def test_xsf_parse_crystal():
name = 'xsf_crystal'
target = ["CRYSTAL\n",
"PRIMVEC\n",
" 5.0000 0.0000 0.0000\n",
" 0.0000 5.0000 0.0000\n",
" 0.0000 0.0000 5.0000\n",
"CONVVEC\n",
" 5.0000 0.0000 0.0000\n",
" 0.0000 5.0000 0.0000\n",
" 0.0000 0.0000 5.0000\n",
"PRIMCOORD\n",
"8 1\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 2.5000 0.0000 0.0000\n",
"Na 2.5000 2.5000 0.0000\n",
"Cl 0.0000 2.5000 0.0000\n",
"Cl 0.0000 0.0000 2.5000\n",
"Na 2.5000 0.0000 2.5000\n",
"Cl 2.5000 2.5000 2.5000\n",
"Na 0.0000 2.5000 2.5000"]
Mol, _ = xsf.parser(name, target)
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ['Na', 'Cl']
assert Mol.getFmt() == 'angstrom'
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert list(map(len, Mol.getBonds(1.1))) == [12, 4, 4, 0, 4, 0, 0, 0]
def test_xsf_parse_crystal_animated_varcell():
name = 'xsf_crystal_anim_varcell'
target = ["ANIMSTEPS 2\n",
"CRYSTAL\n",
"PRIMVEC 1\n",
" 5.0000 0.0000 0.0000\n",
" 0.0000 5.0000 0.0000\n",
" 0.0000 0.0000 5.0000\n",
"PRIMCOORD 1\n",
"8 1\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 2.5000 0.0000 0.0000\n",
"Na 2.5000 2.5000 0.0000\n",
"Cl 0.0000 2.5000 0.0000\n",
"Cl 0.0000 0.0000 2.5000\n",
"Na 2.5000 0.0000 2.5000\n",
"Cl 2.5000 2.5000 2.5000\n",
"Na 0.0000 2.5000 2.5000\n",
"PRIMVEC 2\n",
" 5.0000 0.0000 0.0000\n",
" 0.0000 5.3000 0.0000\n",
" 0.0000 0.0000 5.0000\n",
"PRIMCOORD 2",
"8 1\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 2.5000 0.0000 0.0000\n",
"Na 2.5000 2.5000 0.0000\n",
"Cl 0.0000 2.5000 0.0000\n",
"Cl 0.0000 0.0000 2.5000\n",
"Na 2.5000 0.0000 2.5000\n",
"Cl 2.5000 2.5000 2.5000\n",
"Na 0.0000 2.5000 2.5000"]
Mol, _ = xsf.parser(name, target)
assert Mol.name == name
for step in Mol.steps:
assert step.nat == 8
assert step.ntyp == 2
assert step.getTypes() == ['Na', 'Cl']
assert vec_equal(Mol.steps[0].getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert list(map(len, Mol.steps[0].getBonds(1.1))) ==\
[12, 4, 4, 0, 4, 0, 0, 0]
assert vec_equal(Mol.steps[1].getVec(),
((5, 0, 0), (0, 5.3, 0), (0, 0, 5)))
assert list(map(len, Mol.steps[1].getBonds(1.1))) ==\
[12, 4, 0, 0, 4, 0, 0, 0]
def test_xsf_parse_molecular():
name = 'xsf_molecular'
target = ["# comment\n",
"ATOMS\n",
"O 0.0000 0.0000 0.0000\n",
"H 0.9572 0.0000 0.0000\n",
"H -0.2400 0.9266 0.0000"]
Mol, _ = xsf.parser(name, target)
assert Mol.name == name
assert Mol.nat == 3
assert Mol.ntyp == 2
assert Mol.getTypes() == ['H', 'O']
assert Mol.getFmt() == 'angstrom'
assert atom_equal(Mol.getAtom(0, charge=True, fix=True, hidden=True),
['O', (0, 0, 0), 0.,
[False, False, False], False])
assert atom_equal(Mol.getAtom(2, fmt='bohr'),
['H', (-0.4535, 1.7511, 0)])
assert atom_equal(Mol.getAtom(1, fmt='angstrom'),
['H', (0.9572, 0, 0)])
assert len(Mol.getBonds(1.1)[0]) == 2
def test_xsf_parse_molecule_animated():
name = 'xsf_molecular_anim'
