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# fmt: off
"""
test_gaussian_gjf_input.py, Geoffrey Weal, 23/5/24
This will test the read input for gjf files
Notes
-----
* 23/5/24 -> Wrote test for testing the charge and mutliplicity inputs.
"""
import warnings
from io import StringIO
import pytest
from ase.calculators.calculator import compare_atoms
from ase.io import ParseError, read
# -----------------------------------------------------------
# The following strings give the components of an example gif file
# for two methane molecules.
# The input line of the gjf file.
ORIGINAL_GJF_FILE_PREFIX = """%chk=Preview_s6ozz.chk
# opt freq wb97xd/cc-pvqz geom=connectivity
Title Card Required
"""
# Provide an example of two methane molecules.
ORIGINAL_GJF_FILE_SUFFIX = """
C 0.96604221 0.36299765 0.00000000
H 1.32269663 -0.64581235 0.00000000
H 1.32271505 0.86739584 0.87365150
H 1.32271505 0.86739584 -0.87365150
H -0.10395779 0.36301084 0.00000000
C -4.67798621 -1.41686181 0.00000000
H -4.32133178 -2.42567181 0.00000000
H -4.32131337 -0.91246362 0.87365150
H -4.32131337 -0.91246362 -0.87365150
H -5.74798621 -1.41684862 0.00000000"""
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Provide an example of two methane molecules, which have been identified
# as different fragment.
FRAGMENT_GJF_FILE_SUFFIX = """
C(Fragment=1) 0.96604221 0.36299765 0.00000000
H(Fragment=1) 1.32269663 -0.64581235 0.00000000
H(Fragment=1) 1.32271505 0.86739584 0.87365150
H(Fragment=1) 1.32271505 0.86739584 -0.87365150
H(Fragment=1) -0.10395779 0.36301084 0.00000000
C(Fragment=2) -4.67798621 -1.41686181 0.00000000
H(Fragment=2) -4.32133178 -2.42567181 0.00000000
H(Fragment=2) -4.32131337 -0.91246362 0.87365150
H(Fragment=2) -4.32131337 -0.91246362 -0.87365150
H(Fragment=2) -5.74798621 -1.41684862 0.00000000"""
# -----------------------------------------------------------
# This is the original charge and multiplicity format.
ORIGINAL_CHARGE_MULTIPLICITY = "0 1"
# This is the fragment charge and multiplicity format that should work.
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_1 = '0 1'
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_2 = '0 1 0 1 0 1'
# This is the fragment charge and multiplicity format that should work, even
# if it wont make sense to Gaussian. But for ASE, this is fine, as ASE
# currently only reads in the total charge and the total multiplicity for
# the total system, which is given by the first two digits in this line.
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_3 = '0 1 0 1'
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_4 = '0 1 0 1 0 1 0 1'
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# This is the original Gaussian file that should fail.
ORIGINAL_CHARGE_MULTIPLICITY_FAIL_1 = ' '
ORIGINAL_CHARGE_MULTIPLICITY_FAIL_2 = '0 '
# These are the fragment charge and multiplcities that should fail.
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_1 = '0 '
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_2 = '0 1 0'
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_3 = '0 1 0 1 0'
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_4 = '0 1 0 1 0 1 0'
# -----------------------------------------------------------
def _quiet_parse(input_string):
"""Contains the code for reading in the Gaussian input file into ASE."""
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
return read(StringIO(input_string), format="gaussian-in")
@pytest.fixture()
def reference_system():
"""This is the reference system to compare tests to."""
return _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
ORIGINAL_CHARGE_MULTIPLICITY +
ORIGINAL_GJF_FILE_SUFFIX)
# -----------------------------------------------------------
def test_original_gjf_success(reference_system):
"""Test to make sure an example gjf file that has been written
correctly is being read in correctly."""
atoms = _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
ORIGINAL_CHARGE_MULTIPLICITY +
ORIGINAL_GJF_FILE_SUFFIX)
assert compare_atoms(atoms, reference_system) == []
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def test_fragment_gjf_success_1(reference_system):
"""Test to make sure the first example gjf file that has been written
correctly and contains fragments is being read in correctly."""
atoms = _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_1 +
FRAGMENT_GJF_FILE_SUFFIX)
assert compare_atoms(atoms, reference_system) == []
def test_fragment_gjf_success_2(reference_system):
"""Test to make sure the second example gjf file that has been written
correctly and contains fragments is being read in correctly."""
atoms = _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_2 +
FRAGMENT_GJF_FILE_SUFFIX)
assert compare_atoms(atoms, reference_system) == []
def test_fragment_gjf_success_3(reference_system):
"""Test to make sure the third example gjf file that has been written
correctly and contains fragments is being read in correctly."""
atoms = _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_3 +
FRAGMENT_GJF_FILE_SUFFIX)
assert compare_atoms(atoms, reference_system) == []
def test_fragment_gjf_success_4(reference_system):
"""Test to make sure the fourth example gjf file that has been written
correctly and contains fragments is being read in correctly."""
atoms = _quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_SUCCESS_4 +
FRAGMENT_GJF_FILE_SUFFIX)
assert compare_atoms(atoms, reference_system) == []
# -----------------------------------------------------------
def test_original_gjf_fail_1():
"""Test to make sure the first example gjf file that is expected to fail
does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
ORIGINAL_CHARGE_MULTIPLICITY_FAIL_1 +
ORIGINAL_GJF_FILE_SUFFIX)
def test_original_gjf_fail_2():
"""Test to make sure the second example gjf file that is expected to fail
does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
ORIGINAL_CHARGE_MULTIPLICITY_FAIL_2 +
ORIGINAL_GJF_FILE_SUFFIX)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def test_fragment_gjf_fail_1():
"""Test to make sure the first example gjf file that is expected to fail
and contains fragments does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_1 +
FRAGMENT_GJF_FILE_SUFFIX)
def test_fragment_gjf_fail_2():
"""Test to make sure the second example gjf file that is expected to fail
and contains fragments does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_2 +
FRAGMENT_GJF_FILE_SUFFIX)
def test_fragment_gjf_fail_3():
"""Test to make sure the third example gjf file that is expected to fail
and contains fragments does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_3 +
FRAGMENT_GJF_FILE_SUFFIX)
def test_fragment_gjf_fail_4():
"""Test to make sure the fourth example gjf file that is expected to fail
and contains fragments does infact fail based on the ParseError."""
with pytest.raises(ParseError):
_quiet_parse(ORIGINAL_GJF_FILE_PREFIX +
FRAGMENT_CHARGE_MULTIPLICITY_FAIL_4 +
FRAGMENT_GJF_FILE_SUFFIX)
# -----------------------------------------------------------
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