neighbors(structure, 1e-8)
lattice = Structure([[-0.5, 0.5, 0.5], [0.5, -0.5, 0.5], [0.5, 0.5, -0.5]]) \
.add_atom(0, 0, 0, "Si")
check_against_neighbors(structure, 1e-8)
def mix_atoms(s1, s2, roll=True):
""" Randomly mix cell and atoms from parents.
Mating operation on two parent structures s1 and s2.
Done by mixing randomly atoms from s1 and s2 into the
cell coming from one of them. Returns two offspring
structures.
"""
from random import choice
from itertools import chain
from numpy.linalg import det
from numpy import dot, abs
from ..crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos1 = zip([atom.type for atom in s1], fractional_pos(s1, roll))
sc_pos2 = zip([atom.type for atom in s2], fractional_pos(s2, roll))
result = Structure(s1.cell)
for pos, type in chain(sc_pos1, sc_pos2):
if choice([True, False]):
result.add_atom(*dot(result.cell, pot), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
def str_template(name, scale, cell): from pylada.crystal import Structure structure = Structure() structure.name = name structure.scale = scale structure.cell = cell return structure
def test_system():
from pylada.crystal import Structure
from pylada.vasp import Vasp
a = Vasp()
b = Structure()
assert a.system is None
assert a._input['system'].keyword == 'system'
assert a._input['system'].output_map(vasp=a, structure=b) is None
a.system = 'system'
assert a.system == 'system'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'system'
b.name = 'hello'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(
vasp=a, structure=b)['system'] == 'system: hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
def test_ewald():
""" Ewald Rydberg test """
from numpy import all, abs, sqrt
from pylada.crystal import Structure
from pylada.ewald import ewald
from quantities import angstrom, a0, Ry
structure = Structure([[1, 0, 0],
[0, 1, 0],
[0, 0, 1] ], scale=50 ) \
.add_atom(0, 0, 0, 'A', charge=1e0) \
.add_atom(float(a0.rescale(angstrom) / 50.0), 0, 0, 'A', charge=-1e0)
result = ewald(structure, cutoff=80)
assert abs(result.energy + 2e0 * Ry) < 1e-3
assert all(abs(abs(result[0].force) - [2e0, 0, 0] * Ry / a0) < 1e-3)
assert all(abs(abs(result[1].force) - [2e0, 0, 0] * Ry / a0) < 1e-3)
a = float(a0.rescale(angstrom) / 50.0) / sqrt(2.)
structure = Structure([[1, 0, 0],
[0, 1, 0],
[0, 0, 1] ], scale=50 ) \
.add_atom(0, 0, 0, 'A', charge=1e0) \
.add_atom(0, a, a, 'A', charge=-1e0)
result = ewald(structure, cutoff=80)
assert abs(result.energy + 2e0 * Ry) < 1e-3
assert all(
abs(abs(result[0].force) -
[0, 2. / sqrt(2), 2. / sqrt(2)] * Ry / a0) < 1e-3)
assert all(
abs(abs(result[1].force) -
[0, 2. / sqrt(2), 2. / sqrt(2)] * Ry / a0) < 1e-3)
def test_system():
from pylada.crystal import Structure
from pylada.vasp import Vasp
a = Vasp()
b = Structure()
assert a.system is None
assert a._input['system'].keyword == 'system'
assert a._input['system'].output_map(vasp=a, structure=b) is None
a.system = 'system'
assert a.system == 'system'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system'
b.name = 'hello'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system: hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello'
def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def mix_poscars(s1,s2, roll=True):
""" Crossover operations where atoms are from one and cell from other.
Mating operation on two parent structures s1 and s2.
Done on scaled atomic positions (cubic systems) by
interchanging their cells and scaled positions.
Returns two offspring structures each with the same
number of atoms as the parent from which the atoms
are inhereted.
"""
from random import choice
from numpy import dot
from numpy.linalg import det
from ..crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos2 = zip([atom.type for atom in s2],fractional_pos(s2, roll))
# cell from s1
result = Structure(s1.cell, scal=s1.scale)
# atoms from s2
for type, pos in sc_pos2:
result.add_atom(*dot(result.cell, pos), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
def icsd_cif_b( filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from pylada.misc import bugLev
from . import readCif
rdr = readCif.CifReader( 0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose( cellBasis),
scale = 1,
name = basename( filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
if bugLev >= 5:
print " crystal/read: len(usyms): %d usyms: %s" \
% (len( usyms), usyms,)
print " crystal/read: len(posVecs): %d" % (len(posVecs),)
print " crystal/read: len(mults): %d mults: %s" \
% (len( mults), mults,)
# For each unique type of atom ...
for ii in range( len( usyms)):
if bugLev >= 5:
print " crystal/read: icsd_cif_b: ii: ", ii, \
" usym: ", usyms[ii], \
" mult: ", mults[ii], \
" posVecs: ", posVecs[ii]
# crystal/read: i: 0 symbol: Mo len position: 2
# For each atom of that type ...
for jj in range( mults[ii]):
atpos = dot( transpose( cellBasis), posVecs[ii][jj])
if bugLev >= 5:
print " jj: ", jj, " pos: ", posVecs[ii][jj]
print " atpos: ", atpos
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom( atpos[0], atpos[1], atpos[2], usyms[ii])
if bugLev >= 2:
print " crystal/read: icsd_cif_b: structure:\n", structure
prim = primitive( structure)
if bugLev >= 2:
print " crystal/read: icsd_cif_b: primitive structure:\n", prim
return prim
def pmg_to_pyl(pmg : Structure):
from pylada.crystal import Structure as Pyl_Structure
from pylada.crystal import Atom
pyl = Pyl_Structure(np.transpose(pmg.lattice.matrix))
for i in range(len(pmg)):
if pmg.site_properties:
kwargs = {x: pmg.site_properties[x][i] for x in pmg.site_properties}
else:
kwargs = {}
coords = pmg[i].coords
specie = str(pmg[i].specie)
pyl_atom = Atom(coords[0], coords[1], coords[2], specie, **kwargs)
pyl.add_atom(pyl_atom)
return pyl
def test_ediff():
from pickle import loads, dumps
from pylada.crystal import Structure, supercell
from pylada.vasp.incar._params import Ediff, Ediffg
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])\
.add_atom(0, 0, 0, 'Si')\
.add_atom(0.25, 0.25, 0.25, 'Si')
assert Ediff(None).incar_string(structure=structure) is None
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) - 1e-4 * 2.) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) - 1e-4) < 1e-8 and float(a[2]) > 0e0
assert Ediffg(None).incar_string(structure=structure) is None
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) - 1e-4 * 2.) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) + 1e-4) < 1e-8
structure = supercell(structure, [[1, 0, 0], [0, 1, 0], [0, 0, 1]])
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) - 1e-4 * 8.) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) - 1e-4) < 1e-8 and float(a[2]) > 0e0
