├── .gitignore ├── .vscode └── settings.json ├── ASE_init.ipynb ├── ChemTraYzer_2.0 └── py3 │ ├── analyzing.py │ ├── dbhandler.py │ ├── harvesting.py │ ├── log.py │ ├── master.py │ ├── processing.py │ └── simulation.py ├── Fe Aqueous + CO2 Analysis.ipynb ├── Fe Aqueous + CO2 Long Running Analysis.ipynb ├── Fe Aqueous CO2 Large Analysis.ipynb ├── Fe Aqueous CO2 Small Analysis.ipynb ├── Fe Aqueous CO2 Small Long Analysis.ipynb ├── Fe Aqueous Small Analysis.ipynb ├── Fe Surface Energy.ipynb ├── FeCO3 Bulk Analysis.ipynb ├── FeCO3 Distorted Surfaces Construction BODA.ipynb ├── FeCO3 Distorted Surfaces Construction.ipynb ├── FeCO3 Surfaces Construction.ipynb ├── ForceField Parameters.ipynb ├── HPC_Jupyter ├── CO2 Hydration.ipynb ├── Distorted FeCO3 Slabs with Fixed Middle.ipynb ├── Fe Aqueous + CO2 Large.ipynb ├── Fe Aqueous + CO2 Small Long.ipynb ├── Fe Aqueous + CO2 Small.ipynb ├── Fe Aqueous Small.ipynb ├── FeCO3 Bulk.ipynb ├── LAMMPS Integrate.ipynb ├── Misc Test and Scripts.ipynb ├── Pure Water.ipynb └── Surface Energy of Iron.ipynb ├── HPC_Scripts ├── bonds_analysis.py ├── compress.qin ├── convert_bond.py ├── convert_script.py ├── convert_script.qin ├── convert_script_fast.py ├── convert_script_nocopy_fast.py ├── lammpsrun.py └── minimal_traj_conversion.py ├── Hydration of CO2.ipynb ├── Misc Scripts Usage.ipynb ├── PBSJobSubmissionScript.py ├── README.md ├── Running LAMMPS.ipynb ├── SCM ReaxFF List.ipynb ├── Water Analysis.ipynb ├── finaL_potential_set ├── angles_c_fe.reax ├── angles_c_fe.reax.lib ├── angles_o_c_fe.reax ├── angles_o_c_fe.reax.lib ├── bonds_angles_c_fe.reax ├── bonds_angles_c_fe.reax.lib ├── bonds_c_fe.reax ├── bonds_c_fe.reax.lib ├── bonds_off_diagonal_angles_c_fe.reax ├── bonds_off_diagonal_angles_c_fe.reax.lib ├── bonds_off_diagonal_c_fe.reax ├── bonds_off_diagonal_c_fe.reax.lib ├── off_diagonal_angles_c_fe.reax ├── off_diagonal_angles_c_fe.reax.lib └── off_diagonal_c_fe.reax ├── final_potential_set ├── fe_o_water_fe_o_c_5050.reax ├── fe_o_water_fe_o_c_5050.reax.lib ├── fe_o_water_fe_o_c_full.reax ├── fe_o_water_fe_o_c_full.reax.lib ├── ffield.reax.Fe_O_C ├── ffield.reax.Fe_O_C.lib ├── ffield.reax.Fe_O_C_H └── ffield.reax.Fe_O_C_H.lib ├── gulp.py ├── lammpsrun.py ├── potentials ├── angles_c_fe.reax ├── angles_o_c_fe.reax ├── boda_manual_sub.reax ├── bonds_angles_c_fe.reax ├── bonds_c_fe.reax ├── bonds_off_diagonal_angles_c_fe.reax ├── bonds_off_diagonal_c_fe.reax ├── fe_o_water_fe_o_c_5050.reax ├── fe_o_water_fe_o_c_full.reax ├── fe_o_water_fe_o_c_full_water.reax ├── ffield.reax.Fe_O_C ├── ffield.reax.Fe_O_C_H ├── ffield.reax.O_H ├── ffield.reax.P_Na_Si_S_N_O_H_C ├── off_diagonal_angles_c_fe.reax ├── off_diagonal_c_fe.reax └── reaxff_caco3.lib ├── reaxFF_data.py ├── reaxff_convert.py └── utility_scripts.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiming-xu/LAMMPS_Simulation/HEAD/.gitignore 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