master 2 dev_gen merge

AUTHORS

@@ -4,6 +4,12 @@ cpbd modules, optics functions, CSR,
 tracking module, orbit correction module,
 optimizer, SR module, LH, tutorials
 
+Svitozar Serkez svitozar.serkez@xfel.eu
+genesis2 & genesis4 adaptors,
+coherent radiation class,
+SASE estimator & imitator,
+Stokes parameters class.
+
 Ilya Agapov ilya.agapov@desy.de
 architecture, optimizer, x-ray optics,
 genesis2 adaptor
@@ -17,15 +23,13 @@ space charge, CSR, wakefields, LH
 Gianluca Geloni
 genesis2 adaptor
 
-Svitozar Serkez svitozar.serkez@xfel.eu
-genesis2 & genesis4 adaptors,
-coherent radiation class,
-SASE estimator & imitator,
-Stokes parameters class.
-
 Mykola Veremchuk, Andrei Trebushinin
 Stokes parameters calculation & visualization,
 coherent radiation class, unit tests, examples
 
-Michael Boese michael.boese@desy.de
+Michael Boese
 architecture, cpbd
+
+Christoph Lechner
+adaptors for "GENESIS 1.3", v4 and v2; functions for plotting of simulation results;
+control of MPI simulation jobs

CHANGELOG.md

@@ -42,23 +42,38 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - `remove_coupler_kick` convenience method for Cavity class
 - Integrated quad strengths for `k1` and `k2` convenience getters/setters (`k1l` and `k2l).
 - Added new method `Navigator.add_physics_processes` for adding multiple physics processes at the same time.  This will be a lot fastwe when lots of physics processes are to be added.
+>>>>>>> 6fdd98a24d013057498abd8e9ccf734939ef30e7
 - `Navigator.jump_to` method allowing a `Navigator` instance to jump
   to arbitrary points in z along the magnetic lattice.  Useful as it
   does not require modifying the underling beamling to achieve
   equivalent behaviour.
 - new `__repr__` methods for some common physics processes: `CSR`, `SmoothBeam`, `SpaceCharge` and `WakeTable`.
+- `SmoothBeam` mslice attribute can now be set in the `__init__`.
+- `extract_slice` method on SliceParameters instances
 - modified the 'MagneticLattice.transfer_maps()' method. When using the 'output_at_each_step=True' flag,
   the method returns (Bs, Rs, Ts, S), where 'S' is a list of coordinates after each transfer map.
 - New `WakeTable3` and `Wake3` class for third order Taylor expansion of wakefield tracking.
 - New wake table for the wakefields of parallel plate structure based on analytical results, `WakeTableParallelPlate_origin`, `WakeTableParallelPlate`, 
   `WakeTableParallelPlate3_origin`, `WakeTableParallelPlate3`. The waketables with `origin` use point charge wake at the vicinity of the drive particle, which is the upper limit for wake. 
   The other two waketables contain exponential decay term. The waketables with `3` provide third order Taylor expansion and should be used with `Wake3`.
+
+- added ParticleArray.get_twiss() method which calls get_envelop()
+- Twiss recalculates gamma_x/y and emit_x/y automatically
+- added link between quads to match function, e.g. vars = [{QF: 1.0, QD: -1.0}],
+- Added dispersion auto correction in get_envelope function, it calculates dispersion from statistics and correct it if needed
+- added image analysis functions to utils 
+- added LSC for undulators 
+- added in LSC feature to control size of the slice for transverse beam sizes calculation
+- added new feature to show_density(). now it can plot particles with scatter plot and color of the individual particle will correspond to density - slower but maybe can be visual pleasing for presentations
 
-  
+>>>>>>> 6fdd98a24d013057498abd8e9ccf734939ef30e7
 
 ### Fixed
 
 - fixed bugs in matching function if Drift length is in list of variables. 
+- fixed bug with match function delta constrain
+- fixed geometrical angle approximation in get_envelope function 
+- fixed bug with navigator reset_position() method. now it also call physics process .prepare() method
 
