Merge pull request #141 from ReactionMechanismGenerator/flux_d

Added flux diagrams

environment.yml

@@ -3,6 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.7
+  - pydot
   - cantera=2.6
   - ca-certificates
   - openssl

ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.dot

@@ -0,0 +1,36 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"H(3)" [fillcolor="#DCE5F4", fontsize=8, penwidth=1.7530392047540462, style=filled, xlabel="2.80e-11"];
+"CO(8)" [fontsize=8, penwidth=3.999999999999999, xlabel="4.68e-05"];
+"H2(4)" [fontsize=8, penwidth=3.927639860174137, xlabel="2.95e-05"];
+"OH(5)" [fontsize=8, penwidth=1.6100755035270433, xlabel="1.12e-11"];
+"H(3)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- H2(4) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - H2(4)", penwidth=3.984676425213845];
+"HOCO(10)" [fontsize=8, penwidth=0.5383397186827532, xlabel="1.21e-14"];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.7536269933534743];
+"H(3)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- H2(4)", penwidth=3.7536269933534743];
+"HOCO(10)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- OH(5)", penwidth=3.997757463516357];
+"HOCO(10)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=3.997757463516357];
+"CO2(9)" [fontsize=8, penwidth=3.927639907930275, xlabel="2.95e-05"];
+"H2O(17)" [fontsize=8, penwidth=3.9999999645295996, xlabel="4.68e-05"];
+"OH(5)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- H(3) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H(3)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.9539926576457947];
+"OH(5)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- H2O(17)", penwidth=3.9539926576457947];
+"OCHO(11)" [fontsize=8, penwidth=0.19999999999999937, xlabel="1.40e-15"];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- OCHO(11)", penwidth=3.67123391780574];
+"OH(5)" -> "OCHO(11)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- H2O(17)", penwidth=3.67123391780574];
+"OCHO(11)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.1\n- H(3)", penwidth=3.676279894902382];
+"OCHO(11)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="0.1\n- CO2(9)", penwidth=3.676279894902382];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- OH(5)", penwidth=0.43016435137560394];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- H(3)", penwidth=0.43016435137560394];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- H2(4)", penwidth=0.20000000000000034];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- CO2(9)", penwidth=0.20000000000000034];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="3.6e-08\n+ HOCHO(1)", penwidth=1.4627966491004998];
+"H2(4)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0e-04\n+ OH(5)\n- H2O(17)", penwidth=2.483741242797586];
+"H2(4)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0e-04\n+ OH(5)\n- H(3)", penwidth=2.483741242797586];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- H(3)", penwidth=2.9739529963274607];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- CO2(9)", penwidth=2.9739529963274607];
+}

ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.dot

@@ -0,0 +1,24 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"HOCHO(1)" [fillcolor="#DCE5F4", fontsize=8, penwidth=4.0, style=filled, xlabel="1.69e-01"];
+"CO(8)" [fontsize=8, penwidth=2.6712938924744143, xlabel="4.68e-05"];
+"H2O(17)" [fontsize=8, penwidth=2.671293855796359, xlabel="4.68e-05"];
+"HOCHO(1)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- H2O(17)", penwidth=4.0];
+"HOCHO(1)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=4.0];
+"CO2(9)" [fontsize=8, penwidth=2.596470167350586, xlabel="2.95e-05"];
+"H2(4)" [fontsize=8, penwidth=2.5964701179685017, xlabel="2.95e-05"];
+"HOCHO(1)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.6\n- H2(4)", penwidth=3.9466405710292745];
+"HOCHO(1)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.6\n- CO2(9)", penwidth=3.9466405710292745];
+"H(3)" [fontsize=8, penwidth=0.34783116462852137, xlabel="2.80e-11"];
+"H2(4)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="5.2e-09\n+ OH(5)\n- H2O(17)", penwidth=1.7955577099046087];
+"H2(4)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="5.2e-09\n+ OH(5)\n- H(3)", penwidth=1.7955577099046087];
+"HOCO(10)" [fontsize=8, penwidth=0.7324480422152477, xlabel="1.21e-14"];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="1.8e-12\n+ HOCHO(1)", penwidth=1.1729774870268643];
+"OH(5)" [fontsize=8, penwidth=0.2000000000000002, xlabel="1.12e-11"];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.1e-14\n- OH(5)", penwidth=0.3608065303110556];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="2.1e-14\n- H(3)", penwidth=0.3608065303110556];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="5.3e-15\n+ CO(8)\n- H2(4)", penwidth=0.2];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="5.3e-15\n+ CO(8)\n- CO2(9)", penwidth=0.2];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0e-07\n+ OH(5)\n- H(3)", penwidth=2.138048850394896];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0e-07\n+ OH(5)\n- CO2(9)", penwidth=2.138048850394896];
+}

ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.dot

@@ -0,0 +1,34 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"HOCO(10)" [fillcolor="#DCE5F4", fontsize=8, penwidth=0.5383397186827532, style=filled, xlabel="1.21e-14"];
+"CO(8)" [fontsize=8, penwidth=3.999999999999999, xlabel="4.68e-05"];
+"OH(5)" [fontsize=8, penwidth=1.6100755035270433, xlabel="1.12e-11"];
+"HOCO(10)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- OH(5)", penwidth=3.997757463516357];
+"HOCO(10)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=3.997757463516357];
+"CO2(9)" [fontsize=8, penwidth=3.927639907930275, xlabel="2.95e-05"];
+"H(3)" [fontsize=8, penwidth=1.7530392047540462, xlabel="2.80e-11"];
+"H2O(17)" [fontsize=8, penwidth=3.9999999645295996, xlabel="4.68e-05"];
+"OH(5)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- H(3) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H(3)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.9539926576457947];
+"OH(5)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- H2O(17)", penwidth=3.9539926576457947];
+"OCHO(11)" [fontsize=8, penwidth=0.19999999999999937, xlabel="1.40e-15"];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- OCHO(11)", penwidth=3.67123391780574];
+"OH(5)" -> "OCHO(11)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- H2O(17)", penwidth=3.67123391780574];
+"OCHO(11)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.1\n- H(3)", penwidth=3.676279894902382];
+"OCHO(11)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="0.1\n- CO2(9)", penwidth=3.676279894902382];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- OH(5)", penwidth=0.43016435137560394];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- H(3)", penwidth=0.43016435137560394];
+"H2(4)" [fontsize=8, penwidth=3.927639860174137, xlabel="2.95e-05"];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- H2(4)", penwidth=0.20000000000000034];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- CO2(9)", penwidth=0.20000000000000034];
+"H(3)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- H2(4) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - H2(4)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.7536269933534743];
+"H(3)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- H2(4)", penwidth=3.7536269933534743];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="3.6e-08\n+ HOCHO(1)", penwidth=1.4627966491004998];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- H(3)", penwidth=2.9739529963274607];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- CO2(9)", penwidth=2.9739529963274607];
+}

t3/common.py

@@ -17,6 +17,7 @@
 DATA_BASE_PATH = os.path.join(t3_path, 'tests', 'data')
 SIMULATE_DATA_BASE_PATH = os.path.join(t3_path, 'tests', 'test_simulate_adapters', 'data')
 EXAMPLES_BASE_PATH = os.path.join(t3_path, 'examples')
+SCRATCH_BASE_PATH = os.path.join(t3_path, 'tests', 'scratch')
 IPYTHON_SIMULATOR_EXAMPLES_PATH = os.path.join(t3_path, 'ipython', 'simulator_adapter_examples')
 PROJECTS_BASE_PATH = os.path.join(t3_path, 'Projects')
 VALID_CHARS = "-_=.,%s%s" % (string.ascii_letters, string.digits)

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