data/ADEPT/README.md

ADEPT: Automated molecular Dynamics Engine for Polymer simulaTions

This workflow automates the generation of polymer structures from SMILES, performs molecular dynamics (MD) simulations using LAMMPS, and computes a wide range of polymer properties including density, Tg, Cp, dielectric constant, thermal conductivity, viscosity, and mechanical moduli. It also computes DFT-level monomer electronic properties using Psi4.

The workflow is designed for an HPC cluster with:

• Sun Grid Engine (SGE) or compatible scheduler
• LAMMPS installed as a module
• Conda for Python environment management

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1. Create the Conda Environment

Load the conda module on your HPC:

module load conda

Create the environment:

conda env create -f polymer-workflow.yml

Activate it:

conda activate polymer-workflow

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2. Install PySIMM

PySIMM can be installed inside your conda environment.

Option 1 — Simple install with pip

conda activate polymer-workflow

git clone https://github.com/polysimtools/pysimm.git
cd pysimm
pip install .

Add the following line to your ~/.bashrc (edit the LAMMPS path as needed) export LAMMPS_EXEC="/usr/bin/lmp" source ~/.bashrc

Option 2 — Using complete_install.py

conda activate polymer-workflow

git clone https://github.com/polysimtools/pysimm.git
python pysimm/complete_install.py --pysimm "$PWD"

PySIMM handles polymer chain construction, random-walk polymerization, GAFF2 parameter assignment, RESP/Gasteiger charges, and LAMMPS data file generation.---

3. Load LAMMPS on HPC

LAMMPS is loaded using your cluster's module system. For example:

module load lammps

LAMMPS does not need to be installed inside the conda environment.

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5. Using the Submission Script

To run the first 50 polymers:

qsub -t 1-50 submit.sh

Logs are stored in:

Log_Files/

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6. Property Toggles

Inside submit.sh, you will find:

DO_APG=
DO_OPT=
DO_MONO_ELECTRONIC=
DO_DC=
DO_TC=
DO_TG=
DO_VISC=
DO_EMD=

Set each option to:

• 1 = enable
• 0 = disable

Meaning of Each Toggle

DO_APG

Generates amorphous polymer structures using PySIMM. Builds chains, assigns GAFF2 parameters, RESP/Gasteiger charges, and writes LAMMPS .lmps data files.

DO_OPT

Runs MD equilibration, calculates density (RHO_MD.csv), radius of gyration (RG_MD.csv).

DO_MONO_ELECTRONIC

Runs Psi4 DFT to compute monomer properties: HOMO, LUMO, bandgap, dipole moment, polarizability, monomer refractive index, monomer dielectric constant, total energy.

DO_DC

Computes polymer dielectric properties from MD:

• dipole component
• electronic component
• total dielectric constant
• refractive index
• permittivity

DO_TC

Computes thermal conductivity using NEMD method.

DO_TG

Computes Glass Transition Temperature.

DO_VISC

Computes viscosity, diffusion coefficient, and MSD.

DO_EMD

Computes thermodynamic and mechanical properties:

• specific heat capacity Cp
• thermal diffusivity
• volume expansion coefficient
• linear expansion coefficient
• bulk modulus
• shear modulus
• Young’s modulus
• Poisson’s ratio

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7. Directory Structure (Auto-created)

The workflow will create folders similar to:

POLYMER_DATA/RESULTS/
    RHO_MD.csv
    CP_MD.csv
    DC_MD.csv
    TC_MD.csv
    TG_MD.csv
    VISC_MD.csv

Each PID has its own subfolder under POLYMER_DATA.

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