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import os
import pytest
import numpy as np
import ase
import ase.lattice.cubic
from ase.calculators.castep import (Castep, CastepOption,
CastepParam, CastepCell,
make_cell_dict, make_param_dict,
CastepKeywords)
calc = pytest.mark.calculator
# We use 'fake keywords' to test all the generic CastepOptions and
# whether they work
kw_types = ['Real', 'String', 'Defined', 'Integer Vector',
'Boolean (Logical)', 'Integer', 'Real Vector',
'Block', 'Physical']
kw_levels = ['Dummy', 'Intermediate', 'Expert', 'Basic']
@pytest.fixture
def testing_keywords():
kw_data = {}
for kwt in kw_types:
kwtlow = kwt.lower().replace(' ', '_')
if 'Boolean' in kwt:
kwtlow = 'boolean'
kw = 'test_{0}_kw'.format(kwtlow)
kw_data[kw] = {
'docstring': 'A fake {0} keyword'.format(kwt),
'option_type': kwt,
'keyword': kw,
'level': 'Dummy'
}
# Add the special ones for cell and param that have custom parsers
# Special keywords for the CastepParam object
param_kws = [('continuation', 'String'), ('reuse', 'String')]
param_kw_data = {}
for (pkw, t) in param_kws:
param_kw_data[pkw] = {
'docstring': 'Dummy {0} keyword'.format(pkw),
'option_type': t,
'keyword': pkw,
'level': 'Dummy'
}
param_kw_data.update(kw_data)
# Special keywords for the CastepCell object
cell_kws = [('species_pot', 'Block'),
('symmetry_ops', 'Block'),
('positions_abs_intermediate', 'Block'),
('positions_abs_product', 'Block'),
('positions_frac_intermediate', 'Block'),
('positions_frac_product', 'Block'),
('kpoint_mp_grid', 'Integer Vector'),
('kpoint_mp_offset', 'Real Vector'),
('kpoint_list', 'Block'),
('bs_kpoint_list', 'Block')]
cell_kw_data = {}
for (ckw, t) in cell_kws:
cell_kw_data[ckw] = {
'docstring': 'Dummy {0} keyword'.format(ckw),
'option_type': t,
'keyword': ckw,
'level': 'Dummy'
}
cell_kw_data.update(kw_data)
param_dict = make_param_dict(param_kw_data)
cell_dict = make_cell_dict(cell_kw_data)
return CastepKeywords(param_dict, cell_dict, kw_types, kw_levels,
'Castep v.Fake')
@pytest.fixture
def pspot_tmp_path(tmp_path):
path = os.path.join(tmp_path, 'ppots')
os.mkdir(path)
for el in ase.data.chemical_symbols:
with open(os.path.join(path, '{0}_test.usp'.format(el)), 'w') as fd:
fd.write('Fake PPOT')
return path
@pytest.fixture
def testing_calculator(testing_keywords, tmp_path, pspot_tmp_path):
castep_path = os.path.join(tmp_path, 'CASTEP')
os.mkdir(castep_path)
return Castep(castep_keywords=testing_keywords, directory=castep_path,
castep_pp_path=pspot_tmp_path)
def test_fundamental_params():
# Start by testing the fundamental parts of a CastepCell/CastepParam object
boolOpt = CastepOption('test_bool', 'basic', 'defined')
boolOpt.value = 'TRUE'
assert boolOpt.raw_value is True
float3Opt = CastepOption('test_float3', 'basic', 'real vector')
float3Opt.value = '1.0 2.0 3.0'
assert np.isclose(float3Opt.raw_value, [1, 2, 3]).all()
# Generate a mock keywords object
mock_castep_keywords = CastepKeywords(make_param_dict(), make_cell_dict(),
[], [], 0)
mock_cparam = CastepParam(mock_castep_keywords, keyword_tolerance=2)
mock_ccell = CastepCell(mock_castep_keywords, keyword_tolerance=2)
# Test special parsers
mock_cparam.continuation = 'default'
with pytest.warns(UserWarning):
mock_cparam.reuse = 'default'
assert mock_cparam.reuse.value is None
mock_ccell.species_pot = ('Si', 'Si.usp')
mock_ccell.species_pot = ('C', 'C.usp')
assert 'Si Si.usp' in mock_ccell.species_pot.value
assert 'C C.usp' in mock_ccell.species_pot.value
symops = (np.eye(3)[None], np.zeros(3)[None])
mock_ccell.symmetry_ops = symops
assert """1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.0 0.0 0.0""" == mock_ccell.symmetry_ops.value.strip()
def test_castep_option(testing_keywords):
