PolymerFoulingModeling

A collection of Python and Julia scripts used for generating and simulating multi-phase chemical kinetic models for polymer fouling

Repository structure

📦debutanizer_models
 ┣ 📂basecase # files for the base case debutanizer model
 ┃ ┣ 📂aspen_simulation # files related to process simulation
 ┃ ┃ ┣ 📜Distillation_FEDP_XN_V2_060720_v2.xlsx # output file from Aspen Plus
 ┃ ┃ ┗ 📜aspen_conditions.yml # extracted process conditions (T, P, Cmajor, etc.)
 ┃ ┣ 📂film_mechanism # mechanism files for film growth
 ┃ ┃ ┣ 📜chem_annotated_film.inp
 ┃ ┃ ┣ 📜chem_film_phase.rms
 ┃ ┃ ┣ 📜liquid_species_mapping.yml
 ┃ ┃ ┗ 📜species_dictionary_film.txt
 ┃ ┣ 📂liquid_mechanism # mechanism files for liquid phase oligomerization
 ┃ ┃ ┣ 📜chem.rms
 ┃ ┃ ┣ 📜chem_annotated.inp
 ┃ ┃ ┗ 📜species_dictionary.txt
 ┃ ┣ 📂liquid_mechanism_generation # files to generate liquid phase mechanism using RMG-Py
 ┃ ┃ ┣ 📜input.py
 ┃ ┃ ┣ 📜run_generate_input.sh
 ┃ ┃ ┗ 📜submit_input.sh
 ┃ ┗ 📂submit_scripts
 ┃ ┃ ┣ 📜submit_0.1_liquid_simulation_LLsub.sh
 ┃ ┃ ┣ 📜submit_0.2_film_simulation_LLsub.sh
 ┃ ┃ ┗ 📜submit_0_all_LLsub.sh
 ┗ 📂trace_oxygen_perturbed # files for the trace-oxygen perturbed debutanizer model
 ┃ ┣ 📂aspen_simulation
 ┃ ┃ ┣ 📜Distillation_FEDP_XN_V2_060720_v2_oxygen.xlsx
 ┃ ┃ ┗ 📜aspen_conditions.yml
 ┃ ┣ 📂film_mechanism
 ┃ ┃ ┣ 📜chem_annotated_film.inp
 ┃ ┃ ┣ 📜chem_film_phase.rms
 ┃ ┃ ┣ 📜chem_liquid_film_phase.rms
 ┃ ┃ ┣ 📜liquid_species_mapping.yml
 ┃ ┃ ┗ 📜species_dictionary_film.txt
 ┃ ┣ 📂liquid_mechanism
 ┃ ┃ ┣ 📜chem.rms
 ┃ ┃ ┣ 📜chem_annotated.inp
 ┃ ┃ ┗ 📜species_dictionary.txt
 ┃ ┣ 📂liquid_mechanism_generation
 ┃ ┃ ┗ 📜input.py
 ┃ ┗ 📂submit_scripts
 ┃ ┃ ┣ 📜submit_0.1_liquid_simulation_LLsub.sh
 ┃ ┃ ┣ 📜submit_0.2_film_simulation_LLsub.sh
 ┃ ┃ ┣ 📜submit_0.3_simulate_film_submodel_1D_LLsub.sh
 ┃ ┃ ┣ 📜submit_0_all_LLsub.sh
 ┃ ┃ ┣ 📜submit_10_generate_film_mechanism_LLsub.sh
 ┃ ┃ ┣ 📜submit_11_simulate_film_submodel_LLsub.sh
 ┃ ┃ ┣ 📜submit_12_analyze_film_simulation_and_sensitivity_LLsub.sh
 ┃ ┃ ┣ 📜submit_13_simulate_film_submodel_1D_discretization_studies_LLsub.sh
 ┃ ┃ ┣ 📜submit_14_analyze_debutanizer_film_simulation_1D_discretization_studies_LLsub.sh
 ┃ ┃ ┣ 📜submit_15_analyze_debutanizer_film_simulation_and_sensitivity_1D_LLsub.sh
 ┃ ┃ ┣ 📜submit_16_plotter.sh
 ┃ ┃ ┣ 📜submit_1_extract_and_plot_aspen_conditions_LLsub.sh
 ┃ ┃ ┣ 📜submit_2_generate_rmg_input_LLsub.sh
 ┃ ┃ ┣ 📜submit_3_generate_liquid_mechanism_LLsub.sh
 ┃ ┃ ┣ 📜submit_4_update_parameters_LLsub.sh
 ┃ ┃ ┣ 📜submit_5_time_step_studies.sh
 ┃ ┃ ┣ 📜submit_6_analyze_time_step_studies.sh
 ┃ ┃ ┣ 📜submit_7_simulate_vapor_liquid_submodels_LLsub.sh
 ┃ ┃ ┣ 📜submit_8_get_alpha_for_ASF_distribution_LLsub.sh
 ┃ ┃ ┗ 📜submit_9_analyze_vapor_liquid_simulation_LLsub.sh
 📦QCMD_cell_model
 ┣ 📂film_mechanism
 ┃ ┣ 📜chem_annotated_film.inp
 ┃ ┣ 📜chem_film_phase.rms
 ┃ ┣ 📜liquid_species_mapping.yml
 ┃ ┗ 📜species_dictionary_film.txt
 ┣ 📂liquid_mechanism
 ┃ ┣ 📜chem.rms
 ┃ ┣ 📜chem_annotated.inp
 ┃ ┗ 📜species_dictionary.txt
 ┣ 📂liquid_mechanism_generation
 ┃ ┗ 📜input.py
 ┣ 📂liquid_simulation
 ┃ ┗ 📜simulate_liquid_submodel.jl
 ┗ 📂submit_scripts
 ┃ ┣ 📜submit_0.1_simulation_LLsub.sh
 ┃ ┗ 📜submit_0_all_LLsub.sh

Installation

• git clone RMG-Py (https://github.com/hwpang/RMG-Py), RMG-database (https://github.com/hwpang/RMG-database), and RMS (https://github.com/hwpang/ReactionMechanismSimulator.jl)
• Check out to following commits for the following packages
  • RMG-Py: 87b96e1b0f65145c413ac0fe2761fdf441d35fea on main branch from https://github.com/hwpang/RMG-Py
  • RMG-database: e6d81dba399900568e07f8f79399fd6a62696552 on polymer_fouling_2 branch from https://github.com/hwpang/RMG-database
  • ReactionMechanismSimulator.jl: ba51c2fccddfa7939218b3dcd13e4649b38b4d70 on polymer_fouling_2_20230725 branch from https://github.com/hwpang/ReactionMechanismSimulator.jl
• Install RMG-Py following http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html
  • During installtion, use the following to point to your local RMS instead of the main branch on GitHub

    julia -e 'using Pkg; Pkg.develop(Pkg.PackageSpec(name="ReactionMechanismSimulator",path="/path/to/your/ReactionMechanismSimulator.jl")); Pkg.build("ReactionMechanismSimulator"); using ReactionMechanismSimulator;'
    

• Add these Julia packages

  julia -e 'using Pkg; Pkg.add("CSV"); Pkg.add("DataFrames"); Pkg.add("XLSX");'