| # ADEPT: Automated molecular Dynamics Engine for Polymer simulaTions |
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| 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. |
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| 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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| --- |
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| ## 1. Create the Conda Environment |
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| Load the conda module on your HPC: |
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| ```bash |
| module load conda |
| ``` |
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| Create the environment: |
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| ```bash |
| conda env create -f polymer-workflow.yml |
| ``` |
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| Activate it: |
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| ```bash |
| conda activate polymer-workflow |
| ``` |
| --- |
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| ## 2. Install PySIMM |
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| PySIMM can be installed inside your conda environment. |
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| Option 1 — Simple install with pip |
| ```bash |
| conda activate polymer-workflow |
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| git clone https://github.com/polysimtools/pysimm.git |
| cd pysimm |
| pip install . |
| ``` |
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| Add the following line to your ~/.bashrc (edit the LAMMPS path as needed) |
| export LAMMPS_EXEC="/usr/bin/lmp" |
| source ~/.bashrc |
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| Option 2 — Using complete_install.py |
| ```bash |
| conda activate polymer-workflow |
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| git clone https://github.com/polysimtools/pysimm.git |
| python pysimm/complete_install.py --pysimm "$PWD" |
| ``` |
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| PySIMM handles polymer chain construction, random-walk polymerization, GAFF2 parameter assignment, RESP/Gasteiger charges, and LAMMPS data file generation.--- |
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| ## 3. Load LAMMPS on HPC |
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| LAMMPS is loaded using your cluster's module system. For example: |
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| ```bash |
| module load lammps |
| ``` |
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| LAMMPS does not need to be installed inside the conda environment. |
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| --- |
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| ## 5. Using the Submission Script |
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| To run the first 50 polymers: |
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| ```bash |
| qsub -t 1-50 submit.sh |
| ``` |
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| Logs are stored in: |
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| ```text |
| Log_Files/ |
| ``` |
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| --- |
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| ## 6. Property Toggles |
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| Inside `submit.sh`, you will find: |
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| ```bash |
| DO_APG= |
| DO_OPT= |
| DO_MONO_ELECTRONIC= |
| DO_DC= |
| DO_TC= |
| DO_TG= |
| DO_VISC= |
| DO_EMD= |
| ``` |
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| Set each option to: |
| - `1` = enable |
| - `0` = disable |
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| ### Meaning of Each Toggle |
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| **DO_APG** |
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| Generates amorphous polymer structures using PySIMM. Builds chains, assigns GAFF2 parameters, RESP/Gasteiger charges, and writes LAMMPS `.lmps` data files. |
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| **DO_OPT** |
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| Runs MD equilibration, calculates density (`RHO_MD.csv`), radius of gyration (`RG_MD.csv`). |
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| **DO_MONO_ELECTRONIC** |
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| Runs Psi4 DFT to compute monomer properties: HOMO, LUMO, bandgap, dipole moment, polarizability, monomer refractive index, monomer dielectric constant, total energy. |
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| **DO_DC** |
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| Computes polymer dielectric properties from MD: |
| - dipole component |
| - electronic component |
| - total dielectric constant |
| - refractive index |
| - permittivity |
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| **DO_TC** |
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| Computes thermal conductivity using NEMD method. |
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| **DO_TG** |
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| Computes Glass Transition Temperature. |
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| **DO_VISC** |
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| Computes viscosity, diffusion coefficient, and MSD. |
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| **DO_EMD** |
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| 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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| --- |
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| ## 7. Directory Structure (Auto-created) |
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| The workflow will create folders similar to: |
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| ```text |
| POLYMER_DATA/RESULTS/ |
| RHO_MD.csv |
| CP_MD.csv |
| DC_MD.csv |
| TC_MD.csv |
| TG_MD.csv |
| VISC_MD.csv |
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| ``` |
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| Each PID has its own subfolder under `POLYMER_DATA`. |
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| --- |
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