Configures Arkane to use RMG_DB_PATH

Ensures Arkane and related scripts correctly utilize the RMG_DB_PATH environment variable to locate the RMG database.

Adds flexibility by allowing RMG_ENV_NAME to be specified, defaulting to 'rmg_env' if not provided.

This ensures that Arkane calculations and tests can locate necessary data files.

Author: calvinp0

arc/statmech/arkane.py

@@ -24,7 +24,8 @@
     from arc.species.species import ARCSpecies
 
 
-RMG_DB_PATH, RMG_PATH = settings['RMG_DB_PATH'], settings['RMG_PATH']
+RMG_DB_PATH = settings['RMG_DB_PATH']
+RMG_ENV_NAME = settings.get('RMG_ENV_NAME', 'rmg_env')
 logger = get_logger()
 
 
@@ -445,12 +446,16 @@ def parse_arkane_thermo_output(self, statmech_dir: str) -> None:
             clean_output_directory(os.path.join(self.output_directory, 'Species', species.label))
 
         script_path = os.path.join(ARC_PATH, 'arc', 'scripts', 'save_arkane_thermo.py')
+        env_name = RMG_ENV_NAME
+        rmg_db_path = RMG_DB_PATH or ""
         commands = [f'cd {statmech_dir}',
                     'bash -lc "set -euo pipefail; '
+                    f'export RMG_DB_PATH=\\"{rmg_db_path}\\"; '
+                    f'export RMG_DATABASE=\\"{rmg_db_path}\\"; '
                     'if command -v micromamba >/dev/null 2>&1; then '
-                    f'    micromamba run -n rmg_env python {script_path}; '
+                    f'    micromamba run -n {env_name} python {script_path}; '
                     'elif command -v conda >/dev/null 2>&1 || command -v mamba >/dev/null 2>&1; then '
-                    f'    conda run -n rmg_env python {script_path}; '
+                    f'    conda run -n {env_name} python {script_path}; '
                     'else '
                     '    echo \'❌ Micromamba/Mamba/Conda required\' >&2; exit 1; '
                     'fi"',
@@ -514,11 +519,14 @@ def run_arkane(statmech_dir: str) -> None:
     if not os.path.isfile(input_file):
         logger.error(f'Cannot run Arkane in {statmech_dir} because it does not contain an input.py file.')
         return
-    env_name = 'rmg_env'
-    arkane_cmd = f'python "{RMG_PATH}/Arkane.py" input.py'
+    env_name = RMG_ENV_NAME
+    rmg_db_path = RMG_DB_PATH or ""
+    arkane_cmd = 'python -m arkane input.py'
     arkane_cmd += ' 2> >(tee -a stderr.log >&2) | tee -a stdout.log'
     shell_script = rf'''bash -lc 'set -euo pipefail
 cd "{statmech_dir}"
+export RMG_DB_PATH="{rmg_db_path}"
+export RMG_DATABASE="{rmg_db_path}"
 
 if command -v micromamba >/dev/null 2>&1; then
     micromamba run -n {env_name} {arkane_cmd}
@@ -710,6 +718,8 @@ def get_arkane_model_chemistry(sp_level: 'Level',
         return f"LevelOfTheory(method='{sp_level.method}',software='gaussian')"
 
     qm_corr_file = os.path.join(RMG_DB_PATH, 'input', 'quantum_corrections', 'data.py')
+    if not os.path.isfile(qm_corr_file):
+        qm_corr_file = os.path.join(RMG_DB_PATH, 'quantum_corrections', 'data.py')
 
     atom_energies_start = "atom_energies = {"
     atom_energies_end = "pbac = {"
@@ -768,6 +778,8 @@ def check_arkane_bacs(sp_level: 'Level',
         bool: True if both AECs and BACs are available, False otherwise.
     """
     qm_corr_file = os.path.join(RMG_DB_PATH, 'input', 'quantum_corrections', 'data.py')
+    if not os.path.isfile(qm_corr_file):
+        qm_corr_file = os.path.join(RMG_DB_PATH, 'quantum_corrections', 'data.py')
 
     atom_energies_start = "atom_energies = {"
     atom_energies_end = "pbac = {"

arc/statmech/arkane_test.py

@@ -16,6 +16,7 @@
 from arc.statmech.adapter import StatmechEnum
 from arc.statmech.arkane import ArkaneAdapter
 from arc.statmech.arkane import _level_to_str, _section_contains_key, get_arkane_model_chemistry
+from arc.imports import settings
 
 
 class TestEnumerationClasses(unittest.TestCase):
@@ -108,8 +109,22 @@ def test__str__(self):
     def test_run_statmech_using_molecular_properties(self):
         """Test running statmech using molecular properties."""
         self.arkane_3.compute_thermo()
-        self.assertTrue(os.path.isfile(os.path.join(ARC_PATH, 'arc', 'testing', 'arkane_tests_delete', 'calcs_3',
-                                                    'statmech', 'thermo', 'plots', 'iC3H7.pdf')))
+        plot_path = os.path.join(ARC_PATH, 'arc', 'testing', 'arkane_tests_delete', 'calcs_3',
+                                 'statmech', 'thermo', 'plots', 'iC3H7.pdf')
+        if not os.path.isfile(plot_path):
+            log_dir = os.path.dirname(os.path.dirname(plot_path))
+            stdout_log = os.path.join(log_dir, 'stdout.log')
+            stderr_log = os.path.join(log_dir, 'stderr.log')
+            stdout_text = ''
+            stderr_text = ''
+            if os.path.isfile(stdout_log):
+                with open(stdout_log, 'r') as f:
+                    stdout_text = f.read()
+            if os.path.isfile(stderr_log):
+                with open(stderr_log, 'r') as f:
+                    stderr_text = f.read()
+            self.fail(f'Arkane did not generate {plot_path}.\nstdout.log:\n{stdout_text}\nstderr.log:\n{stderr_text}')
+        self.assertTrue(os.path.isfile(plot_path))
         self.assertAlmostEqual(self.ic3h7.e0, 6.75565e+07)
 
     def test_level_to_str(self):
@@ -123,7 +138,11 @@ def test_level_to_str(self):
 
     def test_section_contains_key(self):
         """Test the _section_contains_key function"""
-        file_path = os.path.join(os.path.dirname(ARC_PATH), 'RMG-database', 'input', 'quantum_corrections', 'data.py')
+        rmg_db_path = settings.get('RMG_DB_PATH')
+        file_path = os.path.join(rmg_db_path, 'input', 'quantum_corrections', 'data.py')
+        if not os.path.isfile(file_path):
+            file_path = os.path.join(rmg_db_path, 'quantum_corrections', 'data.py')
+        self.assertTrue(os.path.isfile(file_path), f'RMG quantum corrections file not found at {file_path}')
         self.assertTrue(_section_contains_key(file_path=file_path,
                                               section_start="atom_energies = {",
                                               section_end="pbac = {",