def test_newk():
from pickle import loads, dumps
from numpy import array, all
from pylada.dftcrystal.properties import Properties
from pylada.dftcrystal.properties.keywords import NewK
from pylada.dftcrystal.input import SetPrint
a = Properties()
assert len(a.output_map()) == 0
a.newk.mp = 5
assert len(a.output_map()) != 0
assert all(array(a.output_map()['newk'].split(), dtype='int64') == [5, 5, 0, 0])
a.newk.printing[66] = -5
assert all(array(a.output_map()['newk'].split(), dtype='int64') == [5, 5, 0, 1, 66, -5])
b = a._input['newk']
assert eval(repr(b), {'NewK': NewK}).output_map()['newk'] == a.output_map()['newk']
assert loads(dumps(b)).output_map()['newk'] == a.output_map()['newk']
assert b.__ui_repr__({})['newk'] == repr(b)
assert b.__ui_repr__({}, defaults=NewK())['newk'] == repr(b)
del b.printing
assert len(b.printing) == 0
assert type(b.printing) is SetPrint
assert b.__ui_repr__({})['newk'] == repr(b)
assert b.__ui_repr__({}, defaults=NewK())['newk'] == '5, None'
assert not b.recompute_fermi
a.newk.recompute_fermi = True
assert b.recompute_fermi
assert all(array(a.output_map()['newk'].split(), dtype='int64') == [5, 5, 1, 0])
assert eval(repr(b), {'NewK': NewK}).output_map()['newk'] == a.output_map()['newk']
assert loads(dumps(b)).output_map()['newk'] == a.output_map()['newk']
assert b.__ui_repr__({})['newk'] == repr(b)
assert b.__ui_repr__({}, defaults=NewK())['newk'] == repr(b)
def test_nosymada(): from pylada.dftcrystal.properties import Properties a = Properties() assert a.nosymada is None assert len(a.output_map()) == 0 a.nosymada = True assert a.print_input() == "NOSYMADA\nEND\n"
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_band():
from pickle import loads, dumps
from collections import namedtuple
from random import randint
from numpy import all, abs, array
from pylada.dftcrystal.properties import Properties
from pylada.dftcrystal.properties.keywords import Band
Shell = namedtuple("Shell", ["charge"])
Functional = namedtuple("Functional", ["basis"])
Extract = namedtuple("Extract", ["functional", "directory", "structure"])
Atom = namedtuple("Atom", ["type"])
class Structure(list):
def __init__(self, *args, **kwargs):
super(Structure, self).__init__(*args, **kwargs)
def eval(self):
return self
shells = {}
shells["Al"] = [Shell(randint(0, 10)) for i in xrange(5)]
shells["Be"] = [Shell(randint(0, 10)) for i in xrange(5)]
functional = Functional(shells)
structure = Structure([Atom(u) for u in ["Al"] * 3 + ["Be"] * 4])
input = Extract(functional, "/dev/null", structure)
kwargs = {"input": input, "filework": False}
nelectrons = sum(u.charge for u in shells["Al"]) * 3 + sum(u.charge for u in shells["Be"]) * 4
a = Properties()
assert len(a.output_map()) == 0
assert len(a.output_map(**kwargs)) == 0
a.band += [[0, 1, 0], [0, 0, 0]], [[0, 0, 0], [1, 0, 0]]
assert all(abs(eval(repr(a.band), {"Band": Band})._lines - a.band._lines) < 1e-8)
assert all(abs(loads(dumps(a.band))._lines - a.band._lines) < 1e-8)
c = a.output_map(**kwargs)["band"].split()
assert all(array(c[:7], dtype="float64") == [2, 10000, 40, 1, nelectrons // 2 + 4, 1, 0])
assert all(abs(array(c[7:], dtype="float64") / 1e4 - a.band._lines.flatten()) < 1e-8)
assert a._input["band"].__ui_repr__({}, name="band")["band"] == repr(a.band)
c = a._input["band"].__ui_repr__({}, name="band", defaults=Band())["band"]
assert all(abs(array(eval(c), dtype="float64") - a.band._lines) < 1e-8)
a.band.maxband = nelectrons // 2 + 1