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) - 1e-4 * 8.) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) + 1e-4) < 1e-8
def test_encut(EncutClass):
from pickle import loads, dumps
from collections import namedtuple
from pylada.crystal import Structure, supercell
from quantities import eV, hartree
Vasp = namedtuple('Vasp', ['species'])
Specie = namedtuple('Specie', ['enmax'])
vasp = Vasp({'Si': Specie(1. * eV), 'Ge': Specie(10.), 'C': Specie(100. * eV)})
name = EncutClass.__name__.upper()
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])\
.add_atom(0, 0, 0, 'Si')\
.add_atom(0.25, 0.25, 0.25, 'Ge')
assert EncutClass(None).incar_string(vasp=vasp, structure=structure) is None
a = loads(dumps(EncutClass(50))).incar_string(vasp=vasp, structure=structure).split()
assert a[0] == name and a[1] == '=' and abs(float(a[2]) - 50) < 1e-8
a = loads(dumps(EncutClass(1.0))).incar_string(vasp=vasp, structure=structure).split()
assert a[0] == name and a[1] == '=' and abs(float(a[2]) - 10.) < 1e-8
structure[0].type = 'C'
a = loads(dumps(EncutClass(2.0))).incar_string(vasp=vasp, structure=structure).split()
assert a[0] == name and a[1] == '=' and abs(float(a[2]) - 2. * 100.) < 1e-8
a = loads(dumps(EncutClass(50. * eV))).incar_string(vasp=vasp, structure=structure).split()
assert a[0] == name and a[1] == '=' and abs(float(a[2]) - 50.) < 1e-8
a = loads(dumps(EncutClass((50. * eV).rescale(hartree)))
).incar_string(vasp=vasp, structure=structure).split()
assert a[0] == name and a[1] == '=' and abs(float(a[2]) - 50.) < 1e-8
assert EncutClass(-50).incar_string(vasp=vasp, structure=structure) is None
assert EncutClass(-50 * eV).incar_string(vasp=vasp, structure=structure) is None
def test_primitive(cell):
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal import supercell, Structure, are_periodic_images as api, primitive, \
is_primitive
lattice = Structure(0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m=True)
structure = supercell(lattice, dot(lattice.cell, cell))
assert not is_primitive(structure)
structure = primitive(structure, 1e-8)
assert is_primitive(structure)
assert abs(structure.volume - lattice.volume) < 1e-8
assert len(structure) == len(lattice)
assert is_integer(dot(structure.cell, inv(lattice.cell)))
assert is_integer(dot(lattice.cell, inv(structure.cell)))
invcell = inv(lattice.cell)
for atom in structure:
assert api(lattice[atom.site].pos, atom.pos, invcell)
assert atom.type == lattice[atom.site].type
assert getattr(lattice[atom.site], 'm',
False) == getattr(atom, 'm', False)
assert (getattr(atom, 'm', False) or atom.site == 0)
def test(path):
from shutil import rmtree
from tempfile import mkdtemp
from pylada.crystal import Structure
from pylada.vasp import Vasp
from epirelax import epitaxial
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
result = epitaxial(vasp, structure, outdir=directory, epiconv=1e-4, comm=default_comm)
assert result.success
finally:
rmtree(directory)
pass
def __init__(self, vasp, dft, gw, outdir="nlep_fit", comm=None, units=None):
from os import makedirs
from os.path import exists
from shutil import rmtree
from boost.mpi import world
from pylada.crystal import Structure
self.gw = gw
self.dft = dft
self.gw.comm = comm
self.dft.comm = comm
# since comm has changed, makes sure there are no issues with caching
self.gw.uncache()
self.dft.uncache()
self.vasp = vasp
self.system = Structure(dft.structure)
self._nbcalls = 0
self.outdir = outdir
self.comm = comm if comm != None else world
self.units = units if units != None else 1e0
self.use_syscall = True
if self.comm.rank == 0 and exists(self.outdir):
rmtree(self.outdir)
makedirs(self.outdir)
self.comm.barrier()
def s28():
""" s28 lattice """
from pylada.crystal import Structure
return Structure( 7.342, -3.671, 0,\
0, 6.35836, 0,\
0, 0, 7.218,\
scale=1, name='s28' )\
.add_atom(1.55419, 2.47041, 1.8045, 'A')\
.add_atom(4.42546, 0.110763, 1.8045, 'A')\
.add_atom(5.03334, 3.77718, 1.8045, 'A')\
.add_atom(1.36234, 2.58118, 5.4135, 'A')\
.add_atom(-2.11681, 3.88795, 5.4135, 'A')\
.add_atom(0.754464, 6.2476, 5.4135, 'A')\
.add_atom(-3.671e-08, 4.23891, 0.241153, 'B')\
.add_atom(-3.671e-08, 4.23891, 3.36785, 'B')\
.add_atom(3.671, 2.11945, 3.85015, 'B')\
.add_atom(3.671, 2.11945, 6.97685, 'B')\
.add_atom(0, 0, 1.8045, 'B')\
.add_atom(0, 0, 5.4135, 'B')\
.add_atom(2.67983, 4.6416, 0, 'X')\
.add_atom(1.98234, 0, 0, 'X')\
.add_atom(-0.99117, 1.71676, 0, 'X')\
.add_atom(2.67983, 4.6416, 3.609, 'X')\
.add_atom(1.98234, 0, 3.609, 'X')\
.add_atom(-0.99117, 1.71676, 3.609, 'X')
def s18():
""" s18 lattice """
from pylada.crystal import Structure
return Structure( 9.296, -4.648, 0,\
0, 8.05057, 0,\
0, 0, 7.346,\
scale=1.1, name='s18' )\
.add_atom(4.648, 5.24897, 4.99528, 'A')\
.add_atom(2.42626, 1.4008, 4.99528, 'A')\
.add_atom(6.86974, 1.4008, 4.99528, 'A')\
.add_atom(0, 2.8016, 1.32228, 'A')\
.add_atom(2.22174, 6.64977, 1.32228, 'A')\
.add_atom(-2.22174, 6.64977, 1.32228, 'A')\
.add_atom(4.64846, 2.68326, 2.29195, 'A')\
.add_atom(-0.0004648, 5.36732, 5.96495, 'A')\
.add_atom(0, 7.76075, 3.673, 'B')\
.add_atom(-2.07301, 4.1702, 3.673, 'B')\
.add_atom(2.07301, 4.1702, 3.673, 'B')\
.add_atom(4.648, 0.289821, 0, 'B')\
.add_atom(6.72101, 3.88038, 0, 'B')\
.add_atom(2.57499, 3.88038, 0, 'B')\
.add_atom(0, 0, 3.673, 'B')\
.add_atom(0, 0, 0, 'B')\
.add_atom(4.648, 5.31338, 1.89527, 'X')\
.add_atom(2.37048, 1.3686, 1.89527, 'X')\
.add_atom(6.92552, 1.3686, 1.89527, 'X')\
.add_atom(0, 2.73719, 5.56827, 'X')\
.add_atom(2.27752, 6.68197, 5.56827, 'X')\
.add_atom(-2.27752, 6.68197, 5.56827, 'X')\
.add_atom(4.64846, 2.68326, 5.28177, 'X')\
.add_atom(-0.0004648, 5.36732, 1.60877, 'X')
def test_b5(u):
""" Test b5 space-group and equivalents """
from numpy import dot
from numpy.random import randint
from pylada.crystal import Structure, which_site
x, y = u, 0.25 - u
lattice = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
assert which_site(lattice[6].pos + [0.5, -0.5, 2], lattice) == 6
for i, atom in enumerate(lattice):
assert which_site(atom.pos, lattice) == i
for j in xrange(10):
newpos = dot(lattice.cell, randint(10, size=(3, )) - 5)
assert which_site(atom.pos + newpos,
lattice) == i, (atom.pos, newpos, i)
def s26():
""" s26 lattice """
from pylada.crystal import Structure
return Structure( 6.997, 0, 3.4985,\
0, 10.83, 5.415,\
0, 0, 3.1435,\
scale=1.1, name='s26' )\
.add_atom(5.24775, 8.65967, 1.86347, 'A')\
.add_atom(8.74625, 13.0003, 1.86347, 'A')\
.add_atom(5.24775, 13.2202, 1.70189, 'A')\
.add_atom(8.74625, 8.43982, 1.70189, 'A')\
.add_atom(8.74625, 5.43774, 2.62671, 'A')\
.add_atom(5.24775, 5.39226, 2.62671, 'A')\
