Welcome to CASPULE’s documentation!

This project uses a single Bash wrapper (create_InitCoor.sh) together with six Python scripts to generate Packmol + Moltemplate input files and produce LAMMPS‐ready data files.

Graphical Summary

Graphical summary of the init-conditions pipeline

Quick Start

  1. Ensure prerequisites are on your PATH - packmol - moltemplate.sh - A LAMMPS binary (e.g., lmp_serial)

  2. Run the pipeline

    bash create_InitCoor.sh

    Behind the scenes, this executes:

    1. python3 LT_writer.py  <n>  <seg_pattern>

    2. python3 writePackmolInput.py  <n>  <NA>  <NB>  <L>  populate_tmp.inp  IC_tmp.xyz

    3. python3 writeSysLT.py  <n>  <NA>  <NB>  <L>  b70_N200_L<L>.lt

    4. packmol < populate_tmp.inp

    5. moltemplate.sh -xyz IC_tmp.xyz b70_N200_L<L>.lt -nocheck

    6. python3 updateColVar.py  IC_tmp.xyz  N400_Rg_L700.colvars  <L>  <n>  <NA>  <NB>  <seg_pattern>

    7. python3 updateInput.py  Template_input.in  <L>

    8. python3 fix_datafiles.py  b70_N200_L<L>.data

  3. After successful execution, you will find:

    IC_tmp.xyz
polyA_n<n>.lt, polyB_n<n>.lt
b70_N200_L<L>.lt
b70_N200_L<L>.data
b70_N200_L<L>.in
N200_Rg_L<L>.colvars
submit_b70_N200_L<L>.sh

    You can then launch LAMMPS with:

    lmp_serial -in b70_N200_L<L>.in

Documentation Sections

Contents: