Setting up Sphinx for documenting start-to-end simulation¶

You need clone the start-to-end repository from GitHub:

git clone https://github.com/chuckie82/start-to-end.git

The index.rst is the master ReST for your project.

You may already have sphinx sphinx installed – you can check by doing:

python -c 'import sphinx'

If that fails grab the latest version of and install it with:

> sudo easy_install -U Sphinx

Let’s see if we can build our html:

make html

If you now point your browser to _build/html/index.html, you should see the site.

To update the document on the web, just push your changes:

git add *.rst
git commit -m "Update all documents"
git push -u origin master

Installing your start-to-end package¶

More instructions to come...

Introduction¶

Documentation for FEL source simulation can be found on this page.

Data access¶

Data in archive can be exported using web browser. Initial FEL source can be downloaded from here:

FEL source web site

with authentication (xfel/desy account)

FEL source web site

If you use this dataset, please acknowledge [SALDIN99].

Output data description¶

The output data is expected in hdf5 format, and the glossary can be found below. FEL source module is responsible for writing out in the format specified below.

Diagnostic (diagnostic_felsrc.py)¶

Fig.1. Pulse irradiance XY map (number of photons per pixel), the title contains size of the pixel;

Fig.2. Pulse time structure, the title contains the pulse energy value.

Input data description¶

The input data is expected in hdf5 format, and the glossary can be found in the link below.

Diagnostic (diagnostic.py)¶

Fig.1. Pulse irradiance XY map (number of photons per pixel), the title contains size of the pixel;

Fig.2. Plot of pulse time structure before and after propagating, the title contains the propagated pulse energy value.

About WPG¶

WPG, WaveProperGator is an interactive simulation framework for coherent X-ray wavefront propagation. WPG provides intuitive interface to the SRW library. The application examples oriented on European XFEL design parameters.

Online documentation page

Input/Output data description¶

The input/output data is expected in hdf5 format, and the glossary can be found below. Photon matter interaction module is responsible for reading in and writing out in the format specified below.

Python script for HDF¶

Script on bitbucket

Input/Output data description¶

The input/output data is expected in hdf5 format, and the glossary can be found below. Coherent diffraction module is responsible for reading in and writing out in the format specified below.

Diagnostic¶

Python script displays /data/data and /data/diffr at completion of the module execution.

Scaling behaviour of SingFEL¶

Calculation time using single processor vs number of atoms is non-linear, perhaps quadratic.

Detector number of pixels: 131x131

Benzoic acid: 15 atoms Chignolin: 2484 atoms 2YBE: 3240 atoms 2NIP: 4735 atoms 4AS4: 4963 atoms

Input/Output data description¶

Test

The input/output data is expected in hdf5 format, and the glossary can be found below. Orientation determination module is responsible for reading in and writing out in the format specified below.

Diagnostics of reconstructed 3D diffraction volume¶

EMC reconstruction parameters..

Input/Output data description¶

The input/output data is expected in hdf5 format, and the glossary can be found below. Phasing module is responsible for reading in and writing out in the format specified below.