# check if the CastepOption assignment and comparison mechanisms work
p1 = CastepParam(testing_keywords)
p2 = CastepParam(testing_keywords)
assert p1._options == p2._options
# Set some values
p1.test_real_kw = 3.0
p1.test_string_kw = 'PBE'
p1.test_defined_kw = True
p1.test_integer_kw = 10
p1.test_integer_vector_kw = [3, 3, 3]
p1.test_real_vector_kw = [3.0, 3.0, 3.0]
p1.test_boolean_kw = False
p1.test_physical_kw = '3.0 ang'
assert p1.test_real_kw.value == '3.0'
assert p1.test_string_kw.value == 'PBE'
assert p1.test_defined_kw.value == 'TRUE'
assert p1.test_integer_kw.value == '10'
assert p1.test_integer_vector_kw.value == '3 3 3'
assert p1.test_real_vector_kw.value == '3.0 3.0 3.0'
assert p1.test_boolean_kw.value == 'FALSE'
assert p1.test_physical_kw.value == '3.0 ang'
assert p1._options != p2._options
def test_castep_cell(testing_keywords):
ccell = CastepCell(testing_keywords, keyword_tolerance=2)
# Here we test the special keywords exclusive to cell
# 1. species_pot
ccell.species_pot = ('H', 'H_test.usp') # Setting with a single value
assert ccell.species_pot.value == """
H H_test.usp"""
ccell.species_pot = [('H', 'H_test.usp'), ('He', 'He_test.usp')] # Two
assert ccell.species_pot.value == """
H H_test.usp
He He_test.usp"""
# 2. symmetry_ops
# Create for example the P-1 spacegroup
R = np.array([np.eye(3), -np.eye(3)])
T = np.zeros((2, 3))
ccell.symmetry_ops = (R, T)
strblock = [l.strip() for l in ccell.symmetry_ops.value.split('\n')
if l.strip() != '']
fblock = np.array([list(map(float, l.split())) for l in strblock])
assert np.isclose(fblock[:3], R[0]).all()
assert np.isclose(fblock[3], T[0]).all()
assert np.isclose(fblock[4:7], R[1]).all()
assert np.isclose(fblock[7], T[1]).all()
# 3. transition state blocks (postponed until fix is merged)
a = ase.Atoms('H', positions=[[0, 0, 1]], cell=np.eye(3) * 2)
ccell.positions_abs_product = a
ccell.positions_abs_intermediate = a
def parse_posblock(pblock, has_units=False):
lines = pblock.split('\n')
units = None
if has_units:
units = lines.pop(0).strip()
pos_lines = []
while len(lines) > 0:
l = lines.pop(0).strip()
if l == '':
continue
el, x, y, z = l.split()
xyz = np.array(list(map(float, [x, y, z])))
pos_lines.append((el, xyz))
return units, pos_lines
pap = parse_posblock(ccell.positions_abs_product.value, True)
pai = parse_posblock(ccell.positions_abs_intermediate.value, True)
assert pap[0] == 'ang'
assert pap[1][0][0] == 'H'
assert np.isclose(pap[1][0][1], a.get_positions()[0]).all()
assert pai[0] == 'ang'
assert pai[1][0][0] == 'H'
assert np.isclose(pai[1][0][1], a.get_positions()[0]).all()
ccell.positions_frac_product = a
ccell.positions_frac_intermediate = a
pfp = parse_posblock(ccell.positions_frac_product.value)
pfi = parse_posblock(ccell.positions_frac_intermediate.value)
assert pfp[1][0][0] == 'H'
assert np.isclose(pfp[1][0][1], a.get_scaled_positions()[0]).all()
assert pfi[1][0][0] == 'H'
assert np.isclose(pfi[1][0][1], a.get_scaled_positions()[0]).all()
# Test example conflict
ccell.kpoint_mp_grid = '3 3 3'
with pytest.warns(UserWarning):
ccell.kpoint_mp_spacing = 10.0
def test_castep_param(testing_keywords):
cparam = CastepParam(testing_keywords, keyword_tolerance=2)
# Special keywords for param
# 1. continuation and reuse
cparam.continuation = True
with pytest.warns(UserWarning):
cparam.reuse = False # This conflicts with the previous one
cparam.continuation = None
cparam.reuse = True
with pytest.warns(UserWarning):
cparam.continuation = True # This conflicts with the previous one
# Test conflict
cparam.cut_off_energy = 500
with pytest.warns(UserWarning):
cparam.basis_precision = 'FINE'
def test_workflow(testing_calculator):
c = testing_calculator
c._build_missing_pspots = False
c._find_pspots = True
c.set_label('test_label_pspots')
atoms = ase.build.bulk('Ag')