.add_atom(3.70491, 6.75359, 0.75444, 'B')\
.add_atom(3.29209, 4.07641, 0.75444, 'B')\
.add_atom(6.79059, 6.75359, 0.75444, 'B')\
.add_atom(7.20341, 4.07641, 0.75444, 'B')\
.add_atom(3.4985, 10.83, 1.57238, 'B')\
.add_atom(6.997, 10.83, 1.57238, 'B')\
.add_atom(7.03898, 14.431, 3.11395, 'X')\
.add_atom(6.95502, 7.22903, 3.11395, 'X')\
.add_atom(10.4535, 14.431, 3.11395, 'X')\
.add_atom(3.54048, 7.22903, 3.11395, 'X')\
.add_atom(1.74925, 5.689, 0.0345785, 'X')\
.add_atom(5.24775, 5.141, 0.0345785, 'X')
def s13():
""" s13 lattice """
from pylada.crystal import Structure
return Structure( 14.462, 7.231, -2.12564,\
0, 2.785, 0,\
0, 0, 9.23657,\
scale=1.1, name='s13' )\
.add_atom(12.2089, 1.30839, 5.17802, 'A')\
.add_atom(13.5267, 1.30839, 8.67683, 'A')\
.add_atom(7.35851, 1.47661, 4.05855, 'A')\
.add_atom(6.04068, 1.47661, 0.559736, 'A')\
.add_atom(9.78368, 1.3925, 4.61828, 'A')\
.add_atom(3.6155, 1.3925, 0, 'A')\
.add_atom(10.1658, 1.31619, 8.0469, 'B')\
.add_atom(15.5698, 1.31619, 5.80795, 'B')\
.add_atom(9.40159, 1.46881, 1.18967, 'B')\
.add_atom(3.9976, 1.46881, 3.42861, 'B')\
.add_atom(5.63677, 1.22429, 6.92742, 'B')\
.add_atom(13.9306, 1.56071, 2.30914, 'B')\
.add_atom(10.8767, 2.56777, 5.62507, 'X')\
.add_atom(14.8588, 2.56777, 8.22978, 'X')\
.add_atom(8.69066, 0.21723, 3.6115, 'X')\
.add_atom(4.70852, 0.21723, 1.00679, 'X')\
.add_atom(-1.06282, 0, 4.61828, 'X')\
.add_atom(0, 0, 0, 'X')
def s41():
""" s41 lattice """
from pylada.crystal import Structure
return Structure( 5.81, 0, 0,\
0, 5.96, 0,\
0, 0, 11.71,\
scale=1.2, name='s41' )\
.add_atom(5.03146, 1.79992, 0.74944, 'A')\
.add_atom(2.12646, 1.18008, 10.9606, 'A')\
.add_atom(0.77854, 4.77992, 5.10556, 'A')\
.add_atom(3.68354, 4.16008, 6.60444, 'A')\
.add_atom(0.77854, 4.16008, 10.9606, 'A')\
.add_atom(3.68354, 4.77992, 0.74944, 'A')\
.add_atom(5.03146, 1.18008, 6.60444, 'A')\
.add_atom(2.12646, 1.79992, 5.10556, 'A')\
.add_atom(3.59058, 0.298, 3.7472, 'B')\
.add_atom(0.68558, 2.682, 7.9628, 'B')\
.add_atom(2.21942, 3.278, 2.1078, 'B')\
.add_atom(5.12442, 5.662, 9.6022, 'B')\
.add_atom(2.21942, 5.662, 7.9628, 'B')\
.add_atom(5.12442, 3.278, 3.7472, 'B')\
.add_atom(3.59058, 2.682, 9.6022, 'B')\
.add_atom(0.68558, 0.298, 2.1078, 'B')\
.add_atom(2.98634, 1.03108, 1.33494, 'X')\
.add_atom(0.08134, 1.94892, 10.3751, 'X')\
.add_atom(2.82366, 4.01108, 4.52006, 'X')\
.add_atom(5.72866, 4.92892, 7.18994, 'X')\
.add_atom(2.82366, 4.92892, 10.3751, 'X')\
.add_atom(5.72866, 4.01108, 1.33494, 'X')\
.add_atom(2.98634, 1.94892, 7.18994, 'X')\
.add_atom(0.08134, 1.03108, 4.52006, 'X')
def s29():
""" s29 lattice """
from pylada.crystal import Structure
return Structure( 4.308, 0, 0,\
0, 13.912, 0,\
0, 0, 7.431,\
scale=1.1, name='s29' )\
.add_atom(3.231, 8.93276, 6.85658, 'A')\
.add_atom(3.231, 11.9352, 6.85658, 'A')\
.add_atom(1.077, 4.97924, 0.574416, 'A')\
.add_atom(1.077, 1.97676, 0.574416, 'A')\
.add_atom(3.231, 1.32039, 4.32023, 'A')\
.add_atom(3.231, 5.63561, 4.32023, 'A')\
.add_atom(1.077, 12.5916, 3.11077, 'A')\
.add_atom(1.077, 8.27639, 3.11077, 'A')\
.add_atom(3.231, 6.97603, 1.55828, 'B')\
.add_atom(3.231, 13.892, 1.55828, 'B')\
.add_atom(1.077, 6.93597, 5.87272, 'B')\
.add_atom(1.077, 0.0200333, 5.87272, 'B')\
.add_atom(3.231, 3.478, 2.16688, 'B')\
.add_atom(1.077, 10.434, 5.26412, 'B')\
.add_atom(3.231, 10.434, 2.22484, 'B')\
.add_atom(1.077, 3.478, 5.20616, 'B')\
.add_atom(3.231, 8.39728, 4.39321, 'X')\
.add_atom(3.231, 12.4707, 4.39321, 'X')\
.add_atom(1.077, 5.51472, 3.03779, 'X')\
.add_atom(1.077, 1.44128, 3.03779, 'X')\
.add_atom(3.231, 2.18001, 6.76072, 'X')\
.add_atom(3.231, 4.77599, 6.76072, 'X')\
.add_atom(1.077, 11.732, 0.670276, 'X')\
.add_atom(1.077, 9.13601, 0.670276, 'X')
def test(path):
from os import makedirs
from os.path import exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
if directory == '/tmp/test' or directory == '/tmp/test/':
if exists(directory): rmtree(directory)
makedirs(directory)
try:
result = vasp(structure, outdir=directory, comm=default_comm)
assert result.success
finally:
if directory != '/tmp/test' and directory != '/tmp/test/':
rmtree(directory)
def test(tmpdir, path):
from numpy import abs
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.relax import epitaxial
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
result = epitaxial(vasp,
structure,
outdir=str(tmpdir),
epiconv=1e-5,
comm=default_comm)
assert result.success
assert abs(result.stress[2, 2]) < 1.0
def test_nelect():
from os.path import dirname
from pickle import loads, dumps
from pylada.vasp import Vasp
from pylada.crystal import Structure
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
scale=5.43, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
a = Vasp()
a.add_specie = "Si", "{0}/pseudos/Si".format(dirname(__file__))
assert a.extraelectron is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 0
assert a.extraelectron == 0
assert a.nelect is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 1
assert a.extraelectron == 1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(
vasp=a, structure=structure)
assert abs(
float(a._input['extraelectron'].output_map(vasp=a, structure=structure)
['nelect']) - 9.0) < 1e-8
assert a._input['nelect'].output_map() is None
a.nelect = 1
a.extraelectron = -1
assert a.extraelectron == -1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(
vasp=a, structure=structure)
assert abs(
float(a._input['extraelectron'].output_map(vasp=a, structure=structure)
['nelect']) - 7.0) < 1e-8
assert a._input['nelect'].output_map() is None
o = a._input['extraelectron']
d = {'ExtraElectron': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(
float(
eval(repr(o), d).output_map(vasp=a, structure=structure)['nelect'])
- 7.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
a.nelect = 8
assert a.nelect == 8
assert a.extraelectron is None
assert 'nelect' in a._input['nelect'].output_map()
assert abs(float(a._input['nelect'].output_map()['nelect']) - 8.0) < 1e-8
assert a._input['extraelectron'].output_map() is None
o = a._input['nelect']
d = {'NElect': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(float(eval(repr(o), d).output_map()['nelect']) - 8.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
def bcc():
""" Creates a BCC lattice with a single site. """
from pylada.crystal import Structure
return Structure(-0.5, 0.5, 0.5,
0.5, -0.5, 0.5,
0.5, 0.5, -0.5,
scale=1, name='bcc' )\
.add_atom(0, 0, 0, 'A')
def fcc():
""" Creates an FCC lattice with a single site. """
from pylada.crystal import Structure
return Structure( 0, 0.5, 0.5,\
0.5, 0, 0.5,\
0.5, 0.5, 0,\
scale=1, name='fcc' )\
.add_atom(0, 0, 0, 'A')
