DopeFlow: DFT Calculation Workflow for Atomic Substitution Problem

This repository contains scripts for managing VASP calculations on a SLURM-based cluster system.

1. job_monitor.sh

A script for submitting and monitoring sequential VASP calculations (Relax → SC → Band → DOS).

Usage

nohup bash job_monitor.sh <calc_type> &

where <calc_type> can be:

• Relax: Structure relaxation
• SC: Self-consistent calculation
• Band: Band structure calculation
• DOS: Density of states calculation

Directory Structure

structure_directory/
├── Relax/
├── SC/
├── DOS/
└── Band/

Required Files

• INCAR_<calc_type>: INCAR file for each calculation type
• sbp_<calc_type>.sh: SLURM submission script for each calculation type
• POTCAR: VASP pseudopotential file
• ../aflow_sym/uniq_poscar_list: List of structures to process
• diverge_structs: (optional) List of structures to skip

2. redo_optics.sh/restart_optics.sh

Scripts for managing optical calculations (SC → DIAG → GW0 → BSE) with automatic error checking and resubmission.

Usage

For normal execution with error checking:

nohup ./redo_optics.sh > redo_optics.log 2>&1 &

For forced restart of all calculations:

nohup ./restart_optics.sh > restart_optics.log 2>&1 &

Required Files

• Direct_dir: File containing list of directories to process
• INCAR files:
  • INCAR_SC
  • INCAR_DIAG
  • INCAR_GW0
  • INCAR_BSE
• SLURM submission scripts:
  • sbp_SC.sh
  • sbp_DIAG.sh
  • sbp_GW0.sh
  • sbp_BSE.sh
• POTCAR_GW: VASP GW pseudopotential file

<calc_type> can be:

• SC: DFT groundstate calculation
• DIAG: DFT "virtual" orbitals (empty states)
• GW0: RPA quasiparticles with single-shot GW
• BSE: BSE calculation

Directory Structure

structure_directory/
├── Optics/
│ ├── SC/
│ ├── DIAG/
│ ├── GW0/
│ └── BSE/

Output Logs

For redo_optics.sh:

• optical_jobs.log: Detailed job submission information
• job_<calc_type>.log: Job counting logs for each calculation type

For restart_optics.sh:

• restart_optical_jobs.log: Detailed job submission information for restarts
• job_<calc_type>_restart.log: Job counting logs for restarted calculations

Features

redo_optics.sh:

• Automatic error detection and job resubmission
• Sequential dependency handling
• Detailed logging of job submissions
• Limits concurrent jobs up to 60 computational nodes

restart_optics.sh:

• Forces restart of all calculations regardless of previous status
• Maintains same workflow and dependencies
• Uses separate log files to avoid confusion with original runs
• Limits concurrent jobs up to 60 computational nodes

Features

job_monitor.sh

• Manages sequential job submissions
• Limits concurrent jobs to 60
• Handles failed calculations
• Supports structure skipping via diverge_structs

redo_optics.sh/restart_optics.sh

• Automatic directory creation and management
• Sequential dependency handling (SC → DIAG → GW0 → BSE)
• Automatic error detection and job resubmission
• Detailed logging of job submissions
• Limits concurrent jobs to 60

Common Issues

1. Missing required files - ensure all INCAR and submission scripts are present
2. Directory permissions - ensure write access in all directories
3. SLURM queue limits - script will wait if queue is full
4. Failed calculations - check individual VASP output files for errors
5. Missing vasprun.xml - script will detect and resubmit affected calculations
6. Failed phonon calculations - use get_err_phon.sh to generate resubmission script

Notes

• Both scripts assume SLURM job scheduler
• Maximum concurrent jobs is set to 60
• Scripts will create necessary directories if they don't exist
• Error handling includes automatic resubmission of failed jobs

3. submit_phonon.sh

A script for managing phonon calculations with automatic supercell generation and job monitoring.

