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# Copyright (c) 2024, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test scan logfiles in cclib"""
import cclib
import numpy
import pytest
from skip import skipForParser
OPT_DONE = cclib.parser.data.ccData.OPT_DONE
OPT_NEW = cclib.parser.data.ccData.OPT_NEW
def is_optnew(optstatus_value) -> bool:
return optstatus_value & OPT_NEW == OPT_NEW
def is_optdone(optstatus_value) -> bool:
return optstatus_value & OPT_DONE == OPT_DONE
class GenericUnrelaxedScanTest:
"""Generic unrelaxed potential energy surface scan unittest."""
@pytest.fixture
def extra(self) -> int:
"""extra indices"""
return 0
@skipForParser("Jaguar", "Not implemented")
def testscannames(self, data) -> None:
assert isinstance(data.scannames, list)
@skipForParser("ORCA", "Not implemented")
@skipForParser("Jaguar", "Not implemented")
def testscanenergies(self, data) -> None:
assert isinstance(data.scanenergies, list)
# This checks the order of magnitude, and unit conversion if nothing else.
numpy.testing.assert_array_less(numpy.array(data.scanenergies), -10000)
@skipForParser("ORCA", "Not implemented")
@skipForParser("Jaguar", "Not implemented")
def testscanparm(self, data) -> None:
assert isinstance(data.scanparm, list)
# Each parameters should have as many values as there are scan
# energies, or optimized point on the PES.
for parm in data.scanparm:
assert len(parm) == len(data.scanenergies)
class GenericRelaxedScanTest(GenericUnrelaxedScanTest):
"""Generic relaxed potential energy surface scan unittest."""
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testnumindices(self, data, extra) -> None:
"""Do the number of indices match number of scan points."""
assert len(data.optdone) == 12 + extra
@skipForParser("Jaguar", "Does not work as expected")
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("ORCA", "Does not work as expected")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testindices(self, data) -> None:
"""Do the indices match the results from geovalues."""
indexes = data.optdone
geovalues_from_index = data.geovalues[indexes]
temp = numpy.all(data.geovalues <= data.geotargets, axis=1)
geovalues = data.geovalues[temp]
numpy.testing.assert_array_equal(geovalues, geovalues_from_index)
@skipForParser("Jaguar", "Not implemented")
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("ORCA", "Not implemented")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testoptstatus(self, data) -> None:
"""Does optstatus contain expected values?"""
# The input coordinates were at a stationary point.
assert is_optdone(data.optstatus[0])
assert len(data.converged_geometries) == len(data.optdone)
for idone in data.optdone:
assert is_optdone(data.optstatus[idone])
if idone != len(data.optstatus) - 1:
assert is_optnew(data.optstatus[idone + 1])
@skipForParser("Jaguar", "Not implemented")
def testscannames(self, data) -> None:
assert isinstance(data.scannames, list)
@skipForParser("Jaguar", "Not implemented")
@skipForParser("ORCA", "Not implemented")
def testscanenergies(self, data) -> None:
assert isinstance(data.scanenergies, list)
# This checks the order of magnitude, and unit conversion if nothing else.
numpy.testing.assert_array_less(numpy.array(data.scanenergies), -10000)
@skipForParser("Jaguar", "Not implemented")
@skipForParser("ORCA", "Not implemented")
def testscanparm(self, data) -> None:
assert isinstance(data.scanparm, list)
# Each parameters should have as many values as there are scan
# energies, or optimized point on the PES.
for parm in data.scanparm:
assert len(parm) == len(data.scanenergies)
class GaussianUnrelaxedScanTest(GenericUnrelaxedScanTest):
"""Customized unrelaxed potential energy surface scan unittest"""
@pytest.fixture
def extra(self) -> int:
"""extra indices"""
return 1
class GaussianRelaxedScanTest(GenericRelaxedScanTest):
"""Customized relaxed potential energy surface scan unittest"""
@pytest.fixture
def extra(self) -> int:
"""extra indices"""
return 1
class JaguarRelaxedScanTest(GenericRelaxedScanTest):
"""Customized relaxed potential energy surface scan unittest"""
@pytest.fixture
def extra(self) -> int:
"""extra indices"""
return 1
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