 ### Removed
 

README.md

@@ -1,172 +1,50 @@
 Accelerator, radiation and x-ray optics simulation framework
 
-# An Introduction to Ocelot
-
-Ocelot is a multiphysics simulation toolkit designed for studying FEL and storage ring-based light sources. Ocelot is written in Python. Its central concept is the writing of python's scripts for simulations with the usage of Ocelot's modules and functions and the standard Python libraries.
-
-Ocelot includes following main modules:
-* **Charged particle beam dynamics module (CPBD)**
-    - optics
-    - tracking
-    - matching
-    - collective effects (description can be found [here](http://vrws.de/ipac2017/papers/wepab031.pdf) and [here](https://journals.aps.org/prab/abstract/10.1103/PhysRevAccelBeams.22.024401))
-        - Space Charge (3D Laplace solver)
-        - CSR (Coherent Synchrotron Radiation) (1D model with arbitrary number of dipoles).
-        - Wakefields (Taylor expansion up to second order for arbitrary geometry).
-    - MOGA (Multi Objective Genetics Algorithm) [ref](http://accelconf.web.cern.ch/AccelConf/ipac2016/papers/thpmb034.pdf).
-* **Native module for spontaneous radiation calculation** (some details can be found [here](http://accelconf.web.cern.ch/AccelConf/ipac2019/papers/wepts017.pdf) and [here](http://scripts.iucr.org/cgi-bin/paper?S1600577519002509))
-* **FEL calculations: interface to GENESIS and pre/post-processing**
-* **Modules for online beam control and online optimization of accelerator performances.**   [ref1](http://accelconf.web.cern.ch/accelconf/IPAC2014/papers/mopro086.pdf), [ref2](https://jacowfs.jlab.org/conf/y15/ipac15/prepress/TUPWA037.PDF), [ref3](http://accelconf.web.cern.ch/AccelConf/ipac2016/papers/wepoy036.pdf), [ref4](https://arxiv.org/pdf/1704.02335.pdf).
-    - This module is being developed in collaboration with other accelerator groups. The module has been migrated to a separate [repository](https://github.com/ocelot-collab/optimizer) (in [ocelot-collab](https://github.com/ocelot-collab) organization) for ease of collaborative development.
-
-Ocelot extensively  uses Python's [NumPy (Numerical Python)](http://numpy.org) and [SciPy (Scientific Python)](http://scipy.org) libraries, which enable efficient in-core numerical and scientific computation within Python and give you access to various mathematical and optimization techniques and algorithms. To produce high quality figures Python's [matplotlib](http://matplotlib.org/index.html) library is used.
-
-It is an open source project and it is being developed by physicists from  [The European XFEL](http://www.xfel.eu/), [DESY](http://www.desy.de/) (Germany), [NRC Kurchatov Institute](http://www.nrcki.ru/) (Russia).
-
-We still have no documentation but you can find a lot of examples in /demos/ folder including this tutorial
-
-## Ocelot user profile
-
-Ocelot is designed for researchers who want to have the flexibility that is given by high-level languages such as Matlab, Python (with Numpy and SciPy) or Mathematica.
-However if someone needs a GUI  it can be developed using Python's libraries like a [PyQtGraph](http://www.pyqtgraph.org/) or [PyQt](http://pyqt.sourceforge.net/Docs/PyQt4/).
-
-
- ## Preliminaries
-
-The tutorial includes 9 examples dedicated to the beam dynamics and optics and 5 to Photon Field Simulation. However, you should have a basic understanding of Computer Programming terminologies. A basic understanding of Python language is a plus.
-
-##### This tutorial requires the following packages:
-
-- Python 3.6 - 3.8
-- `numpy` version 1.8 or later: http://www.numpy.org/
-- `scipy` version 0.15 or later: http://www.scipy.org/
-- `matplotlib` version 1.5 or later: http://matplotlib.org/
-- `ipython` version 2.4 or later, with notebook support: http://ipython.org
-
-**Optional**, but highly recommended for speeding up calculations
-- numexpr (version 2.6.1)
-- pyfftw (version 0.10)
-- numba
-
-**Orbit Correction module**
-- pandas
-
-The easiest way to get these is to download and install the (large) [Anaconda software distribution](https://www.continuum.io/).
-
-Alternatively, you can download and install [miniconda](https://docs.conda.io/en/latest/miniconda.html).
-The following command will install all required packages:
-```
-$ conda install numpy scipy matplotlib jupyter
-```
-
-## Ocelot installation
-##### Anaconda Cloud **recommended**
-The easiest way to install OCELOT is to use Anaconda cloud. In that case use command:
- ```
- $ conda install -c ocelot-collab ocelot
- ``` 
-##### GitHub
-Clone OCELOT from GitHub:
-```
-$ git clone https://github.com/ocelot-collab/ocelot.git
-```
-or download last release [zip file](https://github.com/ocelot-collab/ocelot/archive/v18.02.0.zip).
-Now you can install OCELOT from the source:
-```
-$ python setup.py install
-```
-
-##### PythonPath
-Another way is download ocelot from [GitHub](https://github.com/ocelot-collab/ocelot)
-1. you have to download from GitHub [zip file](https://github.com/ocelot-collab/ocelot/archive/master.zip).
-2. Unzip ocelot-master.zip to your working folder **/your_working_dir/**.
-3. Add **../your_working_dir/ocelot-master** to PYTHONPATH
