Introduction

PMSCO stands for PEARL multiple-scattering cluster calculations and structural optimization. It is a collection of computer programs to calculate photoelectron diffraction patterns, and to optimize structural models based on measured data.

The actual scattering calculation is done by code developed by other parties. PMSCO wraps around those programs and facilitates parameter handling, cluster building, structural optimization and parallel processing. In the current version, the EDAC code developed by F. J. García de Abajo, M. A. Van Hove, and C. S. Fadley (1999) is used for scattering calculations. Instead of EDAC built-in routines, alternatively, the PHAGEN program from MsSpec-1.0 can be used to calculate atomic scattering factors.

Highlights

• angle and energy scanned XPD.
• various scanning modes including energy, manipulator angle (polar/azimuthal), emission angle.
• averaging over multiple domains and emitters.
• global optimization of multiple scans.
• structural optimization algorithms: particle swarm optimization, genetic algorithm, grid scan, table scan.
• detailed reports and graphs of result files.
• calculation of the modulation function.
• calculation of the weighted R-factor.
• automatic parallel processing using OpenMPI.
• compatible with Slurm resource manager on Linux cluster machines.

Installation

PMSCO is written in Python 3.6. The code will run in any recent Linux environment on a workstation or virtual machine. Scientific Linux, CentOS7, Ubuntu and Lubuntu (recommended for virtual machine) have been tested. For optimization jobs, a cluster with 20-50 available processor cores is recommended. The code requires about 2 GB of RAM per process.

Detailed installation instructions and dependencies can be found in the documentation (docs/src/installation.dox). A Doxygen compiler with Doxypypy is required to generate the documentation in HTML format.

The easiest way to set up an environment with all dependencies and without side-effects on other installed software is to use a Singularity container. A Singularity recipe file is part of the distribution, see the PMSCO documentation for details, Singularity must be installed separately. Installation in a virtual box on Windows or Mac is straightforward using pre-compiled images with Vagrant. A Vagrant definition file is included in the distribution.

The public distribution of PMSCO does not contain the EDAC code. Please obtain the EDAC source code from the original author, copy it to the pmsco/edac directory, and apply the edac_all.patch patch.

License

The source code of PMSCO is licensed under the Apache License, Version 2.0. Please read and respect the license agreement.

Please share your extensions of the code with the original author. The gitlab facility can be used to create forks and to submit pull requests. Attribution notices for your contributions shall be added to the NOTICE.md file.

Author

Matthias Muntwiler, mailto:matthias.muntwiler@psi.ch

Copyright

Copyright 2015-2021 by Paul Scherrer Institut

Release Notes

For a detailed list of changes, see the CHANGES.md file.

3.0.0 (2021-02-08)

• Run file interface replaces command line arguments:
  • Specify all run-time parameters in a JSON-formatted text file.
  • Override any public attribute of the project class.
  • Only the name of the run file is needed on the command line.
• The command line interface is still available, some default values and the handling of directory paths have changed. Check your code for compatibility.
• Integrated job scheduling with the Slurm resource manager:
  • Declare all job arguments in the run file and have PMSCO submit the job.
• Graphics scripts for genetic chart and swarm population (experimental feature).
• Update for compatibility with recent Ubuntu (20.04), Anaconda (4.8) and Singularity (3.7).
• Drop compatibility with Python 2.7, minimum requirement is Python 3.6.

2.2.0 (2020-09-04)

This release breaks existing project code unless the listed refactorings are applied.

• Major refactoring: The 'symmetry' calculation level is renamed to 'domain'. The previous Domain class is renamed to ModelSpace, Params to CalculatorParams. The refactorings must be applied to project code as well.
• Included periodic table of elements with electron binding energies and scattering cross-sections.
• Various bug fixes in cluster routines, data file handling, and in the PHAGEN interface.
• Experimental sqlite3 database interface for optimization results.