assert a.band.maxband == nelectrons // 2 + 1
assert all(abs(eval(repr(a.band), {"Band": Band})._lines - a.band._lines) < 1e-8)
assert eval(repr(a.band), {"Band": Band}).maxband == nelectrons // 2 + 1
assert all(abs(loads(dumps(a.band))._lines - a.band._lines) < 1e-8)
assert loads(dumps(a.band)).maxband == nelectrons // 2 + 1
assert a._input["band"].__ui_repr__({}, name="band")["band"] == repr(a.band)
assert a._input["band"].__ui_repr__({}, name="band", defaults=Band())["band"] == repr(a.band)
# check title
assert len(a.output_map(properties=a, **kwargs)["band"].splitlines()[0]) == 0
Extract = namedtuple("Extract", ["functional", "directory", "structure", "title"])
input = Extract(functional, "/dev/null", structure, "hello")
kwargs["input"] = input
assert a.output_map(properties=a, **kwargs)["band"].splitlines()[0] == "hello"
a.band.title = "goodbye"
assert a.output_map(properties=a, **kwargs)["band"].splitlines()[0] == "goodbye"
def test_band():
from pickle import loads, dumps
from collections import namedtuple
from random import randint
from numpy import all, abs, array
from pylada.dftcrystal.properties import Properties
from pylada.dftcrystal.properties.keywords import Band
Shell = namedtuple('Shell', ['charge'])
Functional = namedtuple('Functional', ['basis'])
Extract = namedtuple('Extract', ['functional', 'directory', 'structure'])
Atom = namedtuple('Atom', ['type'])
class Structure(list):
def __init__(self, *args, **kwargs):
super(Structure, self).__init__(*args, **kwargs)
def eval(self): return self
shells = {}
shells['Al'] = [Shell(randint(0, 10)) for i in xrange(5)]
shells['Be'] = [Shell(randint(0, 10)) for i in xrange(5)]
functional = Functional(shells)
structure = Structure([Atom(u) for u in ['Al']*3 + ['Be'] * 4])
input = Extract(functional, '/dev/null', structure)
kwargs = {'input': input, 'filework': False}
nelectrons = sum(u.charge for u in shells['Al']) * 3 \
+ sum(u.charge for u in shells['Be']) * 4
a = Properties()
assert len(a.output_map()) == 0
assert len(a.output_map(**kwargs)) == 0
a.band += [[0, 1, 0], [0, 0, 0]], [[0, 0, 0], [1, 0, 0]]
assert all(abs(eval(repr(a.band), {'Band': Band})._lines - a.band._lines) < 1e-8)
assert all(abs(loads(dumps(a.band))._lines - a.band._lines) < 1e-8)
c = a.output_map(**kwargs)['band'].split()
assert all(array(c[:7], dtype='float64') == [2, 10000, 40, 1, nelectrons//2+4, 1, 0])
assert all(abs(array(c[7:], dtype='float64') / 1e4 - a.band._lines.flatten()) < 1e-8)
assert a._input['band'].__ui_repr__({}, name='band')['band'] == repr(a.band)
c = a._input['band'].__ui_repr__({}, name='band', defaults=Band())['band']
assert all(abs(array(eval(c), dtype='float64') - a.band._lines) < 1e-8)
a.band.maxband = nelectrons // 2 + 1
assert a.band.maxband == nelectrons // 2 + 1
assert all(abs(eval(repr(a.band), {'Band': Band})._lines - a.band._lines) < 1e-8)
assert eval(repr(a.band), {'Band': Band}).maxband == nelectrons // 2 + 1
assert all(abs(loads(dumps(a.band))._lines - a.band._lines) < 1e-8)
assert loads(dumps(a.band)).maxband == nelectrons // 2 + 1
assert a._input['band'].__ui_repr__({}, name='band')['band'] == repr(a.band)
assert a._input['band'].__ui_repr__({}, name='band', defaults=Band())['band'] == repr(a.band)
# check title
assert len(a.output_map(properties=a, **kwargs)['band'].splitlines()[0]) == 0
Extract = namedtuple('Extract', ['functional', 'directory', 'structure', 'title'])
input = Extract(functional, '/dev/null', structure, 'hello')
kwargs['input'] = input
