setup package

actual_usage/VaspReconvergeExample.py

@@ -1,4 +1,4 @@
-from utils.vasp.vasp_resubmitter import CalculationConverger
+from vasp.resubmitter import CalculationConverger
 import os
 
 vasp_resubmitter = CalculationConverger(parent_dir=os.getcwd(),

actual_usage/build_vasp_database.py

@@ -1,4 +1,4 @@
-from utils.vasp.vasp import DatabaseGenerator
+from vasp.database import DatabaseGenerator
 import argparse
 import warnings
 from multiprocessing import cpu_count

actual_usage/update_vasp_db.py

@@ -1,4 +1,4 @@
-from utils.vasp.vasp import DatabaseGenerator
+from vasp.database import DatabaseGenerator
 import argparse
 import warnings
 from multiprocessing import cpu_count

utils/actual_usage/VaspReconvergeExample.py

@@ -0,0 +1,10 @@
+from utils.vasp.vasp_resubmitter import CalculationConverger
+import os
+
+vasp_resubmitter = CalculationConverger(parent_dir=os.getcwd(),
+                                        script_template_dir="/home/hmai/CustodianJobfiles",
+                                        max_submissions = 1000,
+                                        submission_command = "sbatch",
+                                        username="hmai")
+
+vasp_resubmitter.reconverge_all()                                        

utils/actual_usage/build_vasp_database.py

@@ -0,0 +1,42 @@
+from utils.vasp.vasp import DatabaseGenerator
+import argparse
+import warnings
+from multiprocessing import cpu_count
+
+def main():
+    warnings.filterwarnings("ignore")
+
+    # Initialize argument parser
+    parser = argparse.ArgumentParser(description='Find and compress directories based on specified criteria.')
+    parser.add_argument('directory', metavar='DIR', type=str, help='the directory to operate on')
+    parser.add_argument('--extract', action='store_true', help='Extract directories during database generation')
+    parser.add_argument('--max_dir_count', type=int, help='Maximum directory count for database generation')
+    parser.add_argument('--read_all_runs_in_dir', action='store_true', default=False, help='Read all runs in directory')
+    parser.add_argument('--read_error_runs_in_dir', action='store_true', default=False, help='Read directories with errors')
+    args = parser.parse_args()
+
+    datagen = DatabaseGenerator(args.directory,
+                                max_workers=cpu_count())
+
+    # Check if max_dir_count is provided as an argument
+    if args.max_dir_count is not None:
+        max_dir_count = args.max_dir_count
+    else:
+        max_dir_count = 2000  # Default value
+
+    # Call the build_database function with the updated parameters
+    df = datagen.build_database(extract_directories=args.extract,
+                                read_multiple_runs_in_dir=args.read_all_runs_in_dir,
+                                read_error_dirs=args.read_error_runs_in_dir,
+                                max_dir_count=max_dir_count,
+                                tarball_extensions=(".tar.gz", ".tar.bz2"),
+                                cleanup=False,
+                                keep_filenames_after_cleanup=[],
+                                keep_filename_patterns_after_cleanup=[],
+                                filenames_to_qualify=["OUTCAR", "vasprun.xml"],
+                                all_present=True,
+                                df_filename=None,
+                                df_compression=True)
+
+if __name__ == '__main__':
+    main()

actual_usage/compress_here → utils/actual_usage/compress_here

@@ -11,6 +11,6 @@ folder_path="$1"
 path_to_utils="/scratch/pawsey0380/hmai/utils/actual_usage/"
 # Garching
 path_to_utils="/cmmc/u/hmai/personal_dev/utils/actual_usage"
-
+path_to_utils="/root/personal_python_utilities/utils/actual_usage"
 # Run the first Python script and append the output to py.output
 python "$path_to_utils/compression.py" "$folder_path"

utils/actual_usage/update_vasp_db.py

@@ -0,0 +1,34 @@
+from utils.vasp.vasp import DatabaseGenerator
+import argparse
+import warnings
+from multiprocessing import cpu_count
+
+def main():
+    warnings.filterwarnings("ignore")
+
+    # Initialize argument parser
+    parser = argparse.ArgumentParser(description='Find and compress directories based on specified criteria.')
+    parser.add_argument('directory', metavar='DIR', type=str, help='the directory to operate on')
+    parser.add_argument('--max_dir_count', type=int, help='Maximum directory count for database generation')
+    parser.add_argument('--read_all_runs_in_dir', action='store_true', default=False, help='Read all runs in directory')
+    parser.add_argument('--read_error_runs_in_dir', action='store_true', default=False, help='Read directories with errors')
+    args = parser.parse_args()
+
+    datagen = DatabaseGenerator(args.directory,
+                                max_workers=cpu_count())
+
+    # Check if max_dir_count is provided as an argument
+    if args.max_dir_count is not None:
+        max_dir_count = args.max_dir_count
+    else:
+        max_dir_count = 2000  # Default value
+
+    # Call the update_failed_jobs_in_database function with the updated parameters
+    df = datagen.update_failed_jobs_in_database(df_path=args.directory,
+                                                read_error_dirs=args.read_error_runs_in_dir,
+                                                read_multiple_runs_in_dir=args.read_all_runs_in_dir,
+                                                max_dir_count=max_dir_count,
+                                                df_compression=True)
+
+if __name__ == '__main__':
+    main()

chargemol.py → utils/chargemol.py

@@ -213,6 +213,9 @@ def get_ANSBO_profile(self, axis=2, tolerance=0.1):
 
