def test_fdf_gz(sisl_files):
f = sisl_files(osp.join(_dir, 'fdf'), 'main.fdf.gz')
fdf = fdfSileSiesta(f)
# read from gzipped file
assert fdf.get("Main.Foo") == "hello"
assert fdf.get("Main.Bar") == "world"
# read from included non-gzipped file
assert fdf.get("Lvl2.Foo") == "world"
assert fdf.get("Lvl2.Bar") == "hello"
# read from nested included gzipped file
assert fdf.get("Lvl3.Foo") == "world3"
assert fdf.get("Lvl3.Bar") == "hello3"
f = sisl_files(osp.join(_dir, 'fdf'), 'level2.fdf')
fdf = fdfSileSiesta(f)
# read from non-gzipped file
assert fdf.get("Lvl2.Foo") == "world"
assert fdf.get("Lvl2.Bar") == "hello"
# read from included gzipped file
assert fdf.get("Lvl3.Foo") == "world3"
assert fdf.get("Lvl3.Bar") == "hello3"
def test_fdf_argumentparser(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
with open(f, 'w') as fh:
fh.write('Flag1 date\n')
fh.write('Flag1 not-date\n')
fh.write('Flag1 not-date-2\n')
fh.write('Flag3 true\n')
fdfSileSiesta(f).ArgumentParser()
def test_fdf2(self):
f = osp.join(self.d, 'gr.fdf')
self.g.write(fdfSileSiesta(f, 'w'))
g = fdfSileSiesta(f).read_geom()
# Assert they are the same
assert_true(np.allclose(g.cell, self.g.cell))
assert_true(np.allclose(g.xyz, self.g.xyz))
for ia in g:
assert_true(g.atom[ia] == self.g.atom[ia])
def test_fdf2(self):
f = osp.join(self.d, "gr.fdf")
self.g.write(fdfSileSiesta(f, "w"))
g = fdfSileSiesta(f).read_geom()
# Assert they are the same
assert_true(np.allclose(g.cell, self.g.cell))
assert_true(np.allclose(g.xyz, self.g.xyz))
for ia in g:
assert_true(g.atom[ia] == self.g.atom[ia])
def test_fdf2(sisl_tmp, sisl_system):
f = sisl_tmp('gr.fdf', _dir)
sisl_system.g.write(fdfSileSiesta(f, 'w'))
g = fdfSileSiesta(f).read_geometry()
# Assert they are the same
assert np.allclose(g.cell, sisl_system.g.cell)
assert np.allclose(g.xyz, sisl_system.g.xyz)
for ia in g:
assert g.atoms[ia].Z == sisl_system.g.atoms[ia].Z
assert g.atoms[ia].tag == sisl_system.g.atoms[ia].tag
def test_supercell_fail(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
lines = [
'%block Latticevectors',
' 1. 1. 1.',
' 0. 0. 1.',
' 1. 0. 1.',
'%endblock',
]
with open(f, 'w') as fh:
fh.write('\n'.join(lines))
fdfSileSiesta(f).read_supercell()
def test_fdf_units(sisl_tmp, sisl_system):
f = sisl_tmp('gr.fdf', _dir)
fdf = fdfSileSiesta(f, 'w')
g = sisl_system.g
for unit in ['bohr', 'ang', 'fractional', 'frac']:
fdf.write_geometry(g, unit=unit)
g2 = fdfSileSiesta(f).read_geometry()
assert np.allclose(g.cell, g2.cell)
assert np.allclose(g.xyz, g2.xyz)
for ia in g:
assert g.atoms[ia].Z == g2.atoms[ia].Z
assert g.atoms[ia].tag == g2.atoms[ia].tag
def test_xv_preference(sisl_tmp):
g = geom.graphene()
g.write(sisl_tmp('file.fdf', _dir))
g.xyz[0, 0] += 1.
g.write(sisl_tmp('siesta.XV', _dir))
g2 = fdfSileSiesta(sisl_tmp('file.fdf', _dir)).read_geometry(True)
assert np.allclose(g.cell, g2.cell)
assert np.allclose(g.xyz, g2.xyz)
g2 = fdfSileSiesta(sisl_tmp('file.fdf', _dir)).read_geometry(order=['fdf'])
assert np.allclose(g.cell, g2.cell)
g2.xyz[0, 0] += 1.
