Pipeline Overview

create_InitCoor.sh is the orchestrator: edit a few variables at the top, run it once, and you receive a complete LAMMPS start-up folder containing

IC_tmp.xyz — packed bead coordinates (Packmol)
b70_N200_L<L>.data — Moltemplate data file
N200_Rg_L<L>.colvars — colvars tuned to the system size
b70_N200_L<L>.in — production input (+ optional Slurm script)

The diagram below shows the flow; the numbered sections explain every call in the wrapper, which files it consumes, and which files it writes.

Wrapper variables

Bash var	Meaning / effect
`n`	Segment repeat count (`10` → chain length = `10 × len(seg)`)
`seg`	Sticker/spacer pattern `2212212` (`2` = spacer, `1` = sticker)
`NA` / `NB`	Number of A-chains / B-chains (`100` / `100`)
`L`	Half-box length (`500 Å`) → Packmol cube \([-L, L]^3\)

All filenames downstream are built from these numbers, e.g. b70_N200_L500.lt (b = 70 % beads, N200 = 100 + 100 chains).

End-to-end flow

The helper chain executed by create_InitCoor.sh:

LT_writer.py → monomer LT + XYZ
writePackmolInput.py → Packmol recipe
Packmol → IC_tmp.xyz
writeSysLT.py → system LT
Moltemplate → b70_N200_L<L>.data
updateColVar.py → N200_Rg_L<L>.colvars
updateInput.py → b70_N200_L<L>.in + Slurm script
fix_datafiles.py → patch data file
lmp_mpi → run simulation

Detailed step-by-step

3.1 LT_writer.py — build monomer libraries

python3 LT_writer.py "$n" "$seg"

Creates

polyA_n<n>.lt Moltemplate monomer (types 1 & 2)
polyB_n<n>.lt Moltemplate monomer (types 3 & 4)
polyA_n<n>_mono.xyz & polyB_n<n>_mono.xyz (single-monomer XYZ)

Bead taxonomy

ID	Role
1	Sticker (A-chain, specific bonding)
2	Spacer (A-chain, non-specific bonding)
3	Sticker (B-chain, specific bonding)
4	Spacer (B-chain, non-specific bonding)

3.2 writePackmolInput.py — Packmol recipe

python3 writePackmolInput.py "$n" "$NA" "$NB" "$L" \
                             populate_tmp.inp IC_tmp.xyz

Creates populate_tmp.inp containing two structure blocks, each requesting NA or NB copies inside the cube \([-L, L]^3\) with 10 Å clearance.

3.3 Packmol — coordinate packing

packmol < populate_tmp.inp      # → IC_tmp.xyz

Replicates monomers, randomises orientation, outputs one XYZ:

14000
comment line
2  -185.4  -92.7   305.1
1   220.0   44.8   161.9
…

3.4 writeSysLT.py — system-level LT

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

Imports the monomer LTs, instantiates NA + NB polymers, defines back-bone bond/angle types, and writes a Data Boundary block ± (L + 20) Å.

3.5 Moltemplate — LT + XYZ → LAMMPS Data

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

Inputs

packed coordinates IC_tmp.xyz
hierarchy b70_N200_L<L>.lt

Outputs

b70_N200_L<L>.data — canonical LAMMPS Data file
system.in.settings — auxiliary pair/bond/angle styles
*.lt.tmp — intermediate JSON (can be deleted)

The -nocheck flag skips Moltemplate’s expensive overlap checker—we trust Packmol.

3.6 updateColVar.py — patch the colvars template

python3 updateColVar.py IC_tmp.xyz N400_Rg_L700.colvars \
                        "$L" "$n" "$NA" "$NB" "$seg"

Computes radius of gyration from all beads.
Sets upperBoundary = Rg + 10 and upperWalls = Rg + 5.
Generates an atomNumbers list selecting half-chains.
Writes N200_Rg_L<L>.colvars.

3.7 updateInput.py — final .in & Slurm launcher

python3 updateInput.py Template_input.in "$L"

Performs three substitutions in the template:

variable fName → b70_N200_L<L>
read_data → correct Data filename
fix CV_Rg → new .colvars file

Creates

b70_N200_L<L>.in — production input
submit_b70_N200_L<L>.sh — batch script (28 MPI, 3 days)

3.8 fix_datafiles.py — enable dynamic bonds

Search-replace 2 bond types → 3 bond types
Append 50 extra bond per atom

Required for LAMMPS’s fix bond/create/random (EXTRA-BOND package), which forms single-valency sticker–sticker bonds (bond type 3).

3.9 Run LAMMPS

lmp_mpi -in b70_N200_L<L>.in
# or
sbatch submit_b70_N200_L<L>.sh

File cheat-sheet

File	Created by	Consumed by
`polyA_n<n>.lt` / `polyB_n<n>.lt`	`LT_writer.py`	`writeSysLT.py`
`polyA_n<n>_mono.xyz` / `polyB_n<n>_mono.xyz`	`LT_writer.py`	`writePackmolInput.py`
`populate_tmp.inp`	`writePackmolInput.py`	Packmol
`IC_tmp.xyz`	Packmol	`writeSysLT.py`, `updateColVar.py`
`b70_N200_L<L>.lt`	`writeSysLT.py`	Moltemplate
`b70_N200_L<L>.data`	Moltemplate	`fix_datafiles.py`, `updateInput.py`
`N200_Rg_L<L>.colvars`	`updateColVar.py`	`updateInput.py`
`b70_N200_L<L>.in`	`updateInput.py`	LAMMPS
`submit_b70_N200_L<L>.sh`	`updateInput.py`	HPC scheduler