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Minor house-keeping: Define ARC_TESTING_PATH #831

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Merged
ranbenayoun merged 6 commits into from
Feb 9, 2026
+465 −445
Merged

Minor house-keeping: Define ARC_TESTING_PATH #831

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69f99a4
Added ARC's testing folder path to common
alongd Jan 18, 2026
9c86b3c
Use ARC's testing folder in ARC's tests
alongd Jan 18, 2026
7350c87
Minor: Style mod in reaction
alongd Feb 8, 2026
bfd7c4b
Return success from run_arkane()
alongd Feb 8, 2026
abdaba9
Make the install_pyrdl script more flexible
alongd Feb 8, 2026
6b56904
Fix typo in restart functional test
alongd Feb 8, 2026
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24 changes: 12 additions & 12 deletions arc/checks/nmd_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
import numpy as np

import arc.checks.nmd as nmd
from arc.common import ARC_PATH, almost_equal_coords
from arc.common import ARC_PATH, ARC_TESTING_PATH, almost_equal_coords
from arc.job.factory import job_factory
from arc.level import Level
from arc.molecule import Molecule
Expand Down Expand Up @@ -110,7 +110,7 @@ def setUpClass(cls):
H -0.004455 -0.848273 -0.183117
H 1.142454 -0.914148 1.088425""")
cls.rxn_2.ts_species = ARCSpecies(label='TS2', is_ts=True, xyz=cls.ts_2_xyz)
cls.freq_log_path_2 = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'HO2+N2H4_H2O2+N2H3_freq.out')
cls.freq_log_path_2 = os.path.join(ARC_TESTING_PATH, 'freq', 'HO2+N2H4_H2O2+N2H3_freq.out')

cls.displaced_xyz_3 = ({'symbols': ('C', 'N', 'H', 'H', 'H', 'H'), 'isotopes': (13, 14, 1, 1, 1, 1),
'coords': ((1.09466418610, 0.4027481525, -0.40679594165),
Expand Down Expand Up @@ -228,7 +228,7 @@ def setUpClass(cls):
def test_analyze_ts_normal_mode_displacement_simple_rxns(self):
"""Test the analyze_ts_normal_mode_displacement() function with simple reactions."""
# CH4 + OH <=> CH3 + H2O
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'TS_CH4_OH.log')
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'freq', 'TS_CH4_OH.log')
valid = nmd.analyze_ts_normal_mode_displacement(reaction=self.rxn_1,
job=self.generic_job,
amplitude=0.25,
Expand All @@ -246,7 +246,7 @@ def test_analyze_ts_normal_mode_displacement_simple_rxns(self):
self.assertTrue(valid)

# NH2 + N2H3 <=> NH + N2H4:
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'TS_NH2+N2H3.out')
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'freq', 'TS_NH2+N2H3.out')
rxn_3 = ARCReaction(r_species=[ARCSpecies(label='NH2', xyz="""N 0.00000000 -0.00000000 0.14115400
H -0.80516800 0.00000000 -0.49355600
H 0.80516800 -0.00000000 -0.49355600"""),
Expand Down Expand Up @@ -278,7 +278,7 @@ def test_analyze_ts_normal_mode_displacement_simple_rxns(self):
self.assertTrue(valid)

# [CH2]CC=C <=> CCC=[CH] butylene intra H migration:
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'composite',
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'composite',
'TS_butylene_intra_H_migration.out')
rxn_4 = ARCReaction(r_species=[
ARCSpecies(label='butylene',
Expand Down Expand Up @@ -314,7 +314,7 @@ def test_analyze_ts_normal_mode_displacement_simple_rxns(self):
self.assertTrue(valid)

