FireWorks, FilePad and Metadata

Introduction

The Jupyter notebook PythonGoldCluster.ipynb contains two FireWorks sample usage cases. They demonstrate meaningful use of metadata for management of workflow results within FireWork's FilePad.

Content

• PythonGoldCluster.ipynb: a Jupyter notebook working through this demo from setting up workflows to analyze results, i.e. from beginning to end

• A_*.yaml to D_*.yaml: Static yaml descriptions of Fireworks used within the first sample case.

• infiles/*: static LAMMPS input scripts and data files used in both sample cases. The third-party EAM potential file Au-Grochola-JCP05.eam.alloy by

  G. Grochola, S.P. Russo, and I.K. Snook (2005), "On fitting a gold embedded atom method potential using the force matching method", The Journal of Chemical Physics, 123(20), 204719. DOI: 10.1063/1.2124667.

  has been excluded from this repository. You will find it publicly available for download at https://www.ctcms.nist.gov/potentials/system/Au (see infiles/NOTE)

• fig/*: figures and animations used for documentation purposes

• doc/PythonGoldCluster.html: a static HTML-rendered version of the Jupyter notebook. Does not include any interactive trajectory visualizations via nglview.

• doc/FilePad_slides.pdf: static PDF-rendered slides outlining this demonstration's core concepts.

• doc/gold_droplet_impact.mp4: An accompanying gold droplet impact animation not embedded within the static PDF slides.

Requirements

The Jupyter notebook has been tested with FireWorks version 1.9.5. Next to FireWorks, the Python packages

• ase
• matplotlib
• nglview (indirectly via ASE)
• numpy
• pandas
• scipy are used to facilitate demonstrative analysis of results.

The samples have been designed to run on a custom OpenStack instance. An image of this instance is available on request from the author (Johannes Hörmann, johannes.hoermann@imtek.uni-freiburg.de) via the OpenStack service bwCloud (https://bwcloud.ruf.uni-freiburg.de). Without modifications, these samples will not run within the framework of this grk2450-fireworks-tutorial. Most importantly, every Firework's "_category" spec must point to a worker that offers a LAMMPS executable. Likewise, ScriptTask calls of LAMMPS must match this particular worker's setup.

The LAMMPS version used for this demonstration is

LAMMPS (22 Aug 2018)

and the executable has been built with

Active compile time flags:

-DLAMMPS_GZIP
-DLAMMPS_PNG
-DLAMMPS_JPEG
-DLAMMPS_FFMPEG

Installed packages:

COLLOID COMPRESS KOKKOS KSPACE MANYBODY MC MOLECULE MPIIO OPT PYTHON REPLICA
RIGID VORONOI USER-COLVARS USER-DIFFRACTION USER-MOLFILE USER-NETCDF USER-OMP

Contributors:

• Johannes Hörmann (IMTEK, University of Freiburg, johannes.hoermann@imtek.uni-freiburg.de)
• Prof. Lars Pastewka (IMTEK, University of Freiburg, lars.pastewka@imtek.uni-freiburg.de)