assert np.allclose(g.xyz, g2.xyz)
def test_geometry(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
sc_lines = [
'Latticeconstant 1. Ang',
'%block latticeparameters',
' 1. 1. 1. 90. 90. 90.',
'%endblock',
]
lines = [
'NumberOfAtoms 2',
'%block chemicalSpeciesLabel',
' 1 6 C',
' 2 12 H',
'%endblock',
'AtomicCoordinatesFormat Ang',
'%block atomiccoordinatesandatomicspecies',
' 1. 1. 1. 1',
' 0. 0. 1. 1',
' 1. 0. 1. 2',
'%endblock',
]
with open(f, 'w') as fh:
fh.write('\n'.join(sc_lines) + '\n')
fh.write('\n'.join(lines))
fdf = fdfSileSiesta(f, base=sisl_tmp.getbase())
g = fdf.read_geometry()
assert g.na == 2
assert np.allclose(g.xyz, [[1.] * 3,
[0, 0, 1]])
assert g.atom[0].Z == 6
assert g.atom[1].Z == 6
# default read # of atoms from list
with open(f, 'w') as fh:
fh.write('\n'.join(sc_lines) + '\n')
fh.write('\n'.join(lines[1:]))
fdf = fdfSileSiesta(f, base=sisl_tmp.getbase())
g = fdf.read_geometry()
assert g.na == 3
assert np.allclose(g.xyz, [[1.] * 3,
[0, 0, 1],
[1, 0, 1]])
assert g.atom[0].Z == 6
assert g.atom[1].Z == 6
assert g.atom[2].Z == 12
def test_fdf1(self):
f = osp.join(self.d, 'gr.fdf')
self.g.write(fdfSileSiesta(f, 'w'))
fdf = fdfSileSiesta(f)
with fdf:
fdf.readline()
# Be sure that we can read it in a loop
assert_true(fdf.get('LatticeConstant') > 0.)
assert_true(fdf.get('LatticeConstant') > 0.)
assert_true(fdf.get('LatticeConstant') > 0.)
fdf.read_supercell()
fdf.read_geometry()
def test_fdf1(self):
f = osp.join(self.d, "gr.fdf")
self.g.write(fdfSileSiesta(f, "w"))
fdf = fdfSileSiesta(f)
with fdf:
fdf.readline()
# Be sure that we can read it in a loop
assert_true(fdf.get("LatticeConstant") > 0.0)
assert_true(fdf.get("LatticeConstant") > 0.0)
assert_true(fdf.get("LatticeConstant") > 0.0)
fdf.read_sc()
fdf.read_geom()
def test_dry_read(sisl_tmp):
# This test runs the read-functions. They aren't expected to actually read anything,
# it is only a dry-run.
file = sisl_tmp('siesta.fdf', _dir)
geom.graphene().write(file)
fdf = fdfSileSiesta(file)
read_methods = set(m for m in dir(fdf) if m.startswith("read_"))
output = dict(output=True)
kwargs = {
"supercell": output,
"geometry": output,
"grid": dict(name="rho"),
}
with pytest.warns(SislWarning):
assert np.allclose(fdf.read_supercell_nsc(), (1, 1, 1))
read_methods.remove("read_supercell_nsc")
geom_methods = set(f"read_{x}" for x in ("basis", "supercell", "geometry"))
read_methods -= geom_methods
for methodname in read_methods:
kwarg = kwargs.get(methodname[5:], dict())
assert getattr(fdf, methodname)(**kwarg) is None
for methodname in geom_methods:
# Also run these, but dont assert None due to the graphene values being present
# in the fdf. The read functions will still go dry-running through eg. nc-files.
kwarg = kwargs.get(methodname[5:], dict())
getattr(fdf, methodname)(**kwarg)
def test_fdf1(sisl_tmp, sisl_system):
f = sisl_tmp('gr.fdf', _dir)
sisl_system.g.write(fdfSileSiesta(f, 'w'))
fdf = fdfSileSiesta(f)
str(fdf)
with fdf:
fdf.readline()
# Be sure that we can read it in a loop
assert fdf.get('LatticeConstant') > 0.
