def setUp(self):
basis = Basis((1,1,1,0,0,-0.5), kind = 'triclinic')
kp_gamma = numpy.array((0,0,0))[numpy.newaxis,:]
kp_m = numpy.array((0.5, 0.0, 0))[numpy.newaxis,:]
kp_k = numpy.array((2./3, 1./3, 0))[numpy.newaxis,:]
kp_path = numpy.linspace(0,1,30)[:,numpy.newaxis]
kp_path = numpy.concatenate((
kp_gamma*(1-kp_path) + kp_m*kp_path,
kp_m*(1-kp_path) + kp_k*kp_path,
kp_k*(1-kp_path) + kp_gamma*kp_path,
), axis = 0)
d = (basis.transform_to_cartesian(kp_path)**2).sum(axis = 1)
self.bands = UnitCell(
basis,
kp_path,
([[0,0,3]] + d[...,numpy.newaxis]*[[1,2,-3]])*eV,
)
self.bands.meta["Fermi"] = 1*eV
self.weights = self.bands.values/self.bands.values.max()
self.huge_bands = UnitCell(
self.bands,
kp_path,
([BandPlotTest.__pseudo_random__(0,1000,50)*10-5] + d[...,numpy.newaxis]*[BandPlotTest.__pseudo_random__(1000,2000,50)*20-10])*eV,
)
def setUp(self):
basis = Basis((1,1,1,0,0,-0.5), kind = 'triclinic', meta = {"Fermi": 0})
kp_gamma = numpy.array((0,0,0))[numpy.newaxis,:]
kp_m = numpy.array((0.5, 0.0, 0))[numpy.newaxis,:]
kp_k = numpy.array((2./3, 1./3, 0))[numpy.newaxis,:]
kp_path = numpy.linspace(0,1,30)[:,numpy.newaxis]
kp_path = numpy.concatenate((
kp_gamma*(1-kp_path) + kp_m*kp_path,
kp_m*(1-kp_path) + kp_k*kp_path,
kp_k*(1-kp_path) + kp_gamma*kp_path,
), axis = 0)
k = basis.transform_to_cartesian(kp_path)*math.pi/3.**.5*2
e = (1+4*numpy.cos(k[...,1])**2 + 4*numpy.cos(k[...,1])*numpy.cos(k[...,0]*3.**.5))**.5
self.cell = UnitCell(
basis,
kp_path,
e[:,numpy.newaxis]*eV*[[-1.,1.]],
)
self.cell_weights = self.cell.values/self.cell.values.max()
self.grid = Grid(
basis,
(numpy.linspace(0,1,30, endpoint = False)+1./60,numpy.linspace(0,1,30, endpoint = False)+1./60,(0,)),
numpy.zeros((30,30,1,2), dtype = numpy.float64),
)
k = self.grid.cartesian()*math.pi/3.**.5*2
e = (1+4*numpy.cos(k[...,1])**2 + 4*numpy.cos(k[...,1])*numpy.cos(k[...,0]*3.**.5))**.5*eV
self.grid.values[...,0] = -e
self.grid.values[...,1] = e
def test_bands(self):
c = Basis(
numpy.array(((1.000000, -0.577350, 0.000000),
(0.000000, 1.154701, 0.000000),
(0.000000, 0.000000, 0.158745))) * 2 * math.pi /
5.999694 / numericalunits.aBohr)
c = self.parser.bands(c)
assert_standard_bands_path(c)
assert c.values.shape == (400, 34)
assert c.coordinates.shape == (400, 3)
testing.assert_allclose(c.coordinates[0, :],
(0.500000, -0.288675, 0.000000))
testing.assert_allclose(
c.values[0, :],
numpy.array(
(0.500, -0.500, 0.185, -0.185, 0.248, -0.248, 0.067, -0.067,
-0.498, 0.498, -0.498, 0.498, -0.500, 0.500, -0.499, 0.499,
0.500, -0.500, 0.499, -0.499, -0.498, 0.498, -0.498, 0.498,
0.499, -0.499, 0.499, -0.499, 0.496, -0.496, 0.496, -0.496,
