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Added flux diagrams #141

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merged 8 commits into from
Nov 9, 2023
Merged

Added flux diagrams #141

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fd12f0c
Added pydot to env
alongd Oct 24, 2023
3c1620f
Added almost_equal() to tests common
alongd Oct 24, 2023
f275fe8
Added the flux module
alongd Nov 2, 2023
9efc86a
Tests: Added flux tests
alongd Nov 2, 2023
8d83d6c
Added an iPython example with auto-generated figures
alongd Oct 25, 2023
1c50396
Added copy_model() to common
alongd Oct 25, 2023
77026ad
Added the fix_cantera module
alongd Oct 25, 2023
d60fa59
Tests: fix_cantera
alongd Nov 8, 2023
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1 change: 1 addition & 0 deletions environment.yml
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Expand Up @@ -3,6 +3,7 @@ channels:
- conda-forge
dependencies:
- python=3.7
- pydot
- cantera=2.6
- ca-certificates
- openssl
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204 changes: 204 additions & 0 deletions ipython/flux_diagram/Generate Flux Diagram.ipynb
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36 changes: 36 additions & 0 deletions ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.dot
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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];
}
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24 changes: 24 additions & 0 deletions ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.dot
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@@ -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];
}
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34 changes: 34 additions & 0 deletions ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.dot
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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];
}
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1 change: 1 addition & 0 deletions t3/common.py
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Expand Up @@ -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)
Expand Down
149 changes: 149 additions & 0 deletions t3/utils/fix_cantera.py
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"""
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
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