def test(path):
from shutil import rmtree
from tempfile import mkdtemp
from os.path import join
from quantities import eV
from pylada.vasp import Vasp, read_incar
from pylada.crystal import Structure
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
vasp.write_incar(path=join(directory, 'INCAR'), structure=structure)
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
with open(join(directory, 'INCAR'), 'a') as file:
file.write('\nSOMETHing = 0.5\n')
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
assert 'something' in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
finally:
rmtree(directory)
pass
def rock_salt():
""" rock_salt lattice """
from pylada.crystal import Structure
return Structure(1, 0, 0,
0, 1, 0,
0, 0, 1,
scale=1, name='Rock-Salt' )\
.add_atom(0, 0, 0, 'A')\
.add_atom(0.5, 0.5, 0.5, 'B')
def zinc_blende():
""" zinc_blende lattice """
from pylada.crystal import Structure
return Structure(0, 0.5, 0.5,
0.5, 0, 0.5,
0.5, 0.5, 0,
scale=1, name='Zinc-Blende' )\
.add_atom(0, 0, 0, 'A')\
.add_atom(0.25, 0.25, 0.25, 'B')
def crystal(file='fort.34'):
""" Reads CRYSTAL's external format. """
from numpy import array, abs, zeros, any, dot
from numpy.linalg import inv
from ..crystal import which_site
from ..misc import RelativePath
from ..error import IOError
from ..periodic_table import find as find_specie
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file: return crystal(file)
else: file = file.splitlines().__iter__()
# read first line
try: line = file.next()
except StopIteration: raise IOError('Premature end of stream.')
else: dimensionality, centering, type = [int(u) for u in line.split()[:3]]
# read cell
try: cell = array( [file.next().split()[:3] for i in xrange(3)],
dtype='float64' ).T
except StopIteration: raise IOError('Premature end of stream.')
result = Structure( cell=cell, centering=centering,
dimensionality=dimensionality, type=type, scale=1e0 )
# read symmetry operators
result.spacegroup = []
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: op = array( [file.next().split()[:3] for j in xrange(4)],
dtype='float64' )
except StopIteration: raise IOError('Premature end of stream.')
else: op[:3] = op[:3].copy().T
result.spacegroup.append(op)
result.spacegroup = array(result.spacegroup)
# read atoms.
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: line = file.next().split()
except StopIteration: raise IOError('Premature end of stream.')
else: type, pos = int(line[0]), array(line[1:4], dtype='float64')
if type < 100: type = find_specie(atomic_number=type).symbol
result.add_atom(pos=pos, type=type, asymmetric=True)
# Adds symmetrically equivalent structures.
identity = zeros((4, 3), dtype='float64')
for i in xrange(3): identity[i, i] == 1
symops = [u for u in result.spacegroup if any(abs(u - identity) > 1e-8)]
invcell = inv(result.cell)
for atom in [u for u in result]:
for op in symops:
pos = dot(op[:3], atom.pos) + op[3]
if which_site(pos, result, invcell=invcell) == -1:
result.add_atom(pos=pos, type=atom.type, asymmetric=False)
return result
def s1():
""" s1 lattice """
from pylada.crystal import Structure
return Structure( 0, 3.1, 3.1,\
3.1, 0, 3.1,\
3.1, 3.1, 0,\
scale=1, name='s1' )\
.add_atom(3.1, 3.1, 3.1, 'A')\
.add_atom(0, 0, 0, 'B')\
.add_atom(1.55, 1.55, 1.55, 'X')
def test_lattice_is_primitive():
from pylada.crystal import Structure, is_primitive
lattice = Structure(0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m=True)
assert is_primitive(lattice)
def s17():
""" s17 lattice """
from pylada.crystal import Structure
return Structure( 4.244, -2.122, 0,\
0, 3.67541, 0,\
0, 0, 4.563,\
scale=1, name='s17' )\
.add_atom(0, 0, 0, 'A')\
.add_atom(2.122, 1.22514, 2.2815, 'B')\
.add_atom(-2.122e-08, 2.45027, 2.2815, 'X')
def wurtzite():
""" wurtzite lattice """
from pylada.crystal import Structure
return Structure(0.5, 0.5, 0,
-0.866025, 0.866025, 0,
0, 0, 1,
scale=1, name='Wurtzite' )\
.add_atom(0.5, 0.288675, 0, 'A')\
.add_atom(0.5, -0.288675, 0.5, 'A')\
.add_atom(0.5, 0.288675, 0.25, 'B')\
.add_atom(0.5, -0.288675, 0.75, 'B')
def get_madelungenergy(latt_vec_array, charge, epsilon, cutoff):
""" Function returns leading first order correction term, i.e.,
screened Madelung-like lattice energy of point charge
Reference: M. Leslie and M. J. Gillan, J. Phys. C: Solid State Phys. 18 (1985) 973
Parameters
defect = pylada.vasp.Extract object
charge = charge of point defect. Default 1e0 elementary charge
epsilon = dimensionless relative permittivity, SKW: isotropic average of dielectric constant
cutoff = Ewald cutoff parameter
Returns
Madelung (electrostatic) energy in eV
Note:
1. Units in this function are either handled by the module Quantities, or\
defaults to Angstrom and elementary charges
2. Function is adopted from Haowei Peng's version in pylada.defects modules
"""
ewald_cutoff = cutoff * Ry
cell_scale = 1.0 # SKW: In notebook workflow cell parameters are converted to Cartesians and units of Angstroms
# SKW: Create point charge in pylada.crystal.structure class (used for charge model)
# http://pylada.github.io/pylada/userguide/crystal.html
struc = Structure()
struc.cell = latt_vec_array
struc.scale = cell_scale
struc.add_atom(0., 0., 0., "P", charge=charge)
#Anuj_05/22/18: added "cutoff" in ewald syntax
result = ewald(struc, cutoff=ewald_cutoff).energy / epsilon
return -1 * result.rescale(eV)
def first_order_charge_correction(structure, charge=None, epsilon=1e0, cutoff=20.0, **kwargs):
""" First order charge correction of +1 charge in given supercell.
Units in this function are either handled by the module Quantities, or
defaults to Angstroems and elementary charges.
:Parameters:
structure : `pylada.crystal.Structure`
Defect supercell, with cartesian positions in angstrom.
charge
Charge of the point-defect. Defaults to 1e0 elementary charge. If no
units are attached, expects units of elementary charges.
epsilon
dimensionless relative permittivity.
cutoff
Ewald cutoff parameter.
:return: Electrostatic energy in eV.
"""
from quantities import elementary_charge, eV
from pylada.crystal import Structure
from pylada.physics import Ry
from pylada.ewald import ewald
if charge is None:
charge = 1
elif charge == 0:
return 0e0 * eV
if hasattr(charge, "units"):
charge = float(charge.rescale(elementary_charge))
ewald_cutoff = cutoff * Ry
struc = Structure()
struc.cell = structure.cell
struc.scale = structure.scale
struc.add_atom(0e0, 0, 0, "A", charge=charge)
result = ewald(struc, ewald_cutoff).energy / epsilon
return -result.rescale(eV)
def cut_and_splice(s1, s2, roll=True):
""" Cut-n-splice GSGO crossover operation
Mating operation on two parent structures s1 and s2.