0.499, -0.499)) * numericalunits.eV)
testing.assert_allclose(c.coordinates[-1, :],
(-0.503333, -0.282902, 0.000000))
testing.assert_allclose(
c.values[-1, :],
numpy.array(
(0.500, -0.500, 0.185, -0.185, -0.250, 0.247, -0.065, 0.069,
0.497, -0.498, 0.498, -0.497, -0.500, 0.500, 0.499, -0.499,
0.500, -0.500, -0.499, 0.499, -0.498, 0.498, -0.497, 0.498,
0.499, -0.499, 0.499, -0.499, -0.496, 0.496, 0.496, -0.496,
-0.499, 0.499)) * numericalunits.eV)
def setUp(self):
self.cell = Cell(
Basis.triclinic((2.5 * angstrom, 2.5 * angstrom, 10 * angstrom),
(0, 0, .5)),
(
(1. / 3, 1. / 3, .5),
(2. / 3, 2. / 3, .5),
),
['C'] * 2,
).repeated(2, 2, 2)
self.cell2 = Cell(
Basis.triclinic(
(3.9 * angstrom / 2, 3.9 * angstrom / 2, 3.9 * angstrom / 2),
(.5, .5, .5)),
(0, 0, 0),
['Si'],
)
def setUp(self):
self.cell = Cell(
Basis((3.19 * angstrom, 3.19 * angstrom, 10 * angstrom, 0, 0, .5),
kind='triclinic'),
(
(1. / 3, 1. / 3, .5),
(2. / 3, 2. / 3, .6),
(2. / 3, 2. / 3, .4),
),
('Mo', 'S', 'S'),
).repeated(10, 10)
def test_wan90_input(self):
_g = (2, 3, 2)
self.maxDiff = None
grid = uniform_grid(_g).reshape(-1, 3)
cell = Cell(Basis.orthorhombic((2.5 * angstrom, 2.5 * angstrom, 10 * angstrom)),
(
(1. / 3, 1. / 3, .5),
(2. / 3, 2. / 3, .5),
),
['C'] * 2,
)
self.assertEqual(wannier90_input(
cell=cell,
kpts=grid,
kp_grid=_g,
parameters={"some_str": "abc", "some_int": 3, "some_float": 3.0, "some_bool": True},
block_parameters={"some_block": "some_block"},
), "\n".join((
"mp_grid = 2 3 2",
"some_bool = .true.",
"some_float = 3.000000e+00",
"some_int = 3",
"some_str = abc",
"begin atoms_frac",
" C 0.3333333333 0.3333333333 0.5000000000",
" C 0.6666666667 0.6666666667 0.5000000000",
"end atoms_frac",
"begin kpoints",
" 0.0000000000 0.0000000000 0.0000000000",
" 0.0000000000 0.0000000000 0.5000000000",
" 0.0000000000 0.3333333333 0.0000000000",
" 0.0000000000 0.3333333333 0.5000000000",
" 0.0000000000 0.6666666667 0.0000000000",
" 0.0000000000 0.6666666667 0.5000000000",
" 0.5000000000 0.0000000000 0.0000000000",
" 0.5000000000 0.0000000000 0.5000000000",
" 0.5000000000 0.3333333333 0.0000000000",
" 0.5000000000 0.3333333333 0.5000000000",
" 0.5000000000 0.6666666667 0.0000000000",
" 0.5000000000 0.6666666667 0.5000000000",
"end kpoints",
"begin some_block",
" some_block",
"end some_block",
"begin unit_cell_cart",
" 2.5000000000 0.0000000000 0.0000000000",
" 0.0000000000 2.5000000000 0.0000000000",
" 0.0000000000 0.0000000000 10.0000000000",
"end unit_cell_cart",
)))
def setUp(self):
self.cell = Cell(
Basis.triclinic((2.5 * angstrom, 2.5 * angstrom, 10 * angstrom), (0, 0, .5)),
