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# -*- coding: utf-8 -*-
#
# Copyright (c) 2023, 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 os
import unittest
import numpy
import cclib
from skip import skipForParser
__filedir__ = os.path.realpath(os.path.dirname(__file__))
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 GenericRelaxedScanTest_optdone_bool(unittest.TestCase):
"""Generic relaxed potential energy surface scan unittest."""
datatype = cclib.parser.data.ccData_optdone_bool
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
@skipForParser('Molcas','The parser is still being developed so we skip this test')
def testoptdone(self):
"""Is the optimization finished?"""
assert isinstance(self.data.optdone, bool)
assert self.data.optdone
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
@skipForParser('Molcas','The parser is still being developed so we skip this test')
def testindices(self):
"""Do the indices match the results from geovalues."""
assert self.data.optdone and numpy.all(self.data.geovalues[-1] <= self.data.geotargets)
@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):
"""Does optstatus contain expected values?"""
# The input and final coordinates were at a stationary points.
assert is_optnew(self.data.optstatus[0])
assert is_optdone(self.data.optstatus[0])
assert is_optdone(self.data.optstatus[-1])
class GenericUnrelaxedScanTest(unittest.TestCase):
"""Generic unrelaxed potential energy surface scan unittest."""
# extra indices
extra = 0
@skipForParser("Jaguar", "Not implemented")
def testscannames(self):
assert isinstance(self.data.scannames, list)
@skipForParser("ORCA", "Not implemented")
@skipForParser("Jaguar", "Not implemented")
def testscanenergies(self):
assert isinstance(self.data.scanenergies, list)
# This checks the order of magnitude, and unit conversion if nothing else.
numpy.testing.assert_array_less(numpy.array(self.data.scanenergies), -10000)
@skipForParser("ORCA", "Not implemented")
@skipForParser("Jaguar", "Not implemented")
def testscanparm(self):
assert isinstance(self.data.scanparm, list)
# Each parameters should have as many values as there are scan
# energies, or optimized point on the PES.
for parm in self.data.scanparm:
assert len(parm) == len(self.data.scanenergies)
class GenericRelaxedScanTest(GenericUnrelaxedScanTest):
"""Generic relaxed potential energy surface scan unittest."""
# extra indices
extra = 0
@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):
"""Do the number of indices match number of scan points."""
assert len(self.data.optdone) == 12 + self.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):
"""Do the indices match the results from geovalues."""
indexes = self.data.optdone
geovalues_from_index = self.data.geovalues[indexes]
temp = numpy.all(self.data.geovalues <= self.data.geotargets, axis=1)
geovalues = self.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):
"""Does optstatus contain expected values?"""
# The input coordinates were at a stationary point.
assert is_optdone(self.data.optstatus[0])
assert len(self.data.converged_geometries) == len(self.data.optdone)
for idone in self.data.optdone:
assert is_optdone(self.data.optstatus[idone])
if idone != len(self.data.optstatus) - 1:
assert is_optnew(self.data.optstatus[idone+1])
@skipForParser("Jaguar", "Not implemented")
def testscannames(self):
assert isinstance(self.data.scannames, list)
@skipForParser("Jaguar", "Not implemented")
@skipForParser("ORCA", "Not implemented")
def testscanenergies(self):
assert isinstance(self.data.scanenergies, list)
# This checks the order of magnitude, and unit conversion if nothing else.
numpy.testing.assert_array_less(numpy.array(self.data.scanenergies), -10000)
@skipForParser("Jaguar", "Not implemented")
@skipForParser("ORCA", "Not implemented")
def testscanparm(self):
assert isinstance(self.data.scanparm, list)
# Each parameters should have as many values as there are scan
# energies, or optimized point on the PES.
for parm in self.data.scanparm:
assert len(parm) == len(self.data.scanenergies)
class GaussianUnrelaxedScanTest(GenericUnrelaxedScanTest):
"""Customized unrelaxed potential energy surface scan unittest"""
extra = 1
class GaussianRelaxedScanTest(GenericRelaxedScanTest):
"""Customized relaxed potential energy surface scan unittest"""
extra = 1
class JaguarRelaxedScanTest(GenericRelaxedScanTest):
"""Customized relaxed potential energy surface scan unittest"""
extra = 1
class OrcaRelaxedScanTest(GenericRelaxedScanTest):
"""Customized relaxed potential energy surface scan unittest"""
extra = 1
if __name__=="__main__":
import sys
sys.path.insert(1, os.path.join(__filedir__, ".."))
from test_data import DataSuite
suite = DataSuite(['Scan'])
suite.testall()
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