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# fmt: off
"""Test write_input"""
import numpy as np
import pytest
from ase import Atoms
from ase.calculators.siesta.parameters import PAOBasisBlock, Species
@pytest.fixture(name="atoms_h")
def fixture_atoms_h():
"""hydrogen atom"""
return Atoms('H', [(0.0, 0.0, 0.0)])
@pytest.fixture(name="atoms_ch4")
def fixture_atoms_ch4():
"""methane molecule"""
positions = [
[0.000000, 0.000000, 0.000000],
[0.682793, 0.682793, 0.682793],
[-0.682793, -0.682793, 0.682790],
[-0.682793, 0.682793, -0.682793],
[0.682793, -0.682793, -0.682793],
]
return Atoms('CH4', positions)
@pytest.mark.calculator_lite()
@pytest.mark.calculator('siesta')
def test_simple(factory, atoms_h):
"""Test simple fdf-argument case."""
siesta = factory.calc(
label='test_label',
fdf_arguments={'DM.Tolerance': 1e-3})
atoms_h.calc = siesta
siesta.write_input(atoms_h, properties=['energy'])
with open('test_label.fdf', encoding='utf-8') as fd:
lines = fd.readlines()
assert any(line.split() == ['DM.Tolerance', '0.001'] for line in lines)
@pytest.mark.calculator_lite()
@pytest.mark.calculator('siesta')
def test_complex(factory, atoms_h):
"""Test (slightly) more complex case of setting fdf-arguments."""
siesta = factory.calc(
label='test_label',
mesh_cutoff=3000,
fdf_arguments={
'DM.Tolerance': 1e-3,
'ON.eta': (5, 'Ry')})
atoms_h.calc = siesta
siesta.write_input(atoms_h, properties=['energy'])
with open('test_label.fdf', encoding='utf-8') as fd:
lines = fd.readlines()
assert 'MeshCutoff\t3000\teV\n' in lines
assert 'DM.Tolerance\t0.001\n' in lines
assert 'ON.eta\t5\tRy\n' in lines
@pytest.mark.calculator_lite()
@pytest.mark.calculator('siesta')
def test_set_fdf_arguments(factory, atoms_h):
"""Test setting fdf-arguments after initiation."""
siesta = factory.calc(
label='test_label',
mesh_cutoff=3000,
fdf_arguments={
'DM.Tolerance': 1e-3,
'ON.eta': (5, 'Ry')})
siesta.set_fdf_arguments(
{'DM.Tolerance': 1e-2,
'ON.eta': (2, 'Ry')})
siesta.write_input(atoms_h, properties=['energy'])
with open('test_label.fdf', encoding='utf-8') as fd:
lines = fd.readlines()
assert 'MeshCutoff\t3000\teV\n' in lines
assert 'DM.Tolerance\t0.01\n' in lines
assert 'ON.eta\t2\tRy\n' in lines
@pytest.mark.calculator_lite()
@pytest.mark.calculator('siesta')
def test_species(factory, atoms_ch4):
"""Test initiation using Species."""
siesta = factory.calc()
species, numbers = siesta.species(atoms_ch4)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
siesta = factory.calc(species=[Species(symbol='C', tag=1)])
species, numbers = siesta.species(atoms_ch4)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
atoms_ch4.set_tags([0, 0, 0, 1, 0])
species, numbers = siesta.species(atoms_ch4)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
siesta = factory.calc(
species=[
Species(symbol='C', tag=-1),
Species(
symbol='H',
tag=1,
basis_set='SZ',
pseudopotential='somepseudo')])
species, numbers = siesta.species(atoms_ch4)
assert all(numbers == np.array([1, 2, 2, 4, 2]))
siesta = factory.calc(label='test_label', species=species)
siesta.write_input(atoms_ch4, properties=['energy'])
with open('test_label.fdf', encoding='utf-8') as fd:
lines = fd.readlines()
lines = [line.split() for line in lines]
assert ['1', '6', 'C.lda.1'] in lines
assert ['2', '1', 'H.lda.2'] in lines
assert ['4', '1', 'H.4', 'H.4.psml'] in lines
assert ['C.lda.1', 'DZP'] in lines
assert ['H.lda.2', 'DZP'] in lines
assert ['H.4', 'SZ'] in lines
@pytest.mark.calculator_lite()
@pytest.mark.calculator('siesta')
def test_pao_block(factory, atoms_ch4):
"""Test if PAO block can be given as species."""
c_basis = """2 nodes 1.00
0 1 S 0.20 P 1 0.20 6.00
5.00
1.00
1 2 S 0.20 P 1 E 0.20 6.00
6.00 5.00
1.00 0.95"""
basis_set = PAOBasisBlock(c_basis)
species = Species(symbol='C', basis_set=basis_set)
siesta = factory.calc(label='test_label', species=[species])
siesta.write_input(atoms_ch4, properties=['energy'])
with open('test_label.fdf', encoding='utf-8') as fd:
lines = fd.readlines()
lines = [line.split() for line in lines]
assert ['%block', 'PAO.Basis'] in lines
assert ['%endblock', 'PAO.Basis'] in lines
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