(
(1. / 3, 1. / 3, .5),
(2. / 3, 2. / 3, .5),
),
['C'] * 2,
)
coords = (numpy.linspace(0, 1, 11, endpoint=False), numpy.linspace(0, 1, 13, endpoint=False),
numpy.linspace(0, 1, 17, endpoint=False))
self.grid = Grid(
self.cell,
coords,
numpy.zeros((11, 13, 17)),
)
self.grid = self.grid.copy(values=numpy.prod(numpy.sin(self.grid.explicit_coordinates * 2 * numpy.pi), axis=-1))
def test_qe_input(self):
cell = Cell(Basis.orthorhombic((2.5 * angstrom, 2.5 * angstrom, 10 * angstrom)),
(
(1. / 3, 1. / 3, .5),
(2. / 3, 2. / 3, .5),
),
['C'] * 2,
)
self.assertEqual(qe_input(
cell=cell,
relax_mask=3,
parameters={"system": {"a": 3}, "control": {"b": "c"}, "random": {"d": True}},
inline_parameters={"random": "hello"},
pseudopotentials={"C": "C.UPF"},
masses={"C": 3},
), "\n".join((
"&CONTROL",
" b = 'c'",
"/",
"&SYSTEM",
" a = 3",
" ibrav = 0",
" nat = 2",
" ntyp = 1",
"/",
"ATOMIC_SPECIES",
" C 3.000 C.UPF",
"ATOMIC_POSITIONS crystal",
" C 0.33333333333333 0.33333333333333 0.50000000000000 3 3 3",
" C 0.66666666666667 0.66666666666667 0.50000000000000 3 3 3",
"CELL_PARAMETERS angstrom",
" 2.50000000000000e+00 0.00000000000000e+00 0.00000000000000e+00",
" 0.00000000000000e+00 2.50000000000000e+00 0.00000000000000e+00",
" 0.00000000000000e+00 0.00000000000000e+00 1.00000000000000e+01",
"RANDOM hello",
" d = .true.",
)))
self.assertEqual(qe_input(
cell=cell,
relax_mask=(0, 1),
pseudopotentials={"C": "C.UPF"},
), "\n".join((
"&SYSTEM",
" ibrav = 0",
" nat = 2",
" ntyp = 1",
"/",
"ATOMIC_SPECIES",
" C 12.011 C.UPF",
"ATOMIC_POSITIONS crystal",
" C 0.33333333333333 0.33333333333333 0.50000000000000 0 0 0",
" C 0.66666666666667 0.66666666666667 0.50000000000000 1 1 1",
"CELL_PARAMETERS angstrom",
" 2.50000000000000e+00 0.00000000000000e+00 0.00000000000000e+00",
" 0.00000000000000e+00 2.50000000000000e+00 0.00000000000000e+00",
" 0.00000000000000e+00 0.00000000000000e+00 1.00000000000000e+01",
)))
self.assertEqual(qe_input(
parameters=dict(
inputpp=dict(plot_num=3, prefix="tmd"),
plot=dict(fileout='something.xsf', iflag=3),
)
), "\n".join((
"&INPUTPP",
" plot_num = 3",
" prefix = 'tmd'",
"/",
"&PLOT",
" fileout = 'something.xsf'",
" iflag = 3",
"/",
)))
from dfttools.types import Basis, Cell
from dfttools.presentation import svgwrite_unit_cell
from numericalunits import angstrom as a
mos2_basis = Basis(
(3.19*a, 3.19*a, 20*a, 0,0,.5),
kind = 'triclinic'
)
d = 1.57722483162840/20
# Unit cell with 3 atoms
mos2_cell = Cell(mos2_basis, (
(1./3,1./3,.5),
(2./3,2./3,0.5+d),
(2./3,2./3,0.5-d),
), ('Mo','S','S'))
# Rectangular supercell with 6 atoms
mos2_rectangular = mos2_cell.supercell(