Usage

chmod +x submit_phonon.sh
nohup ./submit_phonon.sh > nohup.out 2>&1 &

Required Files

• phonon_list: File containing list of directories to process
• INCAR_PHON: INCAR file for phonon calculations
• sbp_PHON.sh: SLURM submission script for phonon calculations
• Supporting scripts:
  • convert_kpath.sh
  • generate_supercell.sh
  • extract_band_conf.sh
  • preprocess_high_symmetry_points.sh

Directory Structure

structure_directory/
├── Relax/
│ └── CONTCAR
└── PHON/
├── POSCAR-*
├── INCAR
├── POTCAR
└── sbp.sh

Output Logs

• job_PHON.log: Detailed job submission tracking
• Records which phonon calculations have been submitted for each structure

Features

• Automatic supercell generation using VASPKIT
• Batch submission (10 jobs at a time)
• Limits concurrent jobs to 50
• Resumes from last submitted job if interrupted
• Maintains submission history in log file

Workflow

1. Reads structures from phonon_list
2. For each structure:
   • Creates PHON directory
   • Copies CONTCAR from Relax directory
   • Generates primitive cell using VASPKIT
   • Generates supercells
   • Submits jobs in batches
3. Monitors job queue and maintains submission limits
4. Tracks progress in log file

Tips for Phonon Calculations

1. Check supercell size in generate_supercell.sh
2. Monitor convergence in individual phonon calculations
3. Use job_PHON.log to track submission progress
4. Check VASPKIT output for primitive cell generation

4. Post-Processing Scripts

post-proc_phonon.sh

A script for post-processing phonon calculations with automatic error detection and data generation.

Usage

sbatch phonon-pp-job.sh

Features

• Automatic error detection in SLURM output files
• Generates FORCE_SETS using phonopy
• Creates phonon band plots and raw data files
• Handles LaTeX formatting for band labels
• Detailed logging with configurable verbosity

Required Files

• phonon_list: List of structures to process
• Supporting scripts:
  • convert_kpath.sh
  • extract_band_conf.sh
  • preprocess_high_symmetry_points.sh

band_gap-pp.sh

A script for analyzing and categorizing band structures based on their electronic properties.

Usage

./band_gap-pp.sh

Features

• Automatically categorizes structures as Direct, Indirect, or Metallic
• Uses VASPKIT for band structure analysis
• Error detection in SLURM output files
• Generates categorized lists of structures

Output Files

• Direct_dir: List of structures with direct band gaps
• Indirect_dir: List of structures with indirect band gaps
• Metallic_dir: List of structures with metallic/semimetallic band gaps

get_err_phon.sh

A utility script for handling failed phonon calculations.

Usage

./get_err_phon.sh

Features

• Analyzes phonon post-processing logs for errors
• Generates resubmission script for failed calculations
• Handles missing or corrupted vasprun.xml files
• Automatic cleanup and job resubmission

Script Dependencies

• AFLOW
• VASPKIT
• Phonopy

Python Dependencies

Depending on which doping script you use, you'll need different Python packages:

For general substitution WITHOUT symmetry bias:
Example: aflow_sym/rnd_SiGe_doping.py or aflow_sym/NaSiGe_doping.py

• ASE

For using Fingerprint energy as symmetry bias:
Example: aflow_sym/Doping.py

• ASE
• libfp

For explicitly using group-subgroup splitting:
Example: aflow_sym/subgroup_doping.py

• ASE
• Pymatgen
• PyXtal

Environment Setup

Ensure these environment variables are set:

• $AFLOW_HOME: Path to AFLOW executable
• $VASPKIT_HOME: Path to VASPKIT executable
• $PHONOPY_HOME: Path to Phonopy executable

Common Workflow

1. Structure Relaxation (job_monitor.sh Relax)
2. Electronic Structure (job_monitor.sh SC/Band/DOS)
3. Optical Properties (redo_optics.sh)
4. Phonon Calculations (submit_phonon.sh)