DynaRef 6.5.0

This repository contains the Dyna development files.

"Dynamic x-ray reflectivity off- or on-resonant regime for isotropic, magnetic and anisotropic (multi)layer simulations and refinements Program"

About The Project

Dyna is a simulation program for reflectivity and transmittance of x-rays and optics, aimed at determining structural, magnetic and electronic stackings in ultrathin multilayers.

Among so many programs in the field, Dyna has several specificities : it includes anomalous, magnetic and anisotropic components in the index of refraction; it simulates reflectivities either versus angle, or versus x-ray energy, with arbitrary incident and out-going polarizations; it simulates Kerr and Faraday spectra, and transmittance through thin layers.

All the simulations can be simultaneously fitted against one model.

The program integrates a toolbox to create charge and magnetic factors from tables.

Dyna was also designed for pedagogical aims, making easy to slide parameters for on-the-fly effects.

Dyna is an on-going free and open-source project, under Python + Qt, or Matlab environments. Dyna can also be freely downloaded, and support is offered to users upon reasonable request.

Copyright Institut Neel, CNRS, Grenoble, France

Project Collaborators:

• Stéphane Grenier, stephane.grenier@neel.cnrs.fr
• Emmanuelle Jal (PhD, 2010-2013) now at LCPMR CNRS, Paris https://lcpmr.cnrs.fr/content/emmanuelle-jal
• Valentin Chardonnet (PhD) - Emmanuelle Jal's group (LCPMR, Sorbonne Université, Paris)
• Diego Turenne (PhD) - (LCPMR, Sorbonne Université, Paris) diego.turenne@sorbonne-universite.fr
• Nicolas Jaouen Sextants beamline, Synchrotron Soleil, nicolas.jaouen@synchrotron-soleil.fr
• Jean-Marc Tonnerre, jean-marc.tonnerre@neel.cnrs.fr
• Marta Elzo (PhD, 2009-2012)
• Ingrid Hallsteinsen - Padraic Shaffer’s group - Berkeley Nat. Lab.
• Daniel Schick Max-Born-Institute for nonlinear optics and short pulse spectroscopy im Forschungsverbund Berlin e.V.

Questions to:

Stéphane Grenier, stephane.grenier@neel.cnrs.fr

Installation

pip install DynaRef

DynaRef is the name of the package available from Pypi, the DynaRef package contains Dyna. Just launch with:

% dyna

Development install

git clone https://gitlab.com/dynadevgroup/Dyna
cd Dyna
pip install -e .
dyna

Python API

Dyna calculations can run without starting the Qt interface:

from dyna import Experiment, Formalism, load_builtin_sample, run_reflectivity

experiment = Experiment()
experiment.Formalism = Formalism.STEPANOV_ANGLE
experiment.Angle = [0.1, 5.0, 0.01, 0.0]
experiment.Energy[0] = 700.0

result = run_reflectivity(load_builtin_sample("w-si"), experiment)
print(result.x, result.intensity)

For reproducible batch calculations, use a JSON or YAML configuration such as examples/workflows/stepanov-angle.json or examples/workflows/stepanov-angle.yaml:

dyna-sim examples/workflows/stepanov-angle.json --output reflectivity.csv
dyna-sim examples/workflows/stepanov-angle.yaml --output reflectivity.csv
dyna-sim examples/workflows/stepanov-angle.json --output reflectivity.npz

The same file can be used directly from Python:

from dyna import load_config

result = load_config("examples/workflows/stepanov-angle.json").run()
result.save("reflectivity.csv")

Headless fitting is also available from JSON or YAML:

dyna-sim fit examples/workflows/fit-angle.json --summary fit-summary.json --output fitted.csv
dyna-sim fit examples/workflows/fit-angle.yaml --summary fit-summary.json --output fitted.csv

More ready-to-adapt examples are available in examples/README.md.

The graphical interface can also save and load Dyna projects as YAML files. This is the recommended project format for editable samples and experimental parameters; legacy project files can still be loaded. The GUI also provides sample-only YAML import/export actions for reusing the same layer stack across several projects.

Dyna also includes a small built-in YAML sample library:

from dyna import list_samples, load_builtin_sample

print(list_samples())
sample = load_builtin_sample("w-si")

List or export those samples from the command line with dyna-sim samples. The versioned YAML project and sample schema is documented in docs/yaml-format.rst.

Features

• magnetic-sensitive susceptibility, arbitrary magnetic moment direction described by Euler angles, with the limitation of neglictible spin-orbit coupling in the valence states
• anisotropic susceptibility, in the limitation of an uniaxial symmetry along the depth of the film, for the simulation of oriented molecules or orbitally ordered films (not in python code yet)
• structural and magnetic sensitive transmittance.
• Angular/Q scans
• Energy spectra at fix angle or fix Q
• Polarization Analysis, in and out
• Refinement in user-defined interval, with limits on parameters, and constrains between parameters
• Multifit : one system is refined by simultaneous simulations of various data (angle and energy scans, of any polarization, energy or angle configurations).
• Calculates Scattering Factors from Tables
• Calculates Kerr MO rotation and ellipticities, providing that the angles are small, validity to be checked case by case
• (Python Only) Scriptable
• (Matlab only) Genetic Algorithm (requires Optimization Toolbox)

Testing

Integration tests are to be found in the tests folder. Testing is done with pytest, it needs packages listed in tests/requirements_tests.txt. Mainly : pytest, pytest-qt and pytest-env. To launch all integration tests first activate the Dyna's python environement and then in the terminal do:

pytest tests/

These tests mimic common user actions on the interface in order to check a basic minimum viability. As not all functionality is available, some tests have been written but are set to be skipped.

Documentations:

https://pydyna.readthedocs.io