assert a.output_map(properties=a, **kwargs)['band'].splitlines()[0] == 'hello'
a.band.title = 'goodbye'
assert a.output_map(properties=a, **kwargs)['band'].splitlines()[0] == 'goodbye'
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_rdfmwf():
from collections import namedtuple
from shutil import rmtree
from tempfile import mkdtemp
from os.path import join, exists
from os import remove
from pylada.dftcrystal.properties import Properties
from pylada.error import IOError
Extract = namedtuple('Extract', ['directory'])
try:
indir = mkdtemp()
outdir = mkdtemp()
extract = Extract(indir)
a = Properties(input=extract)
assert a.rdfmwf is None
assert len(a.output_map(filework=False)) == 0
assert len(a.print_input(filework=False)) == 0
try: a.output_map(filework=True, workdir=outdir)
except IOError: pass
else: raise Exception()
a.rdfmwf = True
assert len(a.output_map(filework=False)) == 1
assert a.output_map(filework=False)['rdfmwf'] == True
try: a.output_map(filework=True, workdir=outdir)
except IOError: pass
else: raise Exception()
a.rdfmwf = False
assert len(a.output_map(filework=False)) == 0
try: a.output_map(filework=True, workdir=outdir)
except IOError: pass
else: raise Exception()
# now with .f98 file
with open(join(indir, 'crystal.f98'), 'w') as file: file.write('hello')
a.rdfmwf = None
assert len(a.output_map(filework=False)) == 1
assert a.output_map(filework=False)['rdfmwf'] == True
assert not exists(join(outdir, 'fort.98'))
# should fail
a.rdfmwf = False
try: a.output_map(filework=True, workdir=outdir)
except IOError: pass
else: raise Exception()
# now check writing
a.rdfmwf = None
assert not exists(join(outdir, 'fort.98'))
assert a.output_map(filework=True, workdir=outdir)['rdfmwf'] == True
assert exists(join(outdir, 'fort.98'))
remove(join(outdir, 'fort.98'))
a.rdfmwf = True
assert not exists(join(outdir, 'fort.98'))
assert a.output_map(filework=True, workdir=outdir)['rdfmwf'] == True
assert exists(join(outdir, 'fort.98'))
remove(join(indir, 'crystal.f98'))
remove(join(outdir, 'fort.98'))
with open(join(outdir, 'crystal.f98'), 'w') as file: file.write('hello')
assert exists(join(outdir, 'crystal.f98'))
assert not exists(join(outdir, 'fort.98'))
assert a.output_map(filework=True, workdir=outdir, outdir=outdir)['rdfmwf'] == True
assert exists(join(outdir, 'fort.98'))
remove(join(outdir, 'fort.98'))
# now for .f9
with open(join(indir, 'crystal.f9'), 'w') as file: file.write('hello')
a.rdfmwf = None
assert len(a.output_map(filework=False)) == 0
assert not exists(join(outdir, 'fort.9'))
# should fail
a.rdfmwf = True
try: a.output_map(filework=True, workdir=outdir)
except IOError: pass
else: raise Exception()
# now check writing
a.rdfmwf = None
assert not exists(join(outdir, 'fort.9'))
assert len(a.output_map(filework=True, workdir=outdir)) == 0
assert exists(join(outdir, 'fort.9'))
remove(join(outdir, 'fort.9'))
a.rdfmwf = False
assert not exists(join(outdir, 'fort.9'))
assert len(a.output_map(filework=True, workdir=outdir)) == 0
assert exists(join(outdir, 'fort.9'))
remove(join(indir, 'crystal.f9'))
remove(join(outdir, 'fort.9'))
with open(join(outdir, 'crystal.f9'), 'w') as file: file.write('hello')
assert not exists(join(outdir, 'fort.9'))
assert exists(join(outdir, 'crystal.f9'))
assert len(a.output_map(filework=True, workdir=outdir, outdir=outdir)) == 0
assert exists(join(outdir, 'fort.9'))
remove(join(outdir, 'fort.9'))
finally:
try: rmtree(indir)
except: pass
try: rmtree(outdir)
except: pass
