Usage Guide for proposed_mopac

Files descriptions

• main.py - starts proposed_mopac method
• orca_calculate_folder.py - starts ORCA validation calculations
• saddle.py - starts SADDLE validation calculations
• u_functions - contains auxiliary functions for main
• estimation.py - creates plots and calculates KIE
• new_MOPAC_calculator.py - contains new methods for ASE, such as: isotopes labels, extraction functions, inputs modifies functions
• orca_estimation.py - calculates KIE for ORCA validation

How to install proposed mopac

1. You should create conda environment. If you don't have conda, go to install_conda
2. Copy proposed_mopac.yml file to your machine.
3. Type in linux terminal

conda env create -f proposed_mopac.yml

then, activate environment

conda activate proposed_mopac

How to use proposed mopac

1. First, you should copy proposed_mopac_calc directory to your computer
2. Second, create not_opted.xyz file of your molecule system and rename folder proposed_mopac_calc/mop/substance_name to proposed_mopac_calc/mop/YOUR_SYSTEM_NAME
3. Then, paste not_opted.xyz to proposed_mopac_calc/mop/YOUR_SYSTEM_NAME/start
4. Creat starting command, using example, and replace XX with necessary ones.

python3 main.py -x opted_h2o.xyz --eps XX.X --charge X --mult XXXXXXX --step X.XX --isotope X \
--moving_atom_h XX --dest_atom XX --h_neighbour XX --place /mop/YOUR_SYSTEM_NAME/calc --threads 100

necessary parameters

• --eps - dielectric constant, for water 78.4
• --charge - total charge of your system, e.g. 0
• --mult - total multiplicity of your system, e.g. SINGLET
• --step - proton shift length, in Å, e.g. 0.05
• --isotope - isotope H,D or T. E.g. D
• --moving_atom_h - nummber of exchanging H atom in .xyz file. STARTS FROM 0. E.g. 21
• --dest_atom - number of the atom in .xyz file with which the proton is exchanged. E.g. 14
• --h_neighbour - number of the atom in .xyz file with which the proton is connected. E.g. 13
• --place - path to calc folder, e.g. /mop/YOUR_SYSTEM_NAME/calc.
• --threads - number of threads of your processor, e.g. 100

additional parameters

• --other_isotopes - numbers of other H atoms in molecules should be isotopes separated by a space. E.g. 2 3 4
• --freez - numbers of other atoms, that should be freezed in geometry optimization separated by a space. E.g. 2 3 4
• --freez_all_axis - freezing of all axises.

5. Paste this starting comand in new YOUR_SYSTEM_NAME.sh file. This file should be in proposed_mopac_calc folder. Example YOUR_SYSTEM_NAME.sh file:

#!/bin/bash
#export RSH_COMMAND="/usr/bir/ssh -x"
export OMP_NUM_THREADS=70
python3 main.py -x opted_h2o.xyz --eps XX.X --charge X --mult XXXXXXX --step X.XX --isotope X \
--moving_atom_h XX --dest_atom XX --h_neighbour XX --place /mop/YOUR_SYSTEM_NAME/calc --threads 100

6. Start your calculation by created command, or if you have slurm on your machine, you can start calculations with num threads and time.

sbatch -n 100 -t 1:00:00 YOUR_SYSTEM_NAME.sh

7. After calculations done, you can create plots and get KIE.
8. For plots, type:

python3 estimation.py --place /mop/YOUR_SYSTEM_NAME/calc --plot True

9. Determine Transition State (TS) This will create a plot Heat of Formation (HOF) from protons shift/step number. Path to plot /mop/YOUR_SYSTEM_NAME/calc/HOFS.pdf and /mop/YOUR_SYSTEM_NAME/calc/HOFS.png. .pdf HOF from (Stem number), but .png HOF from shift,Å. You shold use .pdf for determine TS point.
10. After you get TS point, e.g. 73 from .pdf, and your isotope was T, you can type:

python3 estimation.py --place /mop/YOUR_SYSTEM_NAME/calc --ts 73 --isotope T

and get KIE value. Also, KIE will be saved in /mop/YOUR_SYSTEM_NAME/calc/kie.txt If your isotope was D, then change on --isotope D

Article Data

data - contains all data for deuterium data_t - contains all data for tritium

We have global file structure:

proposed_mopac

• mop
  • substance_name
    • start
    • calc
• saddle
  • substance_name
    • start
    • end
    • saddle
• for_orca
• main.py
• saddle.py
• u_functions.py
• estimation.py
• new_MOPAC_calculator.py
• orca_estimation.py
• orca_calculate_folder.py
• saddle_example.mop
• substance.sh
• proposed_mopac.yml