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(None):
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_interface():
"""Simple shallow test of the CASTEP interface"""
import os
import re
import tempfile
import warnings
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,
create_castep_keywords,
import_castep_keywords,
CastepVersionError)
# XXX on porting this test to pytest it wasn't skipped as it should be.
# At any rate it failed then. Maybe someone should look into that ...
#
# Hence, call the constructor to trigger our test skipping hack:
Castep()
tmp_dir = tempfile.mkdtemp()
# We have fundamentally two sets of tests: one if CASTEP is present, the other
# if it isn't
has_castep = False
# Try creating and importing the castep keywords first
try:
create_castep_keywords(castep_command=os.environ['CASTEP_COMMAND'],
path=tmp_dir,
fetch_only=20)
has_castep = True # If it worked, it must be present
except KeyError:
print('Could not find the CASTEP_COMMAND environment variable - please'
' set it to run the full set of Castep tests')
except CastepVersionError:
print(
'Invalid CASTEP_COMMAND provided - please set the correct one to '
'run the full set of Castep tests')
try:
castep_keywords = import_castep_keywords(
castep_command=os.environ.get('CASTEP_COMMAND', ''))
except CastepVersionError:
castep_keywords = None
# 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'
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""" in mock_ccell.symmetry_ops.value
# check if the CastepOpt, CastepCell comparison mechanism works
if castep_keywords:
p1 = CastepParam(castep_keywords)
p2 = CastepParam(castep_keywords)
assert p1._options == p2._options
p1._options['xc_functional'].value = 'PBE'
p1.xc_functional = 'PBE'
assert p1._options != p2._options
c = Castep(directory=tmp_dir, label='test_label', keyword_tolerance=2)
if castep_keywords:
c.xc_functional = 'PBE'
else:
c.param.xc_functional = 'PBE' # In "forgiving" mode, we need to specify
lattice = ase.lattice.cubic.BodyCenteredCubic('Li')
print('For the sake of evaluating this test, warnings')
print('about auto-generating pseudo-potentials are')
print('normal behavior and can be safely ignored')
lattice.calc = c
param_fn = os.path.join(tmp_dir, 'myParam.param')
with open(param_fn, 'w') as param:
param.write('XC_FUNCTIONAL : PBE #comment\n')
param.write('XC_FUNCTIONAL : PBE #comment\n')
param.write('#comment\n')
param.write('CUT_OFF_ENERGY : 450.\n')
c.merge_param(param_fn)
assert c.calculation_required(lattice)
if has_castep:
assert c.dryrun_ok()
c.prepare_input_files(lattice)
# detecting pseudopotentials tests
# typical filenames
files = [
'Ag_00PBE.usp', 'Ag_00.recpot', 'Ag_C18_PBE_OTF.usp',
'ag-optgga1.recpot', 'Ag_OTF.usp', 'ag_pbe_v1.4.uspp.F.UPF',
'Ni_OTF.usp', 'fe_pbe_v1.5.uspp.F.UPF', 'Cu_01.recpot'
]
pp_path = os.path.join(tmp_dir, 'test_pp')
os.makedirs(pp_path)
for f in files:
with open(os.path.join(pp_path, f), 'w') as _f:
_f.write('DUMMY PP')
c = Castep(directory=tmp_dir,
label='test_label_pspots',
castep_pp_path=pp_path)
c._pedantic = True
atoms = ase.build.bulk('Ag')
atoms.calc = c
# I know, unittest would be nicer... maybe at a later point
# disabled, but may be useful still
# try:
# # this should yield no files
# atoms.calc.find_pspots(suffix='uspp')
# raise AssertionError
# # this should yield no files
# atoms.calc.find_pspots(suffix='uspp')
# raise AssertionError
# except RuntimeError as e:
# #print(e)
# pass
# # print(e)
# pass
try:
# this should yield non-unique files
atoms.calc.find_pspots(suffix='recpot')
raise AssertionError
except RuntimeError:
pass
# now let's see if we find all...
atoms.calc.find_pspots(pspot='00PBE', suffix='usp')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_00PBE.usp'
atoms.calc.find_pspots(pspot='00', suffix='recpot')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_00.recpot'
atoms.calc.find_pspots(pspot='C18_PBE_OTF', suffix='usp')
assert atoms.calc.cell.species_pot.value.split(
)[-1] == 'Ag_C18_PBE_OTF.usp'
atoms.calc.find_pspots(pspot='optgga1', suffix='recpot')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'ag-optgga1.recpot'
atoms.calc.find_pspots(pspot='OTF', suffix='usp')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_OTF.usp'
atoms.calc.find_pspots(suffix='UPF')
assert (atoms.calc.cell.species_pot.value.split()[-1] ==
'ag_pbe_v1.4.uspp.F.UPF')
# testing regular workflow
c = Castep(directory=tmp_dir,
label='test_label_pspots',
castep_pp_path=pp_path,
find_pspots=True,
keyword_tolerance=2)
c._build_missing_pspots = False
atoms = ase.build.bulk('Ag')
atoms.calc = c
# this should raise an error due to ambuiguity
try:
c._fetch_pspots()
raise AssertionError
except RuntimeError:
pass
for e in ['Ni', 'Fe', 'Cu']:
atoms = ase.build.bulk(e)
atoms.calc = c
c._fetch_pspots()
# test writing to file
tmp_dir = os.path.join(tmp_dir, 'input_files')
c = Castep(directory=tmp_dir,
find_pspots=True,
castep_pp_path=pp_path,
keyword_tolerance=2)
c._label = 'test'
atoms = ase.build.bulk('Cu')
atoms.calc = c
c.prepare_input_files()
with open(os.path.join(tmp_dir, 'test.cell'), 'r') as f:
assert re.search(r'Cu Cu_01\.recpot',
''.join(f.readlines())) is not None
# test keyword conflict management
c = Castep(cut_off_energy=300.)
assert float(c.param.cut_off_energy.value) == 300.0
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
c.basis_precision = 'MEDIUM'
assert issubclass(w[-1].category, UserWarning)
assert "conflicts" in str(w[-1].message)
assert c.param.cut_off_energy.value is None
assert c.param.basis_precision.value.strip() == 'MEDIUM'
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
c.cut_off_energy = 200.0
assert c.param.basis_precision.value is None
assert issubclass(w[-1].category, UserWarning)
assert 'option "cut_off_energy" conflicts' in str(w[-1].message)
# test kpoint setup options
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# This block of tests is going to generate a lot of conflict warnings.
# We already tested that those work, so just hide them from the output.
c = Castep(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'
# test band structure setup
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 = Castep(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]
castep_keywords = None
# Start by testing the fundamental parts of a CastepCell/CastepParam object
boolOpt = CastepOption('test_bool', 'basic', 'defined')
boolOpt.value = 'TRUE'
assert boolOpt.raw_value == 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'
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
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