Added an argparser for sbatch scripts

demo/jobs.in

@@ -0,0 +1,20 @@
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/1/2_analysis/1_cluster/c0-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/1/2_analysis/1_cluster/c1-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/1/2_analysis/1_cluster/c2-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/1/2_analysis/1_cluster/c3-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/2/2_analysis/1_cluster/c0-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/2/2_analysis/1_cluster/c1-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/2/2_analysis/1_cluster/c2-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/2/2_analysis/1_cluster/c3-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/3/2_analysis/1_cluster/c0-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/3/2_analysis/1_cluster/c1-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/3/2_analysis/1_cluster/c2-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/3/2_analysis/1_cluster/c3-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/4/2_analysis/1_cluster/c0-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/4/2_analysis/1_cluster/c1-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/4/2_analysis/1_cluster/c2-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/4/2_analysis/1_cluster/c3-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/5/2_analysis/1_cluster/c0-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/5/2_analysis/1_cluster/c1-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/5/2_analysis/1_cluster/c2-opt/
+/home/kastner/projects/mimochromes/mc6/2_oxo/3_md/5/2_analysis/1_cluster/c3-opt/

demo/jobscript.sh

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+#$ -S /bin/bash             # Specifies interpreting shell for the job
+#$ -N pyEF                  # Identifier for the job
+#$ -l h_rt=48:00:00         # Specify maximum runtime
+#$ -l h_rss=40G             # Specify requested memory
+#$ -q gpusnew               # Specify which queue to submit the job to
+#$ -l gpus=1                # Always set to 1 no matter how many gpus are used.
+#$ -pe smp 2                # Number of parallel processes to run (defines how many GPUs)
+# -fin job_paths.in
+# -fin metal_indices.in
+
+export OMP_NUM_THREADS=2    # Number of threads to be spawned (needs to be the same as -smp)
+source ~/.bashrc   
+conda activate molsimp   
+
+# --geom                      Whether to perform a geometry check
+# --esp                       Whether to perform ESP analysis
+# --jobs_file                 Paths to all the QM jobs
+# --metals_file               The indices of the metals for each job
+
+RUN="/home/kastner/packages/pyEF/pyef/run.py"
+JOBS="/home/kastner/packages/pyEF/demo/jobs.in"
+METALS="/home/kastner/packages/pyEF/demo/metals.in"
+python $RUN --geom --esp --jobs_file $JOBS --metals_file $METALS  > pyEF.log
+

demo/metals.in

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+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486
+486

pyef/run.py

@@ -1,4 +1,7 @@
 import os
+import sys
+import pyef
+import argparse
 from pyef.analysis import Electrostatics
 from pyef.geometry import ErrorAnalysis
 
@@ -55,11 +58,23 @@ def main(jobs, geom_flag, esp_flag, metal_indices):
     # Method to Compute Efield Projections on bonds connected to the atom specified by index in metal_indices
     dataObject.getEFieldData(Efield_data_filename)
 
+def read_file_lines(file_path):
+    """Reads in auxiliary files containing job information"""
+    with open(file_path, 'r') as file:
+        return [line.strip() for line in file.readlines()]
+
 if __name__ == "__main__":
-    geom_flag = False   # Perform a geometry check
-    esp_flag = False    # Perform analysis of electrostatics
-    jobs = ['/home/kastner/DavidMimichrome/mc6_1_2best_c0opt', '/home/kastner/DavidMimichrome/mc6_2_6best_c0opt']
-    metal_indices = [486, 486]
-    main(jobs, geom_flag, esp_flag, metal_indices)
+    # Example: python run.py --geom --esp --jobs_file path/to/jobs.in --metals_file path/to/metals.in  > pyEF.log
+    parser = argparse.ArgumentParser(description="Script Description")
+    parser.add_argument("--geom", action="store_true", help="Perform a geometry check")
+    parser.add_argument("--esp", action="store_true", help="Perform analysis of electrostatics")
+    parser.add_argument("--jobs_file", required=True, help="Path to file containing job paths")
+    parser.add_argument("--metals_file", required=True, help="Path to file containing metal indices")
+
+    args = parser.parse_args()
+    geom_flag = args.geom
+    esp_flag = args.esp
+    jobs = read_file_lines(args.jobs_file)
+    metal_indices = [int(idx) for idx in read_file_lines(args.metals_file)]
 
-    # /home/kastner/DavidMimichrome/mc6_1_2best_c0opt, /home/kastner/DavidMimichrome/mc6_2_6best_c0opt
+    main(jobs, geom_flag, esp_flag, metal_indices)