def test_siesta_zmat():
import os
from ase.calculators.siesta.siesta import Siesta
from ase.constraints import FixAtoms, FixedLine, FixedPlane
from ase import Atoms
pseudo_path = 'pseudos'
if not os.path.exists(pseudo_path): os.makedirs(pseudo_path)
# Make dummy pseudopotentials.
for symbol in 'HCO':
with open('{0}/{1}.lda.psf'.format(pseudo_path, symbol), 'w') as fd:
fd.close()
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0),
(1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = Siesta(label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
assert os.path.isfile(os.path.join(custom_dir, 'C.lda.1.psf'))
assert os.path.isfile(os.path.join(custom_dir, 'O.lda.2.psf'))
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
assert ['cartesian'] in lsl
assert ['%block', 'Zmatrix'] in lsl
assert ['%endblock', 'Zmatrix'] in lsl
assert ['MD.TypeOfRun', 'CG'] in lsl
assert any(
[line.split()[4:9] == ['0', '0', '0', '1', 'C'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '0', '2', 'O'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '1', '3', 'O'] for line in lines])
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"""
species = Species(symbol='C', basis_set=PAOBasisBlock(c_basis))
calc = Siesta(
label='ch4',
basis_set='SZ',
xc='LYP',
mesh_cutoff=300 * Ry,
species=[species],
restart='ch4.XV',
fdf_arguments={
'DM.Tolerance': 1E-5,
'DM.MixingWeight': 0.15,
'DM.NumberPulay': 3,
'MaxSCFIterations': 200,
'ElectronicTemperature': (0.02585, 'eV'), # 300 K
'SaveElectrostaticPotential': True
})
bud.calc = calc
dyn = QuasiNewton(bud, trajectory=traj)
dyn.run(fmax=0.02)
e = bud.get_potential_energy()
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = Siesta(label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
assert os.path.isfile(os.path.join(custom_dir, 'C.lda.1.psf'))
assert os.path.isfile(os.path.join(custom_dir, 'O.lda.2.psf'))
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
assert ['cartesian'] in lsl
assert ['%block', 'Zmatrix'] in lsl
import ase.build
from ase.calculators.siesta.siesta import Siesta
# Test real calculation of the lithium bulk which produced a gapped .EIG file
atoms = ase.build.bulk('Li', cubic=True)
calc = Siesta(kpts=[2,1,1])
atoms.set_calculator(calc)
atoms.get_potential_energy()
assert calc.results['eigenvalues'].shape[:2] == (1, 2) # spins x bands
assert calc.get_k_point_weights().shape == (2,)
assert calc.get_ibz_k_points().shape == (2, 3)
from ase.calculators.calculator import FileIOCalculator
from ase import Atoms
from ase.utils import basestring
# Setup test structures.
h = Atoms('H', [(0.0, 0.0, 0.0)])
co2 = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
ch4 = Atoms('CH4', np.array([
[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]]))
# Test the initialization.
siesta = Siesta()
assert isinstance(siesta, FileIOCalculator)
assert isinstance(siesta.implemented_properties, tuple)
assert isinstance(siesta.default_parameters, dict)
assert isinstance(siesta.name, basestring)
assert isinstance(siesta.default_parameters, dict)
# Test simple fdf-argument case.
atoms = h.copy()
siesta = Siesta(
label='test_label',
fdf_arguments={'DM.Tolerance': 1e-3})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
atoms = h.copy()
atoms.set_calculator(siesta)
def test_siesta():
import numpy as np
from ase.calculators.siesta.siesta import Siesta
from ase.calculators.siesta.parameters import Species, PAOBasisBlock
from ase.calculators.calculator import FileIOCalculator
from ase import Atoms
# Setup test structures.
h = Atoms('H', [(0.0, 0.0, 0.0)])
ch4 = Atoms('CH4', np.array([
[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]]))
# Test the initialization.
siesta = Siesta()
assert isinstance(siesta, FileIOCalculator)
assert isinstance(siesta.implemented_properties, tuple)
assert isinstance(siesta.default_parameters, dict)
assert isinstance(siesta.name, str)
assert isinstance(siesta.default_parameters, dict)
# Test simple fdf-argument case.
atoms = h.copy()
siesta = Siesta(
label='test_label',
fdf_arguments={'DM.Tolerance': 1e-3})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
atoms = h.copy()
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
with open('test_label.fdf', 'r') as fd:
lines = fd.readlines()
assert any([line.split() == ['DM.Tolerance', '0.001'] for line in lines])
