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Tests: libraries util
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@alongd
alongd committed May 18, 2024
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158 changes: 158 additions & 0 deletions tests/test_libraries.py
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#!/usr/bin/env python3
# encoding: utf-8

"""
t3 tests test_libraries module
"""

import os
import shutil

from rmgpy.data.thermo import ThermoLibrary
from rmgpy.species import Species
from rmgpy.thermo import ThermoData
from rmgpy.statmech import Conformer, IdealGasTranslation, NonlinearRotor, HarmonicOscillator

from t3.common import DATA_BASE_PATH
from tests.common import run_minimal
from t3.utils.libraries import add_to_rmg_libraries


def test_add_to_rmg_library():
"""Test adding thermo calculations to an existing thermo library"""
libraries_path = os.path.join(DATA_BASE_PATH, 'libraries')
if not os.path.isdir(libraries_path):
os.makedirs(libraries_path)

spc_1 = Species(
index=1,
label='C2H4',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-20.0, 'kcal/mol'),
S298=(50.0, 'cal/(mol*K)'),
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
HarmonicOscillator(frequencies=([834.50, 973.31, 975.37, 1067.1, 1238.5, 1379.5, 1472.3, 1691.3,
3121.6, 3136.7, 3192.5, 3221.0], 'cm^-1')),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='C=C',
)

spc_2 = Species(
index=2,
label='CH4',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-50.0, 'kcal/mol'),
S298=(100.0, 'cal/(mol*K)'),
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='C',
)

spc_3 = Species(
index=2,
label='C3H7',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-92.0, 'kcal/mol'), # this is different
S298=(12.0, 'cal/(mol*K)'), # this is different
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='[CH2]CC',
)

# 1. Test adding one species to an existing library.
for lib_name, spc_list in [('RMG_library', [spc_1, spc_2]), ('ARC_library', [spc_3])]:
thermo_library = ThermoLibrary(name=lib_name, long_desc=lib_name)
for i, spc in enumerate(spc_list):
thermo_library.load_entry(index=i,
label=spc.label,
molecule=spc.to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.label,
longDesc=spc.label)
thermo_library.save(os.path.join(libraries_path, f'{lib_name}.py'))

t3 = run_minimal()
t3.set_paths()
t3.paths['ARC thermo lib'] = os.path.join(libraries_path, 'ARC_library.py')
t3.paths['T3 thermo lib'] = os.path.join(libraries_path, 'RMG_library.py')
add_to_rmg_libraries(library_name=t3.t3['options']['library_name'],
shared_library_name=t3.t3['options']['shared_library_name'],
paths=t3.paths,
logger=t3.logger)
with open(t3.paths['T3 thermo lib'], 'r') as f:
lines = f.readlines()
for line in [" H298 = (-92,'kcal/mol'),\n",
" S298 = (12,'cal/(mol*K)'),\n",
]:
assert line in lines

# 2. Test adding one species to an existing library when the new library has a species that also exists.
for lib_name, spc_list in [('RMG_library', [spc_1, spc_2]), ('ARC_library', [spc_1, spc_3])]:
thermo_library = ThermoLibrary(name=lib_name, long_desc=lib_name)
for i, spc in enumerate(spc_list):
thermo_library.load_entry(index=i,
label=spc.label,
molecule=spc.to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.label,
longDesc=spc.label)
thermo_library.save(os.path.join(libraries_path, f'{lib_name}.py'))

t3 = run_minimal()
t3.set_paths()
t3.paths['ARC thermo lib'] = os.path.join(libraries_path, 'ARC_library.py')
t3.paths['T3 thermo lib'] = os.path.join(libraries_path, 'RMG_library.py')
add_to_rmg_libraries(library_name=t3.t3['options']['library_name'],
shared_library_name=t3.t3['options']['shared_library_name'],
paths=t3.paths,
logger=t3.logger)
with open(t3.paths['T3 thermo lib'], 'r') as f:
lines = f.readlines()
count = 0
for line in lines:
if 'entry(' in line:
count += 1
assert count == 3


def teardown_module():
"""teardown any state that was previously set up."""
path = os.path.join(DATA_BASE_PATH, 'libraries')
if os.path.isdir(path):
shutil.rmtree(path, ignore_errors=True)
156 changes: 16 additions & 140 deletions tests/test_main.py
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Expand Up @@ -2,20 +2,18 @@
# encoding: utf-8

"""
t3 tests test_tandem module
t3 tests test_main module
"""

import datetime
import os
import shutil
import re

from rmgpy.data.thermo import ThermoLibrary
from rmgpy.reaction import Reaction
from rmgpy.rmg.pdep import PDepNetwork, PDepReaction
from rmgpy.species import Species
from rmgpy.thermo import NASA, ThermoData
from rmgpy.statmech import Conformer, IdealGasTranslation, NonlinearRotor, HarmonicOscillator

from arc.common import read_yaml_file
from arc.species import ARCSpecies
Expand Down Expand Up @@ -51,8 +49,9 @@
'num_sa_per_pressure_range': 3,
'num_sa_per_temperature_range': 3,
'num_sa_per_volume_range': 3,
'save_libraries_directly_in_rmgdb': False,
'profiles_adapter': 'RMG'},
'profiles_adapter': 'RMG',
'shared_library_name': None,
},
'sensitivity': {'ME_methods': ['CSE', 'MSC'],
'SA_threshold': 0.01,
'adapter': 'RMGConstantTP',
Expand Down Expand Up @@ -288,11 +287,16 @@ def test_set_paths():
'iteration': 'T3/Projects/test_minimal_delete_after_usage/iteration_1',
'species dict': 'T3/Projects/test_minimal_delete_after_usage/iteration_1/RMG/chemkin/'
'species_dictionary.txt',
'RMG T3 thermo lib': 'test_minimal_delete_after_usage/Libraries/T3lib.py',
'RMG T3 kinetics lib': 'test_minimal_delete_after_usage/Libraries/T3',
'T3 thermo lib': 'test_minimal_delete_after_usage/Libraries/T3lib.py',
'T3 kinetics lib': 'test_minimal_delete_after_usage/Libraries/T3',
'shared T3 thermo lib': None,
'shared T3 kinetics lib': None,
}
for key, path in t3.paths.items():
assert paths[key] in path
if path is None:
assert paths[key] is None
else:
assert paths[key] in path