-    - **Windows 7:** go to Control Panel -> System and Security -> System -> Advance System Settings -> Environment Variables.
-    and in User variables add **/your_working_dir/ocelot-master/** to PYTHONPATH. If variable PYTHONPATH does not exist, create it
-
-    Variable name: PYTHONPATH
-
-    Variable value: ../your_working_dir/ocelot-master/
-    - Linux:
-    ```
-    $ export PYTHONPATH=/your_working_dir/ocelot-master:$PYTHONPATH
-    ```
-
-#### To launch "ipython notebook" or "jupyter notebook"
-in command line run following commands:
-
-```
-$ ipython notebook
-```
-
-or
-```
-$ ipython notebook --notebook-dir="path_to_your_directory"
-```
-
-or
-```
-$ jupyter notebook --notebook-dir="path_to_your_directory"
-```
-
-#### OCELOT jupyter tutorials
-You can download OCELOT jupyter tutorials (release v18.02) using GitHub link [zip file](https://github.com/ocelot-collab/ocelot/releases/download/v18.02.0/ocelot_jupyter_tutorial.zip).
-
-## Tutorials
-* Preliminaries: Setup & introduction
-#### Beam dynamics
-
-* [Introduction. Tutorial N1. Linear optics](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/1_introduction.ipynb)
-    - Linear optics. Double Bend Achromat (DBA). Simple example of usage OCELOT functions to get periodic solution for a storage ring cell.
-* [Tutorial N2. Tracking](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/2_tracking.ipynb)
-    - Linear optics of the European XFEL Injector.
-    - Tracking. First and second order.
-    - Artificial beam matching - BeamTransform
-* [Tutorial N3. Space Charge](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/3_space_charge.ipynb)
-    - Tracking through RF cavities with SC effects and RF focusing.
-* [Tutorial N4. Wakefields](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/4_wake.ipynb)
-    - Tracking through corrugated structure (energy chirper) with Wakefields
-* [Tutorial N5. CSR](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/5_CSR.ipynb)
-    - Tracking trough bunch compressor with CSR effect.
-* [Tutorial N6. RF Coupler Kick](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/6_coupler_kick.ipynb)
-    - Coupler Kick. Example of RF coupler kick influence on trajjectory and optics.
-* [Tutorial N7. Lattice design](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/7_lattice_design.ipynb)
-    - Lattice design, twiss matching, twiss backtracking
-* [Tutorial N8. Physics process addition. Laser heater](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/8_laser_heater.ipynb)
-    - Theory of Laser Heater, implementation of new Physics Process, track particles w/o laser heater effect.
-* [Tutorial N9. Simple accelerator based THz source](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/9_thz_source.ipynb)
-    - A simple accelerator with the electron beam formation system and an undulator to generate THz radiation.
-
-#### Photon field simulation
-
-* [PFS tutorial N1. Synchrotron radiation module](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/pfs_1_synchrotron_radiation.ipynb).
-    - Simple examples how to calculate synchrotron radiation with OCELOT Synchrotron Radiation Module.
-* [PFS tutorial N2. Coherent radiation module and RadiationField object](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/pfs_2_radiation_field.ipynb).
-* [PFS tutorial N3. Reflection from imperfect highly polished mirror](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/pfs_3_imperfect_mirror.ipynb).
-* [PFS tutorial N4. Converting synchrotron radiation Screen object to RadiationField object for viewing and propagation](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/pfs_4_synchrotron_radiation_visualization.ipynb).
-* [PFS tutorial N5: SASE estimation and imitation](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/pfs_5_SASE_Estimator_and_Imitator.ipynb).
-
-#### Appendixes
-* [Undulator matching](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/undulator_matching.ipynb).
-    - brief theory and example in OCELOT
-* [Some useful OCELOT functions](http://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/small_useful_features.ipynb)
-    - Aperture, RK tracking 
-* [Example of an accelerator section optimization](https://nbviewer.jupyter.org/github/ocelot-collab/ocelot/blob/master/demos/ipython_tutorials/accelerator_optim.ipynb)
-    - A simple demo of accelerator section optimization with a standard scipy numerical optimization method. 
-## Documentation
-The API documentation can be build using [sphinx](https://sphinx.org).
-To do so, you have to clone the repository or download the zip file, as explained in the [ocelot installation section](#ocelot-installation).
-Then you can install all dependencies by running
-``` bash
-python -m pip install -r docs/requirements.txt
-python setup.py install
-```
-Now you can build the documentation by running
-```
-python setup.py build_sphinx
-```
-If these steps succeeded (yes, there are still very many errors and warnings during building the documentation),
-you can browse the HTML documentation by opening `build/sphinx/html/index.html` in your browser.
+# Ocelot
 