# Test (slightly) more complex case of setting fdf-arguments.
siesta = Siesta(
label='test_label',
mesh_cutoff=3000,
fdf_arguments={
'DM.Tolerance': 1e-3,
'ON.eta': (5, 'Ry')})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
atoms = h.copy()
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
with open('test_label.fdf', 'r') as f:
lines = f.readlines()
assert 'MeshCutoff\t3000\teV\n' in lines
assert 'DM.Tolerance\t0.001\n' in lines
assert 'ON.eta\t5\tRy\n' in lines
# Test setting fdf-arguments after initiation.
siesta.set_fdf_arguments(
{'DM.Tolerance': 1e-2,
'ON.eta': (2, 'Ry')})
siesta.write_input(atoms, properties=['energy'])
with open('test_label.fdf', 'r') as f:
lines = f.readlines()
assert 'MeshCutoff\t3000\teV\n' in lines
assert 'DM.Tolerance\t0.01\n' in lines
assert 'ON.eta\t2\tRy\n' in lines
# Test initiation using Species.
atoms = ch4.copy()
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
siesta = Siesta(species=[Species(symbol='C', tag=1)])
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
atoms.set_tags([0, 0, 0, 1, 0])
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
siesta = Siesta(species=[Species(symbol='H', tag=1, basis_set='SZ')])
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 3, 2]))
siesta = Siesta(label='test_label', species=species)
siesta.write_input(atoms, properties=['energy'])
with open('test_label.fdf', 'r') as f:
lines = f.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 ['3', '1', 'H.lda.3'] in lines
assert ['C.lda.1', 'DZP'] in lines
assert ['H.lda.2', 'DZP'] in lines
assert ['H.lda.3', 'SZ'] in lines
# 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 = Siesta(label='test_label', species=[species])
siesta.write_input(atoms, properties=['energy'])
with open('test_label.fdf', 'r') as f:
lines = f.readlines()
lines = [line.split() for line in lines]
assert ['%block', 'PAO.Basis'] in lines
assert ['%endblock', 'PAO.Basis'] in lines
# Setup test structures.
h = Atoms('H', [(0.0, 0.0, 0.0)])
co2 = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
ch4 = Atoms('CH4', np.array([
[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]]))
# Setup required environment variables.
os.environ['SIESTA_PP_PATH'] = '../' + pseudo_path
# Test the initialization.
siesta = Siesta()
assert isinstance(siesta, FileIOCalculator)
assert isinstance(siesta.implemented_properties, tuple)
assert isinstance(siesta.default_parameters, dict)
assert isinstance(siesta.name, str)
assert isinstance(siesta.default_parameters, dict)
# Test simple fdf-argument case.
atoms = h.copy()
siesta = Siesta(
label='test_label',
fdf_arguments={'DM.Tolerance': 1e-3})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
atoms = h.copy()
atoms.set_calculator(siesta)
# Change to test directory.
os.chdir(run_path)
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
# Test simple fdf-argument case.
siesta = Siesta(label='test_label',
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.set_calculator(siesta)
custom_dir = './dir1/'
siesta.set_directory(custom_dir)
siesta.write_input(atoms, properties=['energy'])
assert os.path.isfile(os.path.join(custom_dir, 'C.lda.1.psf'))
assert os.path.isfile(os.path.join(custom_dir, 'O.lda.2.psf'))
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
def __init__(self, *args, **kwargs):
warnings.warn(
"The BaseSiesta calculator class will no longer be supported. "
"Use 'ase.calculators.siesta.Siesta in stead.",
np.VisibleDeprecationWarning)
Siesta.__init__(self, *args, **kwargs)
os.system('touch %s/O.lda.psf' % pseudo_path)
h = Atoms('H', [(0.0, 0.0, 0.0)])
co2 = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
ch4 = Atoms(
'CH4',
np.array([[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]]))
os.chdir(run_path)
os.environ['SIESTA_PP_PATH'] = '../' + pseudo_path
# Test the initialization
siesta = Siesta()
assert isinstance(siesta, FileIOCalculator)
assert isinstance(siesta.implemented_properties, tuple)
assert isinstance(siesta.default_parameters, dict)
assert isinstance(siesta.name, str)
assert isinstance(siesta.default_parameters, dict)
# Test the more complicated species situations
atoms = ch4.copy()
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
siesta = Siesta(species=[Specie(symbol='C', tag=1)])
species, numbers = siesta.species(atoms)
assert all(numbers == np.array([1, 2, 2, 2, 2]))
atoms.set_tags([0, 0, 0, 1, 0])
species, numbers = siesta.species(atoms)