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public release 3.0.0 - see README and CHANGES for details

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README.md
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@ -6,7 +6,7 @@ It is a collection of computer programs to calculate photoelectron diffraction p
and to optimize structural models based on measured data.
The actual scattering calculation is done by code developed by other parties.
PMSCO wraps around that program and facilitates parameter handling, cluster building, structural optimization and parallel processing.
PMSCO wraps around those programs and facilitates parameter handling, cluster building, structural optimization and parallel processing.
In the current version, the [EDAC](http://garciadeabajos-group.icfo.es/widgets/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,
@ -20,11 +20,12 @@ Highlights
- 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, grid search, gradient search.
- 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.
- tested on Linux cluster machines.
- compatible with Slurm resource manager on Linux cluster machines.
Installation
@ -39,13 +40,12 @@ 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](http://www.stack.nl/~dimitri/doxygen/index.html) compiler with Doxypy is required to generate the documentation in HTML or LaTeX format.
A [Doxygen](http://www.stack.nl/~dimitri/doxygen/index.html) 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](https://www.sylabs.io/guides/2.5/user-guide/index.html) container.
A Singularity recipe file is part of the distribution, see the PMSCO documentation for details.
On newer Linux systems (e.g. Ubuntu 18.04), Singularity is available from the package manager.
Installation in a [virtual box](https://www.virtualbox.org/) on Windows or Mac is straightforward using the [Vagrant](https://www.vagrantup.com/) system.
A Vagrant file is included in the distribution.
The easiest way to set up an environment with all dependencies and without side-effects on other installed software is to use a [Singularity](https://www.sylabs.io/guides/3.7/user-guide/index.html) 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](https://www.virtualbox.org/) on Windows or Mac is straightforward using pre-compiled images with [Vagrant](https://www.vagrantup.com/).
A Vagrant definition file is included in the distribution.
The public distribution of PMSCO does not contain the [EDAC](http://garciadeabajos-group.icfo.es/widgets/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.
@ -70,7 +70,7 @@ Matthias Muntwiler, <mailto:matthias.muntwiler@psi.ch>
Copyright
---------
Copyright 2015-2020 by [Paul Scherrer Institut](http://www.psi.ch)
Copyright 2015-2021 by [Paul Scherrer Institut](http://www.psi.ch)
Release Notes
@ -78,6 +78,22 @@ 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)
------------------