Done on scaled atomic positions (cubic systems) by
cutting them in half and mixing their upper and
lower parts.
"""
from random import choice, random
from numpy import dot, abs
from numpy.linalg import det
from pylada.crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos1 = zip([atom.type for atom in s1],fractional_pos(s1, roll=True))
sc_pos2 = zip([atom.type for atom in s2],fractional_pos(s2, roll=True))
result = Structure(s1.cell, scale=s1.scale)
# choose random positions of split-plane
xsep = 0.5 - (random() * 0.45 + 0.15)
# choose direction of split-plane randomly from cell-vectors.
direction = choice(range(3))
for type, pos in sc_pos1:
if pos[direction] >= xsep: result.add_atom(*dot(result.cell, pos), type=type)
for type, pos in sc_pos2:
if pos[direction] < xsep: result.add_atom(*dot(result.cell, pos), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
###############################
from sys import exit
from shutil import rmtree
from os.path import exists, join
from math import ceil, sqrt
from numpy import dot, array, matrix
from numpy.linalg import norm
from boost.mpi import world
from pylada.vff import Vff
from pylada.crystal import Structure, Lattice, fill_structure
from pylada.escan import read_input
input = read_input("input.py")
structure = Structure()
structure.set_cell = (4, 0, 0.5),\
(0, 1, 0),\
(0, 0, 0.5)
structure = fill_structure(structure.cell)
for i, atom in enumerate(structure.atoms):
atom.type = "Si" if i < len(structure.atoms)/2 else "Ge"
result_str = Structure()
result_str.scale = 5.450000e+00
result_str.set_cell = (4.068890e+00, -4.235770e-18, 5.083297e-01),\
(-1.694308e-17, 1.016103e+00, 2.238072e-18),\
(-2.252168e-03, 8.711913e-18, 5.083297e-01)
result_str.weight = 1.000000e+00
result_str.name = ""
# Structure definition.
from pylada.crystal import Structure
from pylada.crystal.defects import third_order_charge_correction
from quantities import eV
structure = Structure()
structure.name = 'Ga2CdO4: b5'
structure.scale = 1.0
structure.energy = -75.497933000000003
structure.weight = 1.0
structure.set_cell = (-0.0001445, 4.3538020, 4.3537935),\
(4.3538700, -0.0001445, 4.3538615),\
(4.3538020, 4.3537935, -0.0001445)
structure.add_atoms = [(7.61911540668, 7.61923876219, 7.61912846850), 'Cd'],\
[(1.08833559332, 1.08834823781, 1.08832253150), 'Cd'],\
[(4.35372550000, 4.35379350000, 4.35372550000), 'Ga'],\
[(4.35379775000, 2.17685850000, 2.17682450000), 'Ga'],\
[(2.17682450000, 4.35386575000, 2.17682875000), 'Ga'],\
[(2.17682875000, 2.17686275000, 4.35379775000), 'Ga'],\
[(2.32881212361, 2.32884849688, 2.32881647755), 'O'],\
[(2.32887187256, 4.20174404476, 4.20169148188), 'O'],\
[(4.20168277385, 2.32891695560, 4.20168347161), 'O'],\
[(4.20168782554, 4.20174474241, 2.32887622633), 'O'],\
[(6.37863887654, 6.37873414925, 6.37863016865), 'O'],\
[(6.37857477364, 4.50584295539, 4.50575516433), 'O'],\
[(4.50576822615, 6.37867004441, 4.50576752839), 'O'],\
[(4.50576317445, 4.50584225759, 6.37857477367), 'O']
# this is converged to less than 1meV
third = third_order_charge_correction(structure, epsilon=10.0, n=20)
assert abs(third - 0.11708438633232088*eV) < 1e-12
# <http://www.gnu.org/licenses/>.
###############################
from pylada.crystal import Structure
from pylada.pcm import Clj, bond_name
from pylada.physics import a0, Ry
from quantities import angstrom, eV, hartree
clj = Clj()
""" Point charge + r^12 + r^6 model. """
clj.ewald_cutoff = 80 * Ry
clj.charges["A"] = -1.0
clj.charges["B"] = 1.0
structure = Structure()
structure.set_cell = (1,0,0),\
(0,1,0),\
(0,0,1)
structure.scale = 50
structure.add_atom = (0,0,0), "A"
structure.add_atom = (a0.rescale(angstrom)/structure.scale,0,0), "B"
print clj.ewald(structure).energy, hartree.rescale(eV)
from pylada.crystal.A2BX4 import b5
from pylada.crystal import fill_structure
from numpy import array
clj.ewald_cutoff = 20 * Ry
lattice = b5()
def make_surface(structure=None, miller=None, nlayers=5, vacuum=15, acc=5):
"""Returns a slab from the 3D structure
Takes a structure and makes a slab defined by the miller indices
with nlayers number of layers and vacuum defining the size
of the vacuum thickness. Variable acc determines the number of
loops used to get the direct lattice vectors perpendicular
and parallel to miller. For high index surfaces use larger acc value
.. warning: (1) cell is always set such that miller is alogn z-axes
(2) nlayers and vacuum are always along z-axes.
:param structure: LaDa structure
:param miller: 3x1 float64 array
Miller indices defining the slab
:param nlayers: integer
Number of layers in the slab
:param vacuum: real
Vacuum thicness in angstroms
:param acc: integer
number of loops for finding the cell vectors of the slab structure
"""
direct_cell = transpose(structure.cell)
reciprocal_cell = 2 * pi * transpose(inv(direct_cell))
orthogonal = [] # lattice vectors orthogonal to miller
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = array([n1, n2, n3])
if dot(pom, miller) == 0 and dot(pom, pom) != 0:
orthogonal.append(array([n1, n2, n3]))
# chose the shortest parallel and set it to be a3 lattice vector
norm_orthogonal = [sqrt(dot(dot(x, direct_cell), dot(x, direct_cell))) for x in orthogonal]
a1 = orthogonal[norm_orthogonal.index(min(norm_orthogonal))]
# chose the shortest orthogonal to miller and not colinear with a1 and set it as a2
in_plane = []
for x in orthogonal:
if dot(x, x) > 1e-3:
v = cross(dot(x, direct_cell), dot(a1, direct_cell))
v = sqrt(dot(v, v))
if v > 1e-3:
in_plane.append(x)
norm_in_plane = [sqrt(dot(dot(x, direct_cell), dot(x, direct_cell))) for x in in_plane]
a2 = in_plane[norm_in_plane.index(min(norm_in_plane))]
a1 = dot(a1, direct_cell)
a2 = dot(a2, direct_cell)
# new cartesian axes z-along miller, x-along a1, and y-to define the right-hand orientation
e1 = a1 / sqrt(dot(a1, a1))
e2 = a2 - dot(e1, a2) * e1
e2 = e2 / sqrt(dot(e2, e2))
e3 = cross(e1, e2)
# find vectors parallel to miller and set the shortest to be a3
parallel = []
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = dot(array([n1, n2, n3]), direct_cell)
if sqrt(dot(pom, pom)) - dot(e3, pom) < 1e-8 and sqrt(dot(pom, pom)) > 1e-3:
parallel.append(pom)
# if there are no lattice vectors parallel to miller
if len(parallel) == 0:
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = dot(array([n1, n2, n3]), direct_cell)
if dot(e3, pom) > 1e-3:
parallel.append(pom)
parallel = [x for x in parallel if sqrt(
dot(x - dot(e1, x) * e1 - dot(e2, x) * e2, x - dot(e1, x) * e1 - dot(e2, x) * e2)) > 1e-3]
norm_parallel = [sqrt(dot(x, x)) for x in parallel]
assert len(norm_parallel) != 0, "Increase acc, found no lattice vectors parallel to (hkl)"
a3 = parallel[norm_parallel.index(min(norm_parallel))]
# making a structure in the new unit cell - defined by the a1,a2,a3
new_direct_cell = array([a1, a2, a3])
assert abs(det(new_direct_cell)) > 1e-5, "Something is wrong your volume is equal to zero"
# make sure determinant is positive
if det(new_direct_cell) < 0.:
new_direct_cell = array([-a1, a2, a3])
#structure = fill_structure(transpose(new_direct_cell),structure.to_lattice())
structure = supercell(lattice=structure, supercell=transpose(new_direct_cell))
# transformation matrix to new coordinates x' = dot(m,x)
m = array([e1, e2, e3])
# seting output structure
out_structure = Structure()
out_structure.scale = structure.scale
out_structure.cell = transpose(dot(new_direct_cell, transpose(m)))
for atom in structure:
p = dot(m, atom.pos)
out_structure.add_atom(p[0], p[1], p[2], atom.type)
# repaeting to get nlayers and vacuum
repeat_cell = dot(out_structure.cell, array([[1., 0., 0.], [0., 1., 0.], [0., 0., nlayers]]))
out_structure = supercell(lattice=out_structure, supercell=repeat_cell)
# checking whether there are atoms close to the cell faces and putting them back to zero
for i in range(len(out_structure)):
scaled_pos = dot(out_structure[i].pos, inv(transpose(out_structure.cell)))
for j in range(3):
if abs(scaled_pos[j] - 1.) < 1e-5:
scaled_pos[j] = 0.
out_structure[i].pos = dot(scaled_pos, transpose(out_structure.cell))
# adding vaccum to the cell
out_structure.cell = out_structure.cell + \
array([[0., 0., 0.], [0., 0., 0.], [0., 0., float(vacuum) / float(out_structure.scale)]])
# translating atoms so that center of the slab and the center of the cell along z-axes coincide
max_z = max([x.pos[2] for x in out_structure])
min_z = min([x.pos[2] for x in out_structure])
center_atoms = 0.5 * (max_z + min_z)
center_cell = 0.5 * out_structure.cell[2][2]
for i in range(len(out_structure)):
out_structure[i].pos = out_structure[i].pos + array([0., 0., center_cell - center_atoms])
# exporting the final structure
return out_structure
def icsd_cif_a(filename, make_primitive=True):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
from pylada import logger
import re
from copy import deepcopy
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
lines = open(filename, 'r').readlines()
logger.info("crystal/read: icsd_cif_a: %s" % filename)
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
logger.debug("crystal/read: icsd_cif_a: sym_big: %s" % sym_big)
logger.debug("crystal/read: icsd_cif_a: sym_end: %s" % sym_end)
symm_ops = ['(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]]
logger.debug("crystal/read: icsd_cif_a: symm_ops a: %s" % symm_ops)
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
logger.debug("crystal/read: icsd_cif_a: symm_ops b: %s" % symm_ops)
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
logger.debug("crystal/read: icsd_cif_a: pos_big: %s" % pos_big)
logger.debug("crystal/read: icsd_cif_a: pos_end: %s" % pos_end)
wyckoff = [[x.split()[0], [x.split()[4], x.split()[5], x.split()[6]], x.split()[7]]
for x in lines[pos_big + 1:pos_end]]
logger.debug("crystal/read: icsd_cif_a: wyckoff a: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
logger.debug("crystal/read: icsd_cif_a: wyckoff b: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
# Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom == 0:
pom = i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
logger.debug("crystal/read: icsd_cif_a: symbols: %s" % symbols)
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
logger.debug("symbol: %s x: %s y: %s z: %s" % (symbol, x, y, z))
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
logger.debug("i: %s pom a: %s" % (i, pom))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
logger.debug("i: %s pom b: %s" % (i, pom))
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u) - array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
logger.debug("new positions for %s: %s" % (symbol, repr(positions[ix])))
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(gamma * pi / 180.) * (-cos(beta * pi / 180.) *
cos(gamma * pi / 180.) + cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
logger.debug("crystal/read: icsd_cif_a: a1: %s" % a1)
logger.debug("crystal/read: icsd_cif_a: a2: %s" % a2)
logger.debug("crystal/read: icsd_cif_a: a3: %s" % a3)
##########################################
from pylada.crystal import Structure, primitive
logger.debug("crystal/read: icsd_cif_a: cell: %s" % cell)
structure = Structure(
transpose(cell),
scale=1,
name=basename(filename))
for i in range(len(symbols)):
logger.debug("crystal/read: icsd_cif_a: i: %s symbol: %s len(position): %i" % (
i, symbols[i], len(positions[i])
))
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
logger.debug("j: %s pos: %s" % (j, positions[i][j]))
logger.debug("atpos: " % atpos)
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i])
logger.info("crystal/read: icsd_cif_a: structure: %s" % structure)
if make_primitive:
prim = primitive(structure)
else:
prim = deepcopy(structure)
logger.info("crystal/read: icsd_cif_a: primitive structure: %s" % prim)
return prim
def test_istruc():
from collections import namedtuple
from pickle import loads, dumps
from os import remove
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import POSCAR, CONTCAR
from pylada.vasp import Vasp
from pylada.crystal import Structure, read, specieset, write
from pylada.error import ValueError
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
Extract = namedtuple("Extract", ['directory', 'success', 'structure'])
a = Vasp()
o = a._input['istruc']
d = {'IStruc': o.__class__}
directory = mkdtemp()
try:
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
assert exists(join(directory, POSCAR))
remove(join(directory, POSCAR))
# check reading from outcar but only on success.
a.restart = Extract(directory, False, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# check reading from outcar but only on success.
a.restart = Extract(directory, True, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) > 1e-8
assert abs(other[1].pos[0] - 0.27) < 1e-8
# Now check CONTCAR
write.poscar(structure, join(directory, CONTCAR))
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# Check some failure modes.