     def get_min_ANSBO(self, axis=2, tolerance=0.1):
         return min(get_ANSBO_all_cleavage_planes(self.struct, self.bond_matrix, axis=axis, tolerance=tolerance))
+
+    def analyse_ANSBO(self, axis=2, tolerance=0.1):
+        return analyse_ANSBO(self.directory, axis=axis, tolerance=tolerance)
 
 def analyse_ANSBO(directory, axis=2, tolerance=0.1):
     """
@@ -512,7 +515,7 @@ def get_ANSBO_all_cleavage_planes(structure, bond_matrix, axis = 2, tolerance =
     ANSBO_profile = []
     for cp in cp_list:
         ANSBO_profile.append(get_ANSBO(structure, bond_matrix, cp))
-    return ANSBO_profile
+    return cp_list, ANSBO_profile
 
 def plot_ANSBO_profile(structure,
                        bond_matrix,

functions.py → utils/functions.py

@@ -7,7 +7,7 @@
 
 from utils.jobfile import jobfile
 potcar_library_path = "/root/POTCAR_Library/GGA"
-potcar_library_path = "/u/hmai/pyiron-resources-cmmc/vasp/potentials/potpaw_PBE"
+#potcar_library_path = "/u/hmai/pyiron-resources-cmmc/vasp/potentials/potpaw_PBE"
 
 sites_to_study = {"S11-RA110-S3-32": [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22],
                   "S3-RA110-S1-11": [20, 22, 24, 26, 28, 30, 32, 34, 36],

jobscript_templates/jobfile-Setonix-base-custodian.sh → utils/jobscript_templates/jobfile-Setonix-base-custodian.sh

@@ -19,11 +19,25 @@ source /scratch/pawsey0380/hmai/mambaforge/bin/activate pymatgen
 echo 'import sys
 
 from custodian.custodian import Custodian
-from custodian.vasp.handlers import VaspErrorHandler, UnconvergedErrorHandler, NonConvergingErrorHandler, PositiveEnergyErrorHandler
 from custodian.vasp.jobs import VaspJob
-
+from custodian.vasp.handlers import (
+    VaspErrorHandler, 
+    NonConvergingErrorHandler,
+    PositiveEnergyErrorHandler,
+    FrozenJobErrorHandler
+)
+from utils.custom_custodian_handlers import Han_CustomVaspErrorHandler
+
+output_filename = {VASPOUTPUTFILENAME}
+
+handlers = [
+    VaspErrorHandler(output_filename=output_filename),
+    Han_CustomVaspErrorHandler(),
+    NonConvergingErrorHandler(),
+    PositiveEnergyErrorHandler(),
+    FrozenJobErrorHandler(output_filename=output_filename)
+]
 output_filename = "vasp.log"
-handlers = [VaspErrorHandler(output_filename=output_filename), UnconvergedErrorHandler(), NonConvergingErrorHandler(), PositiveEnergyErrorHandler()]
 jobs = [VaspJob(sys.argv[1:],
                 output_file=output_filename,
                 suffix = "")]

vasp/vasp.py → utils/vasp/database.py

@@ -11,7 +11,7 @@
 import utils.generic as gen_tools
 from utils.parallel import parallelise
 from utils.vasp.parser.outcar import Outcar
-from utils.vasp.vasp_database import parse_vasp_directory
+from vasp.parser.output import parse_vasp_directory
 
 def find_vasp_directories(parent_dir,
                           filenames=["vasp.log", "INCAR", "POTCAR", "CONTCAR", "KPOINTS", "OUTCAR", "vasprun.xml"],

utils/vasp/test_custodian_finaljobfuckingme.ipynb

@@ -0,0 +1,56 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "\n",
+    "from custodian.custodian import Custodian\n",
+    "from custodian.vasp.handlers import VaspErrorHandler, UnconvergedErrorHandler, NonConvergingErrorHandler, PositiveEnergyErrorHandler\n",
+    "from custodian.vasp.jobs import VaspJob\n",
+    "\n",
+    "output_filename = \"vasp.log\"\n",
+    "handlers = [VaspErrorHandler(output_filename=output_filename), UnconvergedErrorHandler(), NonConvergingErrorHandler(), PositiveEnergyErrorHandler()]\n",
+    "jobs = [VaspJob(sys.argv[1:], output_file=output_filename, suffix = \".relax_1\", final=False, settings_override=[{\"dict\": \"INCAR\", \"action\": {\"_set\": {\"KSPACING\": 0.5}}}]),\n",
+    "        VaspJob(sys.argv[1:], output_file=output_filename, suffix = \".relax_2\", final=False,\n",
+    "                settings_override = [{\"file\": \"CONTCAR\", \"action\": {\"_file_copy\": {\"dest\": \"POSCAR\"}}},\n",
+    "                    {\"dict\": \"INCAR\", \"action\": {\"_set\": {\"KSPACING\": 0.5, \"EDIFF\": 1E-5, \"EDIFFG\": 1E-4}}}], copy_magmom=True),\n",
+    "        VaspJob(sys.argv[1:], output_file=output_filename, suffix = \"\",\n",
+    "                settings_override = [{\"dict\": \"INCAR\", \"action\": {\"_set\": {\"NSW\": 0, \"LAECHG\": True, \"LCHARGE\": True, \"NELM\": 240, \"EDIFF\": 1E-5}}},\n",
+    "                                     {\"file\": \"CONTCAR\", \"action\": {\"_file_copy\": {\"dest\": \"POSCAR\"}}}])]\n",
+    "c = Custodian(handlers, jobs, max_errors=10)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pyiron_workflow",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}