def test():
from tempfile import mkdtemp
from shutil import rmtree
from os.path import join
from numpy import mean, abs, sum
from pylada.dftcrystal import Crystal, Functional, Shell
from pylada.dftcrystal.properties.emass import effective_mass
from pylada import default_comm
functional = Functional()
functional.basis["Si"] = [
Shell(
"s",
a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325],
),
Shell(
"sp",
a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496],
),
Shell("sp", 4.0, a0=[1.22, 1.0, 1.0]),
Shell("sp", 0.0, a0=[0.55, 1.0, 1.0]),
Shell("sp", 0.0, a0=[0.27, 1.0, 1.0]),
]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.dft.spin = False
functional.toldee = 12
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, "Si")
directory = "/tmp/test/" # mkdtemp()
firstdir, seconddir = join(directory, "0"), join(directory, "1")
try:
emass = effective_mass(
functional, crystal, range=0.05, polarpoints=20, nbpoints=10, outdir=directory, comm=default_comm
)
assert emass.success
print emass.bandstructure.kpoints.shape, emass.bandstructure.eigenvalues.shape
print emass.success
print emass.tensors([0, 1, 2])[2][11:15]
# print emass.kpoints
# kpoints = emass.bandstructure.kpoints
# ball = abs(sum(kpoints*kpoints, axis=1)-1e0) < 1e-8
# print kpoints[ball]
# print mean(kpoints[ball], axis=0)
finally:
if directory != "/tmp/test/":
rmtree(directory)
def test():
from tempfile import mkdtemp
from shutil import rmtree
from os.path import join, exists
from os import mkdir
from pylada.dftcrystal import Crystal, Functional, Shell
from pylada.dftcrystal.properties import Properties
from pylada import default_comm
functional = Functional()
functional.basis['Si'] = [
Shell('s', a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325]),
Shell('sp', a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496]),
Shell('sp', 4.0, a0=[1.22, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.55, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.27, 1.0, 1.0]) ]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.dft.spin = True
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
directory = mkdtemp()
if directory == '/tmp/test/':
rmtree(directory)
mkdir(directory)
firstdir, seconddir = join(directory, '0'), join(directory, '1')
try:
si = functional(crystal, outdir=firstdir, comm=default_comm)
assert exists(join(firstdir, 'crystal.f9'))
assert not exists(join(directory, 'crystal.f98'))
properties = Properties(si)
properties.rdfmwf = True
result = properties(outdir=directory, workdir=join(directory, 'try0'))
assert result.success
assert exists(join(directory, 'crystal.f9'))
assert not exists(join(directory, 'crystal.f98'))
properties = Properties(directory)
properties.fmwf = True
result = properties(outdir=directory, workdir=join(directory, 'try1'))
assert not exists(join(directory, 'crystal.f98'))
result = properties(outdir=directory, workdir=join(directory, 'try1'), overwrite=True)
assert result.success
assert exists(join(directory, 'crystal.f98'))
finally:
if directory != '/tmp/test/': rmtree(directory)
def test():
from tempfile import mkdtemp
from shutil import rmtree
from pylada.dftcrystal import Crystal, Functional, Shell
from pylada import default_comm
functional = Functional()
functional.basis["Si"] = [
Shell(
"s",
a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325],
),
Shell(
"sp",
a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496],
),
Shell("sp", 4.0, a0=[1.22, 1.0, 1.0]),
Shell("sp", 0.0, a0=[0.55, 1.0, 1.0]),
Shell("sp", 0.0, a0=[0.27, 1.0, 1.0]),
]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, "Si")
directory = mkdtemp()
try:
results = functional(crystal, outdir=directory, comm=default_comm)
assert results.success
finally:
if directory != "/tmp/test/":
rmtree(directory)
pass
def test():
from tempfile import mkdtemp
from shutil import rmtree
from os.path import join
from numpy import all, array
from quantities import hartree
from pylada.dftcrystal import Crystal, Functional, Shell
from pylada.dftcrystal.properties import Properties
from pylada import default_comm
functional = Functional()
functional.basis['Si'] = [
Shell('s', a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325]),
Shell('sp', a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496]),
Shell('sp', 4.0, a0=[1.22, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.55, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.27, 1.0, 1.0]) ]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.dft.spin = True
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
directory = mkdtemp()
firstdir, seconddir = join(directory, '0'), join(directory, '1')
try:
