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_functional():
from pylada.dftcrystal import Functional, Shell
from pylada.dftcrystal.input import print_input
a = Functional()
assert repr(a) == repr(loads(dumps(a)))
a.basis['H'] = [ Shell( 's', 1.0,
a0=[18.731137, 0.0334946],
a1=[2.8253937, 0.23472695],
a2=[0.6401217, 0.81375733] ),
Shell('s', 0.0, a0=[0.1612778, 1.0]),
Shell('p', 0.0, a0=[1.1, 1.0]) ]
a.shrink = [8, 8, 9], None
a.tolinteg = 8, 8, 8, 8, 14
a.dft.b3lyp = True
a.dft.exchange = 'lda'
a.dft.xxlgrid = True
a.optgeom.maxcycle = 50
a.optgeom.fulloptg = True
assert repr(Functional()) != repr(loads(dumps(a)))
assert repr(a) == repr(loads(dumps(a)))
b = loads(dumps(a))
assert print_input(a.output_map(crystal=a)) == print_input(b.output_map(crystal=b))
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_chemod():
from pickle import loads, dumps
from numpy import all, array, abs
from pylada.dftcrystal import Crystal, Functional, Shell
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]) ]
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
kwargs = {'crystal': functional, 'structure': crystal}
a = functional.basis._input['chemod']
assert len(functional.basis.chemod) == 0
assert a.output_map(**kwargs) is None
assert functional.basis.chemod.breaksym == True
assert loads(dumps(a)).breaksym is True
assert len(loads(dumps(a))) == 0
functional.basis.chemod.keepsym = True
functional.basis.chemod[1] = [2.0, 8.0, 4.0, 0.0, 0.0]
assert 'chemod' in a.output_map(**kwargs)
assert all( abs( array(a.output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
assert a.modisymm(crystal) is None
assert loads(dumps(a)).breaksym is False
assert all( abs( array(loads(dumps(a)).output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
functional.basis.chemod[2] = [2.0, 8.0, 4.0, 0.0, 0.0]
assert 'chemod' in a.output_map(**kwargs)
assert all( abs( array(a.output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
assert loads(dumps(a)).breaksym is False
assert all( abs( array(loads(dumps(a)).output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
assert a.modisymm(crystal) is None
del functional.basis.chemod[1]
assert 'chemod' in a.output_map(**kwargs)
assert all( abs( array(a.output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
assert loads(dumps(a)).breaksym is False
assert all( abs( array(loads(dumps(a)).output_map(**kwargs)['chemod'].split(), dtype='float64')
- [2.0, 1.0, 2.0, 8.0, 4, 0, 0, 2, 2, 8, 4, 0, 0] ) < 1e-8 )
assert a.modisymm(crystal) is None
functional.basis.chemod.breaksym = True
assert 'chemod' in a.output_map(**kwargs)
assert all( abs( array(a.output_map(**kwargs)['chemod'].split(), dtype='float64')
- [1.0, 2.0, 2.0, 8.0, 4, 0, 0] ) < 1e-8 )
assert loads(dumps(a)).breaksym is True
assert all( abs( array(loads(dumps(a)).output_map(**kwargs)['chemod'].split(), dtype='float64')
- [1.0, 2.0, 2.0, 8.0, 4, 0, 0] ) < 1e-8 )
assert a.modisymm(crystal) is not None
assert [2] in a.modisymm(crystal).groups
assert [1] in a.modisymm(crystal).groups
assert len(a.modisymm(crystal).groups) == 2
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
def test_broyden():
from pickles import loads, dumps
from pylada.dftcrystal import Functional
from pylada.dftcrystal.electronic import Broyden
from pylada.error import ValueError, TypeError
a = Functional()
b = a.scf._input['broyden']
assert a.broyden.w0 is None
assert a.broyden.imix is None
assert a.broyden.istart is None
assert b.output_map() is None
assert eval(repr(b), {'Broyden': Broyden}).w0 is None
assert eval(repr(b), {'Broyden': Broyden}).imix is None
assert eval(repr(b), {'Broyden': Broyden}).istart is None
a.broyden.w0 = 1e-4
assert abs(a.broyden.w0 - 1e-4) < 1e-8
assert a.broyden.imix is None
assert a.broyden.istart is None
assert b.output_map() is None
assert abs(eval(repr(b), {'Broyden': Broyden}).w0 - 1e-4) < 1e-8
assert eval(repr(b), {'Broyden': Broyden}).imix is None
assert eval(repr(b), {'Broyden': Broyden}).istart is None
a.broyden.w0 = None
a.broyden.imix = 50
a.broyden.istart = 3
assert a.broyden.w0 is None
assert a.broyden.imix == 50
assert a.broyden.istart == 3
assert eval(repr(b), {'Broyden': Broyden}).w0 is None
assert eval(repr(b), {'Broyden': Broyden}).imix == 50
assert eval(repr(b), {'Broyden': Broyden}).istart == 3
assert b.output_map() is None
a.broyden.w0 = 1e-4
a.broyden.imix = 50
a.broyden.istart = 3
assert abs(a.broyden.w0 - 1e-4) < 1e-8
assert a.broyden.imix == 50
assert a.broyden.istart == 3
assert abs(eval(repr(b), {'Broyden': Broyden}).w0 - 1e-4) < 1e-8
assert eval(repr(b), {'Broyden': Broyden}).imix == 50
assert eval(repr(b), {'Broyden': Broyden}).istart == 3
assert b.output_map() is not None
assert 'broyden' in b.output_map()
assert len(b.output_map()['broyden'].split()) == 3
assert abs(float(b.output_map()['broyden'].split()[0])-1e-4) < 1e-8
assert int(b.output_map()['broyden'].split()[1]) == 50
assert int(b.output_map()['broyden'].split()[2]) == 3
a.broyden[0] = '1e-2'
assert abs(a.broyden.w0 - 1e-2) < 1e-8
assert abs(a.broyden[0] - 1e-2) < 1e-8
a.broyden[1] = 25
assert a.broyden.imix == 25
assert a.broyden[1] == 25
a.broyden[2] = 5
assert a.broyden.istart == 5
assert a.broyden[2] == 5
assert abs(loads(dumps(b))[0] - 1e-2) < 1e-8
assert loads(dumps(b))[1] == 25
assert loads(dumps(b))[2] == 5
a.broyden = None
assert a.broyden.w0 is None
assert a.broyden.imix is None
assert a.broyden.istart is None
a.broyden = ' 1e-2', 25, 5
assert abs(a.broyden[0] - 1e-2) < 1e-8
assert a.broyden[1] == 25
assert a.broyden[2] == 5
try: a.broyden = 0
except TypeError: pass
else: raise Exception()
try: a.broyden = 0, 1
except TypeError: pass
else: raise Exception()
try: a.broyden[1] = 0
except ValueError: pass
else: raise Exception()
try: a.broyden[2] = 1
except ValueError: pass
else: raise Exception()
