User Guide

Contents:

• Compiling and installing
  • Requirements
  • Recommended
  • Procedure
• Setting up Pylada
  • Setting up IPython
  • Running external programs
  • Running MPI calculations
  • Setting up Pylada with PBS/Slurm
• Testing
  • Proof of existence test
  • Battery of tests
  • Failure modes and possible solutions
• Creating and Manipulating crystal structures
  • Playing with the crystal structure
  • More advanced structure manipulation methods
  • Example: Iterating over the shells of a core-shell nanowire
• Interface to VASP
  • A fast primer
  • Configuring Pylada for VASP
  • Reading from pre-existing VASP files
  • Creating and Setting up the vasp functional
  • Executing a VASP calculation
  • Extracting results from VASP calculations
  • A *meta*-functional: Strain relaxation
  • Example: Epitaxial relaxation method
• Organized high-thoughput calculations: job-folders
  • Prep
  • Creating and accessing job-folders
  • Making a job-folder executable
  • Saving and loading folders
• IPython high-throughput interface
  • Prep
  • Manipulating job-folders
  • Launching calculations
  • Collecting results
• NREL Mat DB database interface
  • SQL database overview: Overview of the database system.
  • Flat file database overview: Overview of the database system.
  • Web overview: Overview of the web server system.
  • augmentDb.py: Add additional info to the model table.
  • execMimic.py: Mimic execution for validity testing.
  • fillDbVasp.py: Read files created by wrapUpload and add rows to the model table.
  • queryMatDb.py: Demo query of the NRELMatDB SQL database.
  • readVasp.py: Read and parse an OUTCAR or vasprun.xml file
  • ScanOutcar.py: Extract info from OUTCAR and INCAR files
  • ScanXml.py: Read and parse a vasprun.xml file
  • wrapReceive.py: Receive results sent by wrapUpload.sh
  • wrapUpload.py: Locate, extract, and upload results to the server running wrapReceive.
• NREL Scheduler interface
  • schedMain
  • Example A: static files
  • Example B: VASP