From c1232f34032db2ea4ff6c3903801abcac71d5124 Mon Sep 17 00:00:00 2001
From: Alon Grinberg Dana <alon@technion.ac.il>
Date: Wed, 25 Oct 2023 23:14:32 +0300
Subject: [PATCH] Added the fix_cantera module

To automatically solve issues in RMG-generated Cantera files such as duplicate reaction issues
---
 t3/utils/fix_cantera.py | 149 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 149 insertions(+)
 create mode 100644 t3/utils/fix_cantera.py

diff --git a/t3/utils/fix_cantera.py b/t3/utils/fix_cantera.py
new file mode 100644
index 00000000..99e61e9b
--- /dev/null
+++ b/t3/utils/fix_cantera.py
@@ -0,0 +1,149 @@
+"""
+t3 utils fix_cantera module
+A module to automatically fix issues with RMG-generated Cantera files, mainly resolving mislabeled duplicate reactions.
+"""
+import os
+
+from typing import List, Optional
+
+import shutil
+import time
+import traceback
+
+import cantera as ct
+
+from arc.common import read_yaml_file, save_yaml_file
+
+
+def get_traceback(model_path: str) -> Optional[str]:
+    """
+    Try loading the Cantera model and return the traceback if it fails.
+
+    Args:
+        model_path (str): The path to the cantera YAML model file.
+
+    Returns:
+        Optional[str]: The traceback if the model fails to load.
+    """
+    tb = None
+    try:
+        ct.Solution(model_path)
+    except ct.CanteraError:
+        tb = traceback.format_exc()
+    return tb
+
+
+def fix_cantera(model_path: str):
+    """
+    Fix a Cantera model that has incorrectly marked duplicate reactions.
+    Creates a backup copy of the Cantera model and fixes the content of the original file in place.
+
+    Args:
+        model_path (str): The path to the cantera YAML model file.
+
+    Returns:
+        bool: Whether the model was fixed.
+    """
+    shutil.copyfile(model_path, model_path + '.bak')
+    done, fixed = False, False
+    counter = 0
+    while not done and counter < 1000:
+        counter += 1
+        tb = get_traceback(model_path)
+        if tb is None:
+            done = True
+            break
+        else:
+            if 'Undeclared duplicate reactions detected' in tb:
+                fix_undeclared_duplicate_reactions(model_path, tb)
+                fixed = True
+            elif 'No duplicate found for declared duplicate reaction' in tb:
+                fix_no_duplicate_found(model_path, tb)
+                fixed = True
+            else:
+                print(f'Could not fix {model_path}:\n\n{tb}')
+                break
+        time.sleep(1)
+    if fixed:
+        print(f'Fixing Cantera model {model_path} (and creating a backup copy with a .bak extension).')
+    else:
+        os.remove(model_path + '.bak')
+    return done
+
+
+def fix_undeclared_duplicate_reactions(model_path: str, tb: str):
+    """
+    Fix a Cantera model that has undeclared duplicate reactions.
+
+    Args:
+        model_path (str): The path to the cantera YAML model file.
+        tb (str): The traceback.
+    """
+    content = read_yaml_file(model_path)
+    rxns = get_dup_rxn_indices(tb)
+    print(f'Marking reactions {", ".join([str(r) for r in rxns])} as duplicate.')
+    for i in rxns:
+        content['reactions'][i - 1]['duplicate'] = True
+    save_yaml_file(model_path, content)
+
+
+def fix_no_duplicate_found(model_path: str, tb: str):
+    """
+    Fix a Cantera model that has a reaction marked as duplicate by mistake with no other duplicate reaction.
+
+    Args:
+        model_path (str): The path to the cantera YAML model file.
+        tb (str): The traceback.
+    """
+    content = read_yaml_file(model_path)
+    rxns = get_mistakenly_marked_dup_rxns(tb)
+    for i in rxns:
+        if 'duplicate' in content['reactions'][i].keys():
+            print(f'Marking reaction {i} as non-duplicate.')
+            del content['reactions'][i]['duplicate']
+    save_yaml_file(model_path, content)
+
+
+def get_dup_rxn_indices(tb: str) -> List[int]:
+    """
+    Get the duplicate reactions from the traceback.
+
+    Args:
+        tb (str): The traceback.
+
+    Returns:
+        List[int]: The reactions indices.
+    """
+    rxns = list()
+    if tb is None:
+        return rxns
+    lines = tb.split('\n')
+    read = False
+    for line in lines:
+        if 'Undeclared duplicate reactions detected:' in line:
+            read = True
+        if '|  Line |' in line:
+            break
+        if read and 'Reaction' in line:
+            rxns.append(int(line.split()[1].split(':')[0]))
+    return rxns
+
+
+def get_mistakenly_marked_dup_rxns(tb: str) -> List[int]:
+    """
+    Get the duplicate reactions from the traceback.
+
+    Args:
+        tb (str): The traceback.
+
+    Returns:
+        List[int]: The reactions indices.
+    """
+    rxns = list()
+    if tb is None:
+        return rxns
+    lines = tb.split('\n')
+    for line in lines:
+        if 'No duplicate found for declared duplicate reaction number' in line:
+            rxns.append(int(line.split()[8]))
+    return rxns