# NCC + H <=> CH3CHNH2 + H2:
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'TS0_composite_2044.out')
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'composite', 'TS0_composite_2044.out')
ea_xyz = """N 1.27511929 -0.21413688 -0.09829069
C 0.04568411 0.51479456 0.24529057
C -1.17314611 -0.39875221 0.01838707
Expand Down Expand Up @@ -345,7 +345,7 @@ def test_analyze_ts_normal_mode_displacement_simple_rxns(self):
self.assertTrue(valid)

# NH3 + H <=> NH2 + H2
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'TS_NH3+H=NH2+H2.out')
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'freq', 'TS_NH3+H=NH2+H2.out')

rxn_6 = ARCReaction(r_species=[ARCSpecies(label='NH3', smiles='N'), ARCSpecies(label='H', smiles='[H]')],
p_species=[ARCSpecies(label='NH2', smiles='[NH2]'), ARCSpecies(label='H2', smiles='[H][H]')])
Expand All @@ -356,7 +356,7 @@ def test_analyze_ts_normal_mode_displacement_simple_rxns(self):

def test_analyze_ts_normal_mode_displacement_correct_and_incorrect_data(self):
"""Test the analyze_ts_normal_mode_displacement() function with correct and incorrect TSs for iC3H7 <=> nC3H7."""
base_path = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'C3H7')
base_path = os.path.join(ARC_TESTING_PATH, 'composite', 'C3H7')
log_file_paths = {'iC3H7': os.path.join(base_path, 'iC3H7.gjf'),
'nC3H7': os.path.join(base_path, 'nC3H7.gjf'),
'TS1': os.path.join(base_path, 'TS1.log'), # an iC3H7-like saddle point
Expand Down Expand Up @@ -411,7 +411,7 @@ def test_analyze_ts_normal_mode_displacement_correct_and_incorrect_data(self):
def test_analyze_ts_normal_mode_displacement_for_hypervalence_nitrogen(self):
"""Test the analyze_ts_normal_mode_displacement() function for a hypervalence nitrogen."""
# C2H5NO2 <=> C2H5ONO
self.generic_job.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'C2H5NO2__C2H5ONO.out')
self.generic_job.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'composite', 'C2H5NO2__C2H5ONO.out')
valid = nmd.analyze_ts_normal_mode_displacement(reaction=self.rxn_3,
job=self.generic_job,
amplitude=0.25,
Expand Down Expand Up @@ -561,7 +561,7 @@ def test_get_bond_length_in_reaction(self):

def test_classic_intra_h_migration_through_all_major_functions(self):
"""Test the intermediate stages the nmd module takes for processing the classic intra H migration reaction."""
xyz_path = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'C3H7', 'TS3.log')
xyz_path = os.path.join(ARC_TESTING_PATH, 'composite', 'C3H7', 'TS3.log')
standard_ts_orientation_xyz = check_xyz_dict(xyz_path)
freqs, nmd_array = parse_normal_mode_displacement(xyz_path)
self.assertAlmostEqual(float(freqs[0]), -1927.862, 2)
Expand Down Expand Up @@ -626,9 +626,9 @@ def test_classic_intra_h_migration_through_all_major_functions(self):
self.assertAlmostEqual(reactive_bonds_diffs[1], 1.52941596, places=5)

rxn = ARCReaction(r_species=[ARCSpecies(label='iC3H7', smiles='C[CH]C',
xyz=os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'C3H7', 'iC3H7.gjf'))],
xyz=os.path.join(ARC_TESTING_PATH, 'composite', 'C3H7', 'iC3H7.gjf'))],
p_species=[ARCSpecies(label='nC3H7', smiles='[CH2]CC',
xyz=os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'C3H7', 'nC3H7.gjf'))])
xyz=os.path.join(ARC_TESTING_PATH, 'composite', 'C3H7', 'nC3H7.gjf'))])
rxn.ts_species = ARCSpecies(label='TS', is_ts=True, xyz=xyz_path)
r_bonds, _ = rxn.get_bonds(r_bonds_only=True)
non_reactive_bonds = list()
Expand Down
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