target = ["ANIMSTEPS 3\n",
"ATOMS 1\n",
"O 0.0000 0.0000 0.0000\n",
"H 0.9572 0.0000 0.0000\n",
"H -0.2400 0.9266 0.0000\n",
"ATOMS 2\n",
"O 0.0000 0.0000 0.0000\n",
"H -0.9572 0.0000 0.0000\n",
"H 0.2400 0.9266 0.0000\n",
"ATOMS 3\n",
"O 0.0000 0.0000 0.0000\n",
"H -0.9572 0.0000 0.0000\n",
"H 0.2400 -0.9266 0.0000"]
Mol, _ = xsf.parser(name, target)
assert len(Mol) == 3
assert Mol.name == name
assert Mol.getFmt() == 'angstrom'
for step in Mol.steps:
assert step.nat == 3
assert step.ntyp == 2
assert step.getTypes() == ['H', 'O']
assert len(step.getBonds(1.1)[0]) == 2
def test_xsf_parse_datagrid3d():
name = 'xsf_datagrid3d'
target = ["CRYSTAL\n",
"PRIMVEC\n",
" 5.0000 0.0000 0.0000\n",
" 0.0000 5.0000 0.0000\n",
" 0.0000 0.0000 5.0000\n",
"PRIMCOORD\n",
"8 1\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 2.5000 0.0000 0.0000\n",
"Na 2.5000 2.5000 0.0000\n",
"Cl 0.0000 2.5000 0.0000\n",
"Cl 0.0000 0.0000 2.5000\n",
"Na 2.5000 0.0000 2.5000\n",
"Cl 2.5000 2.5000 2.5000\n",
"Na 0.0000 2.5000 2.5000\n",
"BEGIN_BLOCK_DATAGRID_3D\n",
"3D_TESTGRID\n",
"BEGIN_DATAGRID_3D_UNKNOWN1\n",
" 5 5 5\n",
" 0.0 0.0 0.0\n",
" 5.0 0.0 0.0\n",
" 0.0 5.0 0.0\n",
" 0.0 0.0 5.0\n",
" 0.000 1.000 2.000 5.196 8.000\n",
" 1.000 1.414 2.236 5.292 8.062\n",
" 2.000 2.236 2.828 5.568 8.246\n",
" 3.000 3.162 3.606 6.000 8.544\n",
" 4.000 4.123 4.472 6.557 8.944\n",
"\n",
" 1.000 1.414 2.236 5.292 8.062\n",
" 1.414 1.732 2.449 5.385 8.124\n",
" 2.236 2.449 3.000 5.657 8.307\n",
" 3.162 3.317 3.742 6.083 8.602\n",
" 4.123 4.243 4.583 6.633 9.000\n",
"\n",
" 2.000 2.236 2.828 5.568 8.246\n",
" 2.236 2.449 3.000 5.657 8.307\n",
" 2.828 3.000 3.464 5.916 8.485\n",
" 3.606 3.742 4.123 6.325 8.775\n",
" 4.472 4.583 4.899 6.856 9.165\n",
"\n",
" 3.000 3.162 3.606 6.000 8.544\n",
" 3.162 3.317 3.742 6.083 8.602\n",
" 3.606 3.742 4.123 6.325 8.775\n",
" 4.243 4.359 4.690 6.708 9.055\n",
" 5.000 5.099 5.385 7.211 9.434\n",
"\n",
" 4.000 4.123 4.472 6.557 8.944\n",
" 4.123 4.243 4.583 6.633 9.000\n",
" 4.472 4.583 4.899 6.856 9.165\n",
" 5.000 5.099 5.385 7.211 9.434\n",
" 5.657 5.745 6.000 7.681 9.798\n",
"END_DATAGRID_3D\n",
"BEGIN_DATAGRID_3D_UNKNOWN2\n",
" 3 3 3\n",
" 0.5 0.5 0.5\n",
" 5.0 0.0 0.0\n",
" 0.0 5.0 0.0\n",
" 0.0 0.0 5.0\n",
" 0.000 1.000 -3.000 2.000 3.000\n",
" -3.000 -2.000 -2.000 -3.000 4.000\n",
" 5.000 -3.000 6.000 7.000 -3.000\n",
" -2.000 -2.000 -3.000 -1.000 -1.000\n",
" -1.000 -1.000 -1.000 -1.000 -1.000\n",
" -1.000 -1.000\n",
"END_DATAGRID_3D\n",
"END_BLOCK_DATAGRID_3D\n"]
Mol, _ = xsf.parser(name, target)
assert len(Mol) == 2
assert vec_equal(Mol.steps[0].getVolOffset(), [0, 0, 0])
assert vec_equal(Mol.steps[1].getVolOffset(), [0.5, 0.5, 0.5])
assert vec_equal(Mol.getVol(), (((0, 4), (2, 6)),
((1, 5), (3, 7))))
assert vec_equal(Mol.getVolGradient(), 0)
assert Mol.getVolGradient().shape == (3, 2, 2, 2)