+Ocelot is an open-source multiphysics simulation toolkit for accelerator physics.  
+It is designed to model Free Electron Lasers (FELs), storage rings, and transport lines using a modular and scriptable Python interface.
+
+- **Website**: [https://www.ocelot-collab.com](https://www.ocelot-collab.com)
+- **Documentation**: [https://www.ocelot-collab.com/docs/docu/intro](https://www.ocelot-collab.com/docs/docu/intro)
+- **Tutorials**: [https://www.ocelot-collab.com/docs/tutorial/intro](https://www.ocelot-collab.com/docs/tutorial/intro)
+- **Source code**: [https://github.com/ocelot-collab/ocelot](https://github.com/ocelot-collab/ocelot)
+- **Bug reports**: [https://github.com/ocelot-collab/ocelot/issues](https://github.com/ocelot-collab/ocelot/issues)
+- **License**: [GPL-3.0 license](https://github.com/ocelot-collab/ocelot/blob/master/LICENSE)
+
+---
+
+## Features
+
+Ocelot provides:
+
+- A modular framework for beam dynamics simulations (tracking, optics, matching)
+- Physics processes including:
+  - Space charge
+  - Coherent synchrotron radiation (CSR)
+  - Wakefields
+  - and many more
+- A framework for FEL-related studies and synchrotron calculation
+- Jupyter-based interactive tutorials for education and development
+
+
+---
+
+## Getting Started
+
+For requirements and installation instructions, see the official guide:  
+👉 [**Installation & Setup**](https://www.ocelot-collab.com/docs/docu/intro)
+
+To explore tutorials, visit:  
+👉 [**Tutorial Overview**](https://www.ocelot-collab.com/docs/tutorial/intro)  
+👉 [**Student-Friendly Introduction**](https://www.ocelot-collab.com/docs/tutorial/tutorial-beam-dynamics/for_students)
+
+---
+
+We welcome feedback, contributions, and new ideas from the accelerator community!
+
+- [How to create a pull request](https://www.ocelot-collab.com/docs/docu/how-to/pull_request)
+- [How to add unit tests](https://www.ocelot-collab.com/docs/docu/how-to/unit_test)
+- [How to create your own Physics Process class](https://www.ocelot-collab.com/docs/docu/how-to/phys_proc)
 
 **Disclaimer:** The OCELOT code comes with absolutely NO warranty. The authors of the OCELOT do not take any responsibility for any damage to equipments or personnel injury that may result from the use of the code.

conda-recipe/meta.yaml

@@ -1,29 +1,38 @@
 package:
   name: ocelot
-  version: '24.03.0'
+  version: "25.07.0"
 
 source:
-  git_rev: 24.03.0
   git_url: https://github.com/ocelot-collab/ocelot.git
+  git_tag: v25.07.0
+
+build:
+  noarch: python
+  script: python -m pip install . --no-deps -vv
 
 requirements:
-  build:
-    - python
+  host:
+    - python >=3.9
+    - pip
     - setuptools
-    - numpy >=1.9
+  run:
+    - python >=3.9
+    - numpy
     - scipy
     - matplotlib
     - pandas
-    - alabaster==0.7.12
-    - Sphinx==3.2.1
-    - sphinxcontrib-jsmath==1.0.1
-  run:
-    - python
-    - numpy >=1.9
-    - scipy
-
+    - h5py
 
 about:
   home: https://github.com/ocelot-collab/ocelot
-  license: GNU General Public License v3.0
-  license_file: LICENSE
+  license: GPL-3.0
+  license_file: LICENSE
+  summary: "Accelerator, radiation, and x-ray optics simulation framework"
+  description: |
+    OCELOT is a simulation toolkit for modeling beam dynamics and synchrotron radiation in accelerators.
+  doc_url: https://ocelot-collab.github.io
+  dev_url: https://github.com/ocelot-collab/ocelot
+
+extra:
+  recipe-maintainers:
+    - sergey-tomin