write.poscar(structure, join(directory, CONTCAR))
structure[0].type = 'Ge'
a.restart = None
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
structure[0].type = 'Si'
structure.add_atom(0.25,0,0, 'Si')
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
finally: rmtree(directory)
vff.lattice.set_types = ("In", "Ga"), ("As",)
vff.lattice.scale = 6.5
vff.add_bond = "In", "As", (2.62332, 21.6739, -112.0, 150.0)
vff.add_bond = "Ga", "As", (2.44795, 32.1530, -105.0, 150.0)
vff.add_angle = "As", "Ga", "As", ("tet", -4.099, 9.3703)
vff.add_angle = "Ga", "As", "Ga", ("tet", -4.099, 9.3703)
vff.add_angle = "In", "As", "In", ("tet", -5.753, 5.7599)
vff.add_angle = "As", "In", "As", ("tet", -5.753, 5.7599)
vff.add_angle = "Ga", "As", "In", (-0.35016, -4.926, 7.5651)
vff.minimizer.verbose = True
vff.minimizer.type = "gsl_bfgs2"
vff.minimizer.itermax = 1
vff.minimizer.tolerance = 1e-5
vff.minimizer.uncertainties = 1e-3
structure = Structure()
# structure.set_cell = (00.0, 0.5, 0.5),\
# (0.50, 0.0, 0.5),\
# (0.50, 0.5, 0.0)
# structure.add_atoms = ((0.00, 0.00, 0.00), "In"),\
# ((0.25, 0.25, 0.25), "As")
structure.set_cell = (10.0, 0.5, 0.5),\
(0.00, 0.0, 0.5),\
(0.00, 0.5, 0.0)
structure.add_atoms = ((0.00, 0.00, 0.00), "Ga"),\
((0.25, 0.25, 0.25), "As"),\
((1.00, 0.00, 0.00), "Ga"),\
((1.25, 0.25, 0.25), "As"),\
((2.00, 0.00, 0.00), "In"),\
((2.25, 0.25, 0.25), "As"),\
((3.00, 0.00, 0.00), "In"),\
def test_ingaas():
from numpy import abs, all, dot, array
from quantities import eV, angstrom
from pylada.crystal import Structure
vff = functional()
structure = Structure( 10.0, 0.5, 0.5,
0.00, 0.0, 0.5,
0.00, 0.5, 0.0, scale=6.5 )\
.add_atom(pos=(0.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(0.25, 0.25, 0.25), type="As") \
.add_atom(pos=(1.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(1.25, 0.25, 0.25), type="As") \
.add_atom(pos=(2.00, 0.00, 0.00), type="In") \
.add_atom(pos=(2.25, 0.25, 0.25), type="As") \
.add_atom(pos=(3.00, 0.00, 0.00), type="In") \
.add_atom(pos=(3.25, 0.25, 0.25), type="As") \
.add_atom(pos=(4.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(4.25, 0.25, 0.25), type="As") \
.add_atom(pos=(5.00, 0.00, 0.00), type="In") \
.add_atom(pos=(5.25, 0.25, 0.25), type="As") \
.add_atom(pos=(6.00, 0.00, 0.00), type="In") \
.add_atom(pos=(6.25, 0.25, 0.25), type="As") \
.add_atom(pos=(7.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(7.25, 0.25, 0.25), type="As") \
.add_atom(pos=(8.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(8.25, 0.25, 0.25), type="As") \
.add_atom(pos=(9.00, 0.00, 0.00), type="Ga") \
.add_atom(pos=(9.25, 0.25, 0.25), type="As")
epsilon = array([[1e0, 0.1, 0], [0.1, 1e0, 0], [0, 0, 1e0]])
structure.cell = dot(epsilon, structure.cell)
for atom in structure: atom.pos = dot(epsilon, atom.pos)
out = vff._pyeval(structure)
assert abs(out.energy - 12.7962141476*eV) < 1e-8
assert abs(vff.energy(structure) - 12.7962141476*eV) < 1e-8
stress = array([[ 0.07050804, 0.04862879, 0.00025269],
[ 0.04862879, 0.07050804, -0.00025269],
[ 0.00025269, -0.00025269, 0.06073765]]) * eV/angstrom**3
assert all(abs(out.stress - stress) < 1e-6)
assert all(abs(vff.jacobian(structure)[0] - stress) < 1e-6)
gradients = array([u.gradient for u in out])
check_gradients = array( [[ 9.15933995e-16, -5.96744876e-15, 1.12373933e+00],
[ 2.22044605e-16, -9.43689571e-15, -1.12373933e+00],
[ 6.19921859e-02, -6.19921859e-02, 1.00514227e+00],
[ -5.99520433e-15, 2.19269047e-15, -1.12373933e+00],
[ 7.66544525e-02, -7.66544525e-02, 1.02138259e+00],
[ 3.82409256e-01, -3.82409256e-01, -1.65478066e+00],
[ -1.89756333e-02, 1.89756333e-02, 1.15847492e+00],
[ -4.16333634e-17, 8.81239526e-16, -1.09205526e+00],
[ -7.54665596e-02, 7.54665596e-02, 1.14107325e+00],
[ -3.64621516e-01, 3.64621516e-01, -5.74094841e-01],
[ 7.66544525e-02, -7.66544525e-02, 1.02138259e+00],
[ 3.82409256e-01, -3.82409256e-01, -1.65478066e+00],
[ -1.89756333e-02, 1.89756333e-02, 1.15847492e+00],
[ -1.19973476e-14, -2.32591724e-14, -1.09205526e+00],
[ -1.37458746e-01, 1.37458746e-01, 1.25967031e+00],
[ -3.64621516e-01, 3.64621516e-01, -5.74094841e-01],
[ -7.77156117e-16, -3.10862447e-15, 1.12373933e+00],
[ 8.29891711e-15, 0.00000000e+00, -1.12373933e+00],
[ 3.33066907e-15, 7.16093851e-15, 1.12373933e+00],
[ -4.44089210e-16, 7.85482790e-15, -1.12373933e+00]])
assert all(abs(gradients - check_gradients) < 1e-8)
assert all(abs(vff.jacobian(structure)[1].magnitude - check_gradients) < 1e-8)
def castep(file):
""" Tries to read a castep structure file. """
from numpy import array, dot
from ..periodic_table import find as find_specie
from ..error import IOError, NotImplementedError, input as InputError
from ..misc import RelativePath
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file: return castep(file)
else: file = file.splitlines()
file = [l for l in file]
def parse_input(input):
""" Retrieves blocks from CASTEP input file. """
current_block = None
result = {}
for line in file:
if '#' in line: line = line[:line.find('#')]
if current_block is not None:
if line.split()[0].lower() == '%endblock':
current_block = None
continue
result[current_block] += line
elif len(line.split()) == 0: continue
elif len(line.split()[0]) == 0: continue
elif line.split()[0].lower() == '%block':
name = line.split()[1].lower().replace('.', '').replace('_', '')
if name in result:
raise InputError('Found two {0} blocks in input.'.format(name))
result[name] = ""
current_block = name
else:
name = line.split()[0].lower().replace('.', '').replace('_', '')
if name[-1] in ['=' or ':']: name = name[:-1]
if name in result:
raise InputError('Found two {0} tags in input.'.format(name))
data = line.split()[1:]
if len(data) == 0: result[name] = None; continue
if data[0] in [':', '=']: data = data[1:]
result[name] = ' '.join(data)
return result
def parse_units(line):
from quantities import a0, meter, centimeter, millimeter, angstrom, emass, \
amu, second, millisecond, microsecond, nanosecond, \
picosecond, femtosecond, elementary_charge, coulomb,\
hartree, eV, meV, Ry, joule, cal, erg, hertz, \
megahertz, gigahertz, tera, kelvin, newton, dyne, \
h_bar, UnitQuantity, pascal, megapascal, gigapascal,\
bar, atm, milli, mol
auv = UnitQuantity('auv', a0*Ry/h_bar) # velocity
units = { 'a0': a0, 'bohr': a0, 'm': meter, 'cm': centimeter,
'mm': millimeter, 'ang': angstrom, 'me': emass, 'amu': amu,
's': second, 'ms': millisecond, 'mus': microsecond,
'ns': nanosecond, 'ps': picosecond, 'fs': femtosecond,
'e': elementary_charge, 'c': coulomb, 'hartree': hartree,
'ha': hartree, 'mha': 1e-3*hartree, 'ev': eV, 'mev': meV,
'ry': Ry, 'mry': 1e-3*Ry, 'kj': 1e3*joule, 'mol': mol,
'kcal': 1e3*cal, 'j': joule, 'erg': erg, 'hz': hertz,
'mhz': megahertz, 'ghz': gigahertz, 'thz': tera*hertz,
'k': kelvin, 'n': newton, 'dyne': dyne, 'auv': auv, 'pa': pascal,
'mpa': megapascal, 'gpa': gigapascal, 'atm': atm, 'bar': bar,
'atm': atm, 'mbar': milli*bar }
line = line.replace('cm-1', '1/cm')
return eval(line, units)
input = parse_input(file)
if 'latticecart' in input:
data = input['latticecart'].splitlines()
if len(data) == 4:
units = parse_units(data[0])
data = data[1:]
else: units = 1
cell = array([l.split() for l in data], dtype='float64')
elif 'latticeabc' in input:
raise NotImplementedError('Cannot read lattice in ABC format yet.')
else:
raise InputError('Could not find lattice block in input.')