def test_restart():
Expand Down Expand Up @@ -466,15 +470,15 @@ def test_process_arc_run():
t3.process_arc_run()
assert t3.species[0]['converged'] is True
assert t3.species[1]['converged'] is False
assert os.path.isfile(t3.paths['RMG T3 thermo lib'])
with open(t3.paths['RMG T3 thermo lib'], 'r') as f:
assert os.path.isfile(t3.paths['T3 thermo lib'])
with open(t3.paths['T3 thermo lib'], 'r') as f:
lines = f.readlines()
for line in ['name = "T3"\n',
"Species imipramine_ol_2_ket_4 (run time: 1 day, 8:24:38)\n",
' label = "imipramine_ol_2_ket_4",\n',
" E0 = (-171.078,'kJ/mol'),\n"]:
assert line in lines
os.remove(t3.paths['RMG T3 thermo lib'])
os.remove(t3.paths['T3 thermo lib'])


def test_get_current_rmg_tol():
Expand Down Expand Up @@ -921,133 +925,6 @@ def test_add_reaction():
assert rmg_rxn_1.products[1].label == 's12_NO'


def test_add_to_rmg_library():
"""Test adding thermo calculations to an existing thermo library"""
libraries_path = os.path.join(DATA_BASE_PATH, 'libraries')
if not os.path.isdir(libraries_path):
os.makedirs(libraries_path)

spc_1 = Species(
index=1,
label='C2H4',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-20.0, 'kcal/mol'),
S298=(50.0, 'cal/(mol*K)'),
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
HarmonicOscillator(frequencies=([834.50, 973.31, 975.37, 1067.1, 1238.5, 1379.5, 1472.3, 1691.3,
3121.6, 3136.7, 3192.5, 3221.0], 'cm^-1')),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='C=C',
)

spc_2 = Species(
index=2,
label='CH4',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-50.0, 'kcal/mol'),
S298=(100.0, 'cal/(mol*K)'),
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='C',
)

spc_3 = Species(
index=2,
label='C3H7',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-92.0, 'kcal/mol'), # this is different
S298=(12.0, 'cal/(mol*K)'), # this is different
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
],
spin_multiplicity=1,
optical_isomers=1,
),
smiles='[CH2]CC',
)

# 1. Test adding one species to an existing library.
for lib_name, spc_list in [('RMG_library', [spc_1, spc_2]), ('ARC_library', [spc_3])]:
thermo_library = ThermoLibrary(name=lib_name, long_desc=lib_name)
for i, spc in enumerate(spc_list):
thermo_library.load_entry(index=i,
label=spc.label,
molecule=spc.to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.label,
longDesc=spc.label)
thermo_library.save(os.path.join(libraries_path, f'{lib_name}.py'))

t3 = run_minimal()
t3.set_paths()
t3.paths['ARC thermo lib'] = os.path.join(libraries_path, 'ARC_library.py')
t3.paths['RMG T3 thermo lib'] = os.path.join(libraries_path, 'RMG_library.py')
t3.add_to_rmg_libraries()
with open(t3.paths['RMG T3 thermo lib'], 'r') as f:
lines = f.readlines()
for line in [" H298 = (-92,'kcal/mol'),\n",
" S298 = (12,'cal/(mol*K)'),\n",
]:
assert line in lines

# 2. Test adding one species to an existing library when the new library has a species that also exists.
for lib_name, spc_list in [('RMG_library', [spc_1, spc_2]), ('ARC_library', [spc_1, spc_3])]:
thermo_library = ThermoLibrary(name=lib_name, long_desc=lib_name)
for i, spc in enumerate(spc_list):
thermo_library.load_entry(index=i,
label=spc.label,
molecule=spc.to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.label,
longDesc=spc.label)
thermo_library.save(os.path.join(libraries_path, f'{lib_name}.py'))

t3 = run_minimal()
t3.set_paths()
t3.paths['ARC thermo lib'] = os.path.join(libraries_path, 'ARC_library.py')
t3.paths['RMG T3 thermo lib'] = os.path.join(libraries_path, 'RMG_library.py')
t3.add_to_rmg_libraries()
with open(t3.paths['RMG T3 thermo lib'], 'r') as f:
lines = f.readlines()
count = 0
for line in lines:
if 'entry(' in line:
count += 1
assert count == 3


def test_dump_species():
"""Test dump species for restart purposes"""
# create an empty `iteration_5` directory
Expand Down Expand Up @@ -1166,7 +1043,7 @@ def test_check_overtime():


def teardown_module():
"""teardown any state that was previously setup with a setup_module method."""
"""teardown any state that was previously set up."""

# delete log files
for i in range(10):
Expand Down Expand Up @@ -1196,7 +1073,6 @@ def teardown_module():
os.path.join(DATA_BASE_PATH, 'determine_species', 'log_archive'),
os.path.join(DATA_BASE_PATH, 'pdep_network', 'log_archive'),
os.path.join(DATA_BASE_PATH, 'process_arc', 'log_archive'),
os.path.join(DATA_BASE_PATH, 'libraries'),
os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'output'),
os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'log_and_restart_archive'),
]:
Expand Down

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