https://github.com/anselmoo/edrixs

An open source toolkit for simulating RIXS spectra based on ED

https://github.com/anselmoo/edrixs

Repository

An open source toolkit for simulating RIXS spectra based on ED

README.rst

===============================
edrixs
===============================

.. image:: https://img.shields.io/pypi/v/edrixs.svg
        :target: https://pypi.python.org/pypi/edrixs

.. image:: https://mybinder.org/badge_logo.svg
 :target: https://mybinder.org/v2/gh/NSLS-II/edrixs.git/master?urlpath=lab

An open source toolkit for simulating RIXS spectra based on exact diagonalization (ED) for strongly correlated materials.
`It is developed `_ as part of `COMSCOPE project `_ in the Center for Computational Material Spectroscopy and Design, Brookhaven National Laboratory

* Free software: GNU General Public License Version 3
* Documentation: https://nsls-ii.github.io/edrixs.
* Launch a `MyBinder Session `_ to try the code.

Features
--------

* ED solver
* XAS spectra
* RIXS spectra

How to cite
-----------
If you are using the EDRIXS code to do some studies and would like to publish your great works, it would be really appreciated if you can cite the following paper:

``EDRIXS: An open source toolkit for simulating spectra of resonant inelastic x-ray scattering, Y.L. Wang, G. Fabbris, M.P.M. Dean and G. Kotliar``, `Computer Physics Communications,243, 151 (2019) `_, `arXiv:1812.05735 `_.


Install via Anaconda for Linux and macOS
----------------------------------------

  .. code-block:: bash

     $ conda create --name edrixs_env python=3.7
     $ conda activate edrixs_env
     $ conda install -c conda-forge edrixs


Run edrixs in docker
--------------------
To make life easier, we have built a docker image based on Ubuntu Linux (18.04) for edrixs, so you don't need to struggle with the installation anymore.
The docker image can be used on any OS as long as the `docker `_ application are available.
Follow these steps to use the docker image:

* Install the `docker `_ application on your system and `learn how to use it `_.
* Once the docker is running, create a directory to store data in your host OS and launch a container to run edrixs

    .. code-block:: bash

       $ mkdir /dir/on/your/host/os   # A directory on your host OS
       $ docker pull edrixs/edrixs    # pull latest version
       $ docker run -it -p 8888:8888 -u rixs -w /home/rixs -v /dir/on/your/host/os:/home/rixs/data edrixs/edrixs

  it will take a while to pull the image from `Docker Hub `_ for the first time, while, it will launch the local one very fast at the next time.

  * ``-p 8888:8888`` maps container's port 8888 to host port 8888.
  * ``-u rix`` means using a default user ``rixs`` to login the Ubuntu Linux, the password is ``rixs``.
  * ``-v /dir/on/your/host/os:/home/rixs/dat`` means mounting the directory ``/dir/on/your/host/os`` from your host OS to  ``/home/rixs/data`` on the Ubuntu Linux in the container.

* After launching the container, you will see ``data`` and ``edrixs_examples`` in ``/home/rixs`` directory. If you want to save the data from edrixs calculations to your host system, you need to work in ``/home/rixs/data`` directory.

    .. code-block:: bash

       $ cd /home/rixs/data
       $ cp -r ../edrixs_examples .
       $ Play with edrixs ...

  Note that any changes outside ``/home/rixs/data`` will be lost when this container stops. You can only use your host OS to make interactive plots. Use ``sudo apt-get install`` to install softwares if they are needed.

* Type ``exit`` in the container to exit. You can delete all the stopped containers by

   .. code-block:: bash

      $ docker rm $(docker ps -a -q)

* You can delete the edrixs image by

   .. code-block:: bash

      $ docker rmi edrixs/edrixs


Install from source
-------------------
* Required tools and libraries

   * Fortran compiler: gfortran and ifort are supported
   * MPI environment: openmpi and mpich are tested
   * mpif90 (binding with gfortran or ifort) and mpicc (binding with gcc)
   * Python3
   * BLAS and LAPACK: gfortran+OpenBLAS or ifort+MKL
   * arpack-ng (with mpi enabled)
   * Numpy
   * Scipy
   * Sympy
   * Matplotlib
   * mpi4py
   * Sphinx
   * Numpydoc

  Be sure to compile OpenBLAS, arpack-ng, mpi4py and edrixs with the same (MPI) Fortran compiler.

* Install edrixs

    .. code-block:: bash

       $ pip install -v .

  There will be problems when using gfortran with MKL, so we recommend ``gfortran+OpenBLAS`` or ``ifort+MKL``. The executable ``.x`` files will be installed in the ``bin`` directory of the active python environment.
  The fortran library and compiled python extension are built using ``cmake`` which can be configured by setting the ``CMAKE_CONFIGURE_ARGS`` environment variable.

Please see our `online documentation `_ for more details of installation.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use edrixs in your research, please cite it as below.
title: An open source toolkit for simulating RIXS spectra based on ED
version: 0.0.6
date-released: 2020-07-09
url: "https://github.com/NSLS-II/edrixs"
preferred-citation:
  type: article
  authors:
  - family-names: "Wang"
    given-names: "Y.L."
  - family-names: "Fabbris"
    given-names: "G."
  - family-names: "Dean"
    given-names: "M.P.M."
  - family-names: "Kotliar"
    given-names: "G."
  doi: "10.1016/j.cpc.2019.04.018"
  journal: "Computer Physics Communications"
  month: 9
  start: 151 # First page number
  end: 165 # Last page number
  title: "EDRIXS: An open source toolkit for simulating spectra of resonant inelastic x-ray scattering"
  volume: 243
  year: 2019

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