# create structure
result = Structure(cell, scale=units)
# now look for position block.
units = None
if 'positionsfrac' in input:
posdata, isfrac = input['positionsfrac'].splitlines(), True
elif 'positionsabs' in input:
posdata, isfrac = input['positionsabs'].splitlines(), False
try: units = parse_units(posdata[0])
except: units = None
else: posdata = posdata[1:]
else: raise InputError('Could not find position block in input.')
# and parse it
for line in posdata:
line = line.split()
if len(line) < 2:
raise IOError( 'Wrong file format: line with less ' \
'than two items in positions block.')
pos = array(line[1:4], dtype='float64')
if isfrac: pos = dot(result.cell, pos)
try: dummy = int(line[0])
except: type = line[0]
else: type = find_specie(atomic_number=dummy).symbol
result.add_atom(pos=pos, type=type)
if len(line) == 5: result[-1].magmom = float(line[4])
return result
def poscar(path="POSCAR", types=None):
""" Tries to read a VASP POSCAR file.
:param path: Path to the POSCAR file. Can also be an object with
file-like behavior.
:type path: str or file object
:param types: Species in the POSCAR.
:type types: None or sequence of str
:return: `pylada.crystal.Structure` instance.
"""
import re
from os.path import join, exists, isdir
from copy import deepcopy
from numpy import array, dot, transpose
from numpy.linalg import det
from quantities import angstrom
from . import Structure
# if types is not none, converts to a list of strings.
if types is not None:
if isinstance(types, str): types = [types] # can't see another way of doing this...
elif not hasattr(types, "__iter__"): types = [str(types)] # single lone vasp.specie.Specie
else: types = [str(s) for s in types]
if path is None: path = "POSCAR"
if not hasattr(path, 'read'):
assert exists(path), IOError("Could not find path %s." % (path))
if isdir(path):
assert exists(join(path, "POSCAR")), IOError("Could not find POSCAR in %s." % (path))
path = join(path, "POSCAR")
result = Structure()
poscar = path if hasattr(path, "read") else open(path, 'r')
try:
# gets name of structure
result.name = poscar.readline().strip()
if len(result.name) > 0:
if result.name[0] == "#": result.name = result.name[1:].strip()
# reads scale
scale = float(poscar.readline().split()[0])
# gets cell vectors.
cell = []
for i in range(3):
line = poscar.readline()
assert len(line.split()) >= 3,\
RuntimeError("Could not read column vector from poscar: %s." % (line))
cell.append( [float(f) for f in line.split()[:3]] )
result.cell = transpose(array(cell))
vol = det(cell)
if scale < 1.E-8 : scale = abs(scale/vol) **(1.0/3)
result.scale = scale * angstrom
# checks for vasp 5 input.
is_vasp_5 = True
line = poscar.readline().split()
for i in line:
if not re.match(r"[A-Z][a-z]?", i):
is_vasp_5 = False
break
if is_vasp_5:
text_types = deepcopy(line)
if types is not None and not set(text_types).issubset(set(types)):
raise RuntimeError( "Unknown species in poscar: {0} not in {1}."\
.format(text_types, types) )
types = text_types
line = poscar.readline().split()
assert types is not None, RuntimeError("No atomic species given in POSCAR or input.")
# checks/reads for number of each specie
assert len(types) >= len(line), RuntimeError("Too many atomic species in POSCAR.")
nb_atoms = [int(u) for u in line]
# Check whether selective dynamics, cartesian, or direct.
first_char = poscar.readline().strip().lower()[0]
selective_dynamics = False
if first_char == 's':
selective_dynamics = True
first_char = poscar.readline().strip().lower()[0]
# Checks whether cartesian or direct.
is_direct = first_char not in ['c', 'k']
# reads atoms.
for n, specie in zip(nb_atoms, types):
for i in range(n):
line = poscar.readline().split()
pos = array([float(u) for u in line[:3]], dtype="float64")
if is_direct: pos = dot(result.cell, pos)
result.add_atom(pos=pos, type=specie)
if selective_dynamics:
for which, freeze in zip(line[3:], ['x', 'y', 'z']):
if which.lower()[0] == 't':
result[-1].freeze = getattr(result[-1], 'freeze', '') + freeze
finally: poscar.close()
return result
def icsd_cif_a( filename):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
import re
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
from pylada.misc import bugLev
lines = open(filename,'r').readlines()
if bugLev >= 2:
print " crystal/read: icsd_cif_a: filename: ", filename
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x)>0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x)>0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x)>0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
#if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
if bugLev >= 5:
print " crystal/read: icsd_cif_a: sym_big: ", sym_big
print " crystal/read: icsd_cif_a: sym_end: ", sym_end
symm_ops = [ '(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'\
for x in lines[sym_big+1:sym_end-1] ]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symm_ops a: ", symm_ops
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symm_ops b: ", symm_ops
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
if bugLev >= 5:
print " crystal/read: icsd_cif_a: pos_big: ", pos_big
print " crystal/read: icsd_cif_a: pos_end: ", pos_end
wyckoff = [ [x.split()[0],[x.split()[4],x.split()[5],x.split()[6]],x.split()[7]]\
for x in lines[pos_big+1:pos_end] ]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: wyckoff a: ", wyckoff
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4])+0.5) != 0]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: wyckoff b: ", wyckoff
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
############## Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom ==0: pom=i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list(set([w[0] for w in wyckoff]))
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symbols: ", symbols
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x,y,z = w[1][0],w[1][1],w[1][2]
if bugLev >= 5:
print " symbol: ", symbol, " x: ", x, " y: ", y, " z: ", z
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
if bugLev >= 5:
print " i: ", i, " pom a: ", pom
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.: pom[j] = pom[j]+1.
if pom[j] >= 0.999: pom[j] = pom[j]-1.
if bugLev >= 5:
print " i: ", i, " pom b: ", pom
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u)-array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
if bugLev >= 5:
print " new positions for ", symbol, ": ", positions[ix]
################ CELL ####################
a1 = a*array([1.,0.,0.])
a2 = b*array([cos(gamma*pi/180.),sin(gamma*pi/180.),0.])
c1 = c*cos(beta*pi/180.)
c2 = c/sin(gamma*pi/180.)*(-cos(beta*pi/180.)*cos(gamma*pi/180.) + cos(alpha*pi/180.))
a3 = array([c1, c2, sqrt(c**2-(c1**2+c2**2))])
cell = array([a1,a2,a3])
if bugLev >= 2:
print " crystal/read: icsd_cif_a: a1: ", a1
print " crystal/read: icsd_cif_a: a2: ", a2
print " crystal/read: icsd_cif_a: a3: ", a3
# a1: [ 3.15 0. 0. ]
# a2: [-1.575 2.72798002 0. ]
# a3: [ 7.53157781e-16 1.30450754e-15 1.23000000e+01]
##########################################
from pylada.crystal import Structure, primitive
if bugLev >= 2:
print " crystal/read: icsd_cif_a: cell: ", cell
# [[ 3.15000000e+00 0.00000000e+00 0.00000000e+00]
# [ -1.57500000e+00 2.72798002e+00 0.00000000e+00]
# [ 7.53157781e-16 1.30450754e-15 1.23000000e+01]]
structure = Structure(
transpose( cell),
scale = 1,
name = basename( filename))
for i in range(len(symbols)):
if bugLev >= 5:
print " crystal/read: icsd_cif_a: i: ", i, \
" symbol: ", symbols[i], \
" len position: ", len(positions[i])
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot( transpose(cell), positions[i][j])
if bugLev >= 5:
print " j: ", j, " pos: ", positions[i][j]
print " atpos: ", atpos
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom( atpos[0], atpos[1], atpos[2], symbols[i])
if bugLev >= 2:
print " crystal/read: icsd_cif_a: structure:\n", structure
prim = primitive( structure)
if bugLev >= 2:
print " crystal/read: icsd_cif_a: primitive structure:\n", prim
return prim