(1,0,0),
(-1,2,0),
(0,0,1)
)
# Rectangular sheet with a defect
mos2_defect = mos2_rectangular.normalized()
mos2_defect.discard((mos2_defect.values == "S") * (mos2_defect.coordinates[:,1] < .5) * (mos2_defect.coordinates[:,2] < .5))
# Prepare a sheet
mos2_sheet = Cell.stack(*((mos2_rectangular,)*3 + (mos2_defect,) + (mos2_rectangular,)*3), vector = 'y')
from dfttools.types import Basis, Cell
from dfttools.presentation import svgwrite_unit_cell
from numericalunits import angstrom as a
si_basis = Basis((3.9 * a / 2, 3.9 * a / 2, 3.9 * a / 2, .5, .5, .5),
kind='triclinic')
si_cell = Cell(si_basis, (.5, .5, .5), 'Si')
svgwrite_unit_cell(si_cell, 'output.svg', size=(440, 360), show_cell=True)
from dfttools.types import Basis, Cell
from dfttools import presentation
from matplotlib import pyplot
from numericalunits import eV
import numpy
# A reciprocal basis
basis = Basis((1, 1, 1, 0, 0, -0.5), kind='triclinic', meta={"Fermi": 0})
# G-K path
kp = numpy.linspace(0, 1, 100)[:, numpy.newaxis] * numpy.array(
((1. / 3, 2. / 3, 0), ))
# A dummy grid Cell with correct kp-path
bands = Cell(
basis,
kp,
numpy.zeros((100, 2), dtype=numpy.float64),
)
# Calculate graphene band
k = bands.cartesian() * numpy.pi / 3.**.5 * 2
e = (1 + 4 * numpy.cos(k[..., 1])**2 +
4 * numpy.cos(k[..., 1]) * numpy.cos(k[..., 0] * 3.**.5))**.5 * eV
# Set the band values
bands.values[..., 0] = -e
bands.values[..., 1] = e
# Assign some weights
from dfttools.types import Basis, Cell
from dfttools.presentation import svgwrite_unit_cell
from numericalunits import angstrom as a
graphene_basis = Basis(
(2.46*a, 2.46*a, 6.7*a, 0,0,.5),
kind = 'triclinic'
)
# Unit cell
graphene_cell = Cell(graphene_basis, (
(1./3,1./3,.5),
(2./3,2./3,.5),
), ('C','C'))
# Moire matching vectors
moire = [1, 26, 6, 23]
# A top layer
l1 = graphene_cell.supercell(
(moire[0],moire[1],0),
(-moire[1],moire[0]+moire[1],0),
(0,0,1)
)
# A bottom layer
l2 = graphene_cell.supercell(
(moire[2],moire[3],0),
(-moire[3],moire[2]+moire[3],0),
(0,0,1)
from dfttools.types import Basis, Grid
from dfttools import presentation
from numericalunits import angstrom
from matplotlib import pyplot
import numpy
grid = Grid(
Basis((1 * angstrom, 1 * angstrom, 1 * angstrom, 0, 0, -0.5),
kind='triclinic'),
(
numpy.linspace(0, 1, 30, endpoint=False),
numpy.linspace(0, 1, 30, endpoint=False),
numpy.linspace(0, 1, 30, endpoint=False),
),
numpy.zeros((30, 30, 30)),
)
grid.values = numpy.prod(numpy.sin(grid.explicit_coordinates() * 2 * numpy.pi),
axis=-1)
presentation.matplotlib_scalar(grid,
pyplot.gca(), (0.1, 0.1, 0.1),
'z',
show_cell=True)
pyplot.show()