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NotImplementedError: Can't check isomorphism of lists with 4 species/molecules

Open NUSCondy opened this issue 3 years ago • 0 comments

Hi, I am trying to merge two models with the script in RMG-Py/scripts. This time it seems that it's the problem of isomorphism. I am confused since I think RMG could check the repeatability in the models. Could you tell me how to check the isomorphism problems in two models? The followings are the error info:

**Ignoring common species and reactions from model #1... Added 493 out of 493 (100.0%) unique species from model #1. Added 2643 out of 2643 (100.0%) unique reactions from model #1. Ignoring common species and reactions from model #2... Species CH3OCHO thermo from model 1 did not match that of model 2. Species CH3OCO thermo from model 1 did not match that of model 2. Species CH2OCHO thermo from model 1 did not match that of model 2. Reaction CH3 + OH <=> CH2(S) + H2O kinetics from model 1 did not match that of model 2. Reaction C2H + O <=> CO + CHV kinetics from model 1 did not match that of model 2. Traceback (most recent call last): File "//home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main python(**vars(ns)) File "//home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python scope = runpy.run_path(script, run_name="main") File "//home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "//home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "//home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/zhuqiren/RMG-Py/scripts/mergeModels.py", line 52, in main() File "/home/zhuqiren/RMG-Py/scripts/mergeModels.py", line 48, in main merge_models.main() File "/home/zhuqiren/RMG-Py/rmgpy/tools/mergemodels.py", line 94, in main execute(input_model_files, kwargs) File "/home/zhuqiren/RMG-Py/rmgpy/tools/mergemodels.py", line 111, in execute final_model = combine_models(models) File "/home/zhuqiren/RMG-Py/rmgpy/tools/mergemodels.py", line 148, in combine_models final_model = final_model.merge(model) File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 118, in merge if rxn.is_isomorphic(rxn0, either_direction=True): File "rmgpy/reaction.py", line 434, in rmgpy.reaction.Reaction.is_isomorphic File "rmgpy/reaction.py", line 476, in rmgpy.reaction.Reaction.is_isomorphic File "rmgpy/reaction.py", line 1503, in rmgpy.reaction.same_species_lists NotImplementedError: Can't check isomorphism of lists with 4 species/molecules

NUSCondy avatar Dec 13 '21 03:12 NUSCondy