atoms.calc = c
# Should find them automatically!
c._fetch_pspots()
assert os.path.isfile(os.path.join(c._directory, 'Ag_test.usp'))
# Try creating input files
c.prepare_input_files()
assert os.path.isfile(os.path.join(c._directory, c._label + '.cell'))
assert os.path.isfile(os.path.join(c._directory, c._label + '.param'))
def test_set_kpoints(testing_calculator):
c = testing_calculator
c.set_kpts([(0.0, 0.0, 0.0, 1.0)])
assert c.cell.kpoint_list.value == '0.0 0.0 0.0 1.0'
c.set_kpts(((0.0, 0.0, 0.0, 0.25), (0.25, 0.25, 0.3, 0.75)))
assert (c.cell.kpoint_list.value ==
'0.0 0.0 0.0 0.25\n0.25 0.25 0.3 0.75')
c.set_kpts(c.cell.kpoint_list.value.split('\n'))
assert (c.cell.kpoint_list.value ==
'0.0 0.0 0.0 0.25\n0.25 0.25 0.3 0.75')
c.set_kpts([3, 3, 2])
assert c.cell.kpoint_mp_grid.value == '3 3 2'
c.set_kpts(None)
assert c.cell.kpoints_list.value is None
assert c.cell.kpoint_list.value is None
assert c.cell.kpoint_mp_grid.value is None
c.set_kpts('2 2 3')
assert c.cell.kpoint_mp_grid.value == '2 2 3'
c.set_kpts({'even': True, 'gamma': True})
assert c.cell.kpoint_mp_grid.value == '2 2 2'
assert c.cell.kpoint_mp_offset.value == '0.25 0.25 0.25'
c.set_kpts({'size': (2, 2, 4), 'even': False})
assert c.cell.kpoint_mp_grid.value == '3 3 5'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
atoms = ase.build.bulk('Ag')
atoms.calc = c
c.set_kpts({'density': 10, 'gamma': False, 'even': None})
assert c.cell.kpoint_mp_grid.value == '27 27 27'
assert c.cell.kpoint_mp_offset.value == '0.018519 0.018519 0.018519'
c.set_kpts({'spacing': (1 / (np.pi * 10)),
'gamma': False, 'even': True})
assert c.cell.kpoint_mp_grid.value == '28 28 28'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
def test_band_structure_setup(testing_calculator):
c = testing_calculator
from ase.dft.kpoints import BandPath
atoms = ase.build.bulk('Ag')
bp = BandPath(cell=atoms.cell,
path='GX',
special_points={'G': [0, 0, 0], 'X': [0.5, 0, 0.5]})
bp = bp.interpolate(npoints=10)
c.set_bandpath(bp)
kpt_list = c.cell.bs_kpoint_list.value.split('\n')
assert len(kpt_list) == 10
assert list(map(float, kpt_list[0].split())) == [0., 0., 0.]
assert list(map(float, kpt_list[-1].split())) == [0.5, 0.0, 0.5]
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