assert fdf.get('LatticeConstant') > 0.
assert fdf.get('LatticeConstant') > 0.
fdf.read_supercell()
fdf.read_geometry()
def test_get_block(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
with open(f, 'w') as fh:
fh.write('%block MyBlock\n date\n%endblock\n')
fdf = fdfSileSiesta(f)
assert isinstance(fdf.get('MyBlock'), list)
assert fdf.get('MyBlock')[0] == 'date'
assert 'block' in fdf.print("MyBlock", fdf.get("MyBlock"))
def test_re_read(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
with open(f, 'w') as fh:
fh.write('Flag1 date\n')
fh.write('Flag1 not-date\n')
fh.write('Flag1 not-date-2\n')
fdf = fdfSileSiesta(f)
for i in range(10):
assert fdf.get('Flag1') == 'date'
def test_supercell(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
lines = [
'Latticeconstant 1. Ang',
'%block Latticevectors',
' 1. 1. 1.',
' 0. 0. 1.',
' 1. 0. 1.',
'%endblock',
]
with open(f, 'w') as fh:
fh.write('\n'.join(lines))
cell = np.array([[1.] * 3, [0, 0, 1], [1, 0, 1]])
sc = fdfSileSiesta(f).read_supercell()
assert np.allclose(sc.cell, cell)
lines = [
'Latticeconstant 1. Bohr',
'%block Latticevectors',
' 1. 1. 1.',
' 0. 0. 1.',
' 1. 0. 1.',
'%endblock',
]
with open(f, 'w') as fh:
fh.write('\n'.join(lines))
sc = fdfSileSiesta(f).read_supercell()
assert np.allclose(sc.cell, cell * unit_convert('Bohr', 'Ang'))
cell = np.diag([2.] * 3)
lines = [
'Latticeconstant 2. Ang',
'%block Latticeparameters',
' 1. 1. 1. 90. 90. 90.',
'%endblock',
]
with open(f, 'w') as fh:
fh.write('\n'.join(lines))
sc = fdfSileSiesta(f).read_supercell()
assert np.allclose(sc.cell, cell)
def test_get_set(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
with open(f, 'w') as fh:
fh.write('Flag1 date\n')
fdf = fdfSileSiesta(f)
assert fdf.get('Flag1') == 'date'
fdf.set('Flag1', 'not-date')
assert fdf.get('Flag1') == 'not-date'
fdf.set('Flag1', 'date')
assert fdf.get('Flag1') == 'date'
fdf.set('Flag1', 'date-date')
assert fdf.get('Flag1') == 'date-date'
fdf.set('Flag1', 'date-date', keep=False)
def test_h2_dynamical_matrix(sisl_files):
si = fdfSileSiesta(sisl_files(_dir, 'H2_dynamical_matrix.fdf'))
trans_inv = [True, False]
sum0 = trans_inv[:]
hermitian = trans_inv[:]
eV2cm = 8065.54429
hw_true = [-88.392650, -88.392650, -0.000038, -0.000001, 0.000025, 3797.431825]
from itertools import product
for ti, s0, herm in product(trans_inv, sum0, hermitian):
dyn = si.read_dynamical_matrix(trans_inv=ti, sum0=s0, hermitian=herm)
hw = dyn.eigenvalue().hw
if ti and s0 and herm:
assert np.allclose(hw * eV2cm, hw_true, atol=1e-4)
def test_geom_order(sisl_tmp):
gfdf = geom.graphene()
gxv = gfdf.copy()
gxv.xyz[0, 0] += 0.5
gnc = gfdf.copy()
gnc.xyz[0, 0] += 0.5
gfdf.write(sisl_tmp('siesta.fdf', _dir))
# Create fdf-file
fdf = fdfSileSiesta(sisl_tmp('siesta.fdf', _dir))
assert fdf.read_geometry(True, order=['nc']) is None