si = functional(crystal, outdir=firstdir, comm=default_comm)
properties = Properties(si)
properties.band = [0, 0, 0], [1, 0, 0], [1, 0, 0], [0, 1, 0]
result0 = properties(outdir=firstdir)
assert result0.success
assert all(abs(result0.bandstructure.eigenvalues[0] - result0.bandstructure.eigenvalues[1]) < 1e-6)
test = [ [-64.55637917, -64.55637522, -3.64877203, -3.64854929,
-1.98183315, -1.98183315, -1.98183315, -1.98097196,
-1.98097196, -1.98097196, 1.00052165, 1.49996607,
1.49996607, 1.49996607, 1.63212276, 1.63212276,
1.63212276, 1.66407077],
[-64.55637917, -64.55637522, -3.64877203, -3.64854929,
-1.98183315, -1.98183315, -1.98183315, -1.98097196,
-1.98097196, -1.98097196, 1.00052165, 1.49996607,
1.49996607, 1.49996607, 1.63212276, 1.63212276,
1.63212276, 1.66407077] ] * hartree
assert all(abs(result0.bandstructure.eigenvalues[0,0] - test[0]) < 1e-8)
assert all(abs(result0.bandstructure.eigenvalues[0,-1] - test[1]) < 1e-8)
test = array([[ 6.66666667e-02, 0, 0],
[ 1.33333333e-01, 0, 0],
[ 2.00000000e-01, 0, 0],
[ 2.66666667e-01, 0, 0],
[ 3.33333333e-01, 0, 0],
[ 4.00000000e-01, 0, 0],
[ 4.66666667e-01, 0, 0],
[ 5.33333333e-01, 0, 0],
[ 6.00000000e-01, 0, 0],
[ 6.66666667e-01, 0, 0],
[ 7.33333333e-01, 0, 0],
[ 8.00000000e-01, 0, 0],
[ 8.66666667e-01, 0, 0],
[ 9.33333333e-01, 0, 0],
[ 1.00000000e+00, 0, 0],
[ 1.06666667e+00, 0, 0],
[ 9.58333333e-01, 4.16666667e-02, 0],
[ 9.16666667e-01, 8.33333333e-02, 0],
[ 8.75000000e-01, 1.25000000e-01, 0],
[ 8.33333333e-01, 1.66666667e-01, 0],
[ 7.91666667e-01, 2.08333333e-01, 0],
[ 7.50000000e-01, 2.50000000e-01, 0],
[ 7.08333333e-01, 2.91666667e-01, 0],
[ 6.66666667e-01, 3.33333333e-01, 0],
[ 6.25000000e-01, 3.75000000e-01, 0],
[ 5.83333333e-01, 4.16666667e-01, 0],
[ 5.41666667e-01, 4.58333333e-01, 0],
[ 5.00000000e-01, 5.00000000e-01, 0],
[ 4.58333333e-01, 5.41666667e-01, 0],
[ 4.16666667e-01, 5.83333333e-01, 0],
[ 3.75000000e-01, 6.25000000e-01, 0],
[ 3.33333333e-01, 6.66666667e-01, 0],
[ 2.91666667e-01, 7.08333333e-01, 0],
[ 2.50000000e-01, 7.50000000e-01, 0],
[ 2.08333333e-01, 7.91666667e-01, 0],
[ 1.66666667e-01, 8.33333333e-01, 0],
[ 1.25000000e-01, 8.75000000e-01, 0],
[ 8.33333333e-02, 9.16666667e-01, 0],
[ 4.16666667e-02, 9.58333333e-01, 0],
[ -1.11022302e-16, 1.00000000e+00, 0]])
assert all(abs(result0.bandstructure.kpoints - test) < 1e-8)
functional.dft.spin = False
si = functional(crystal, outdir=seconddir, comm=default_comm)
properties = Properties(si)
properties.band = [0, 0, 0], [1, 0, 0], [1, 0, 0], [0, 1, 0]
result1 = properties(outdir=seconddir)
assert result1.success
assert all(abs(result1.bandstructure.eigenvalues - result0.bandstructure.eigenvalues[0]) < 1e-6)
assert all(abs(result1.bandstructure.kpoints - result0.bandstructure.kpoints) < 1e-6)
finally:
if directory != '/tmp/test/': rmtree(directory)
def test_breaksym():
from pylada.dftcrystal import Crystal, Functional, Shell, DisplaceAtoms, read
functional = Functional()
functional.basis['Si'] = [
Shell('s', a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325]),
Shell('sp', a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496]),
Shell('sp', 4.0, a0=[1.22, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.55, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.27, 1.0, 1.0]) ]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.optgeom.keepsymm = True
functional.optgeom.enabled = True
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
crystal.append('breaksym')
crystal.append(DisplaceAtoms().add_atom(0.01, 0, 0, 1))
string = functional.print_input(structure=crystal)
assert string.splitlines()[10] == 'KEEPSYMM'
cry, func = read(string)
assert cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.keepsymm
functional.optgeom.keepsymm = False
string = functional.print_input(structure=crystal)
assert string.splitlines()[10] == 'OPTGEOM'
cry, func = read(string)
assert cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.breaksym
crystal[0] = 'keepsymm'
string = functional.print_input(structure=crystal)
assert string.splitlines()[11] == 'BREAKSYM'
cry, func = read(string)
assert not cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.breaksym
functional.optgeom.keepsymm = True
string = functional.print_input(structure=crystal)
assert string.splitlines()[11] == 'OPTGEOM'
cry, func = read(string)
assert not cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.keepsymm
string = crystal.print_input()
crystal.append('keepsymm')
crystal.append('keepsymm')
assert crystal.print_input() == string
crystal.append('breaksym')
assert crystal.print_input() != string
assert len(crystal.print_input().splitlines()) == len(string.splitlines()) + 1
