File size: 4,098 Bytes
930ea3d | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 | #!/bin/bash
#===============================
# Submission Script
#==============================================================
#$ -S /bin/bash
#$ -pe mpi-48 48
#$ -q hpc
#$ -o Log_Files/$JOB_NAME.o$JOB_ID.$TASK_ID
#$ -e Log_Files/$JOB_NAME.e$JOB_ID.$TASK_ID
#$ -cwd
#==============================================================
# --- Environment Setup ---
module purge
module load conda/24.7.1
conda activate polymer-workflow
module load lammps/29Aug24/intel/24.2
export MKL_INTERFACE_LAYER=""
export OMP_NUM_THREADS=1
#==============================================================
export NSLOTS="$NSLOTS"
initial_dir=$(pwd)
# SMILES CSV (for array jobs)
SMILES_FILE="SMILES.csv"
#==============================================================
# --- USER CONFIG ---
#==============================================================
#
# === USAGE EXAMPLE ===
#
# Run from SMILES.csv (array jobs), e.g. first 10 rows (after header):
# qsub -t 1-10 submit.sh
#
#===============================
#==============================================================
# --- PROPERTY TOGGLES (1=run, 0=skip;
#==============================================================
DO_APG=1 # Amorphous generation:
# ✅ Build amorphous polymer structure (.lmps)
# --- Charge method for APG (choose one) ---
CHARGE_METHOD="RESP" # Options: "RESP" or "GASTEIGER"
#(Use RESP if Dielectric Constant is calculating)
# Note: RESP is time consuming compared to GASTEIGER
DO_OPT=1 # Optimization / Equilibration: (Output Files: POLYMER_DATA/RESULTS)
# ✅ Equilibration runs (POLYMER_DATA/OPTIMIZATION/PID/PID_eq1.data, PID_eq2.data)
# ✅ Density calculation (RHO_MD.csv)
# ✅ Radius of gyration (RG_MD.csv)
# Property calculations
DO_MONO_ELECTRONIC=1 # Monomer electronic properties:(DFT)
# ✅ HOMO (Highest Occupied Molecular Orbital) (HOMO_DFT.csv)
# ✅ LUMO (Lowest Unoccupied Molecular Orbital) (LUMO_DFT.csv)
# ✅ Band gap energy (BANDGAP_DFT.csv)
# ✅ Dipole moment (MU_DFT.csv)
# ✅ Dipole polarizability (ALPHA_DFT.csv)
# ✅ Total energy (ETOTAL_DFT.csv)
# ✅ Dielectric constant-electronic component (monomer) (EDCMONO_DFT.csv) (Rough estimate only, use MD data)
# ✅ Refractive index- (monomer) (ERIMONO_DFT.csv) (Rough estimate only, use MD data)
DO_DC=1 # Polymer electronic properties (MD)
# ✅ Dielectric constant- dipole component (polymer) (DCD_MD.csv)
# ✅ Dielectric constant- electronic component (polymer) (DCE_MD.csv)
# ✅ Dielectric constant- total (Polymer) (DC_MD.csv)
# ✅ Refractive index- (Polymer) (RI_MD.csv)
# ✅ Permittivity - (Polymer) (PE_MD.csv)
DO_TC=1 # Thermal conductivity (TC_MD.csv)
DO_TG=1 # Glass transition temperature:
# ✅ Passes Tg from TG_EXP.csv (PID,Tg); (TG_MD.csv)
DO_VISC=1 # Viscosity: Passes Tg from TG_EXP.csv (PID,Tg);
# ✅ Viscosity (per your LAMMPS input) (VISC_MD.csv)
# ✅ Diffusion coefficient (D_MD.csv)
# ✅ Mean square displacement (MSD)
DO_EMD=1
# ✅ Specific heat (Cp) (CP_MD.csv)
# ✅ Thermal diffusivity (alphaT) (ALPHAT_MD.csv)
# ✅ Volume expansion coefficient (alphaP) (ALPHAP_MD.csv)
# ✅ Linear expansion coefficient (alphaL) (ALPHAL_MD.csv)
# ✅ Bulk Modulus (K_MD.csv)
# ✅ Shear Modulus (G_MD.csv)
# ✅ Youngs Modulus (E_MD.csv)
# ✅ Poisson ratio (NU_MD.csv)
#==============================================================
CSV_START_LINE=2 # 2 = skip header; set to 1 if no header
# Export config so child jobs (manual list mode) inherit these values
export SMILES_FILE CSV_START_LINE
export DO_APG DO_MONO_ELECTRONIC DO_OPT DO_TC DO_TG DO_VISC DO_DC DO_EMD
export CHARGE_METHOD
export initial_dir
#==============================================================
# --- Run (files.sh handles dispatch vs per-PID workflow) ---
#==============================================================
source Files/files.sh
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