gxv.write(sisl_tmp('siesta.XV', _dir))
gnc.write(sisl_tmp('siesta.nc', _dir))
# Should read from XV
g = fdf.read_geometry(True)
assert np.allclose(g.xyz, gxv.xyz)
g = fdf.read_geometry(order=['nc', 'fdf'])
assert np.allclose(g.xyz, gnc.xyz)
g = fdf.read_geometry(order=['fdf', 'nc'])
assert np.allclose(g.xyz, gfdf.xyz)
g = fdf.read_geometry(order=['xv', 'nc'])
assert np.allclose(g.xyz, gxv.xyz)
def test_fdf_fe_basis(sisl_files):
geom = fdfSileSiesta(sisl_files(_dir, 'fe.fdf')).read_geometry()
assert geom.no == 15
assert geom.na == 1
def test_include(sisl_tmp):
f = sisl_tmp('file.fdf', _dir)
with open(f, 'w') as fh:
fh.write('Flag1 date\n')
fh.write('# Flag2 comment\n')
fh.write('Flag2 date2\n')
fh.write('# Flag3 is read through < from file hello\n')
fh.write('Flag3 Sub < hello\n')
fh.write('FakeInt 1\n')
fh.write('Test 1. eV\n')
fh.write(' %INCLUDE file2.fdf\n')
fh.write('TestRy 1. Ry\n')
fh.write('%block Hello < hello\n')
fh.write('TestLast 1. eV\n')
hello = sisl_tmp('hello', _dir)
with open(hello, 'w') as fh:
fh.write('Flag4 hello\n')
fh.write('# Comments should be discarded\n')
fh.write('Flag3 test\n')
fh.write('Sub sub-test\n')
file2 = sisl_tmp('file2.fdf', _dir)
with open(file2, 'w') as fh:
fh.write('Flag4 non\n')
fh.write('FakeReal 2.\n')
fh.write(' %incLude file3.fdf')
file3 = sisl_tmp('file3.fdf', _dir)
with open(file3, 'w') as fh:
fh.write('Sub level\n')
fh.write('Third level\n')
fh.write('MyList [1 , 2 , 3]\n')
fdf = fdfSileSiesta(f, base=sisl_tmp.getbase())
assert fdf.includes() == [Path(hello), Path(file2), Path(file3)]
assert fdf.get('Flag1') == 'date'
assert fdf.get('Flag2') == 'date2'
assert fdf.get('Flag3') == 'test'
assert fdf.get('Flag4') == 'non'
assert fdf.get('FLAG4') == 'non'
assert fdf.get('Fakeint') == 1
assert fdf.get('Fakeint', '0') == '1'
assert fdf.get('Fakereal') == 2.
assert fdf.get('Fakereal', 0.) == 2.
assert fdf.get('test', 'eV') == pytest.approx(1.)
assert fdf.get('test', with_unit=True)[0] == pytest.approx(1.)
assert fdf.get('test', with_unit=True)[1] == 'eV'
assert fdf.get('test',
unit='Ry') == pytest.approx(unit_convert('eV', 'Ry'))
assert fdf.get('testRy') == pytest.approx(unit_convert('Ry', 'eV'))
assert fdf.get('testRy', with_unit=True)[0] == pytest.approx(1.)
assert fdf.get('testRy', with_unit=True)[1] == 'Ry'
assert fdf.get('testRy', unit='Ry') == pytest.approx(1.)
assert fdf.get('Sub') == 'sub-test'
assert fdf.get('Third') == 'level'
assert fdf.get('test-last', with_unit=True)[0] == pytest.approx(1.)
assert fdf.get('test-last', with_unit=True)[1] == 'eV'
# Currently lists are not implemented
#assert np.allclose(fdf.get('MyList'), np.arange(3) + 1)
#assert np.allclose(fdf.get('MyList', []), np.arange(3) + 1)
# Read a block
ll = open(sisl_tmp('hello', _dir)).readlines()
ll.pop(1)
assert fdf.get('Hello') == [l.replace('\n', '').strip() for l in ll]
