edrixs 0.0.8

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 (only Linux now)

$ 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

  $ 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.

  $ 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

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

• You can delete the edrixs image by

  $ 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 Fortran parts of edrixs

  $ cd src
  $ make F90=mpif90 LIBS="-L/usr/local/lib -lopenblas -lparpack -larpack"
  $ make install

  where, you may need to change F90 and LIBS according to your specific environment. There will be problems when using gfortran with MKL, so we recommend gfortran+OpenBLAS or ifort+MKL. libedrixsfortran.a will be generated, which will be used when building python interface. The executable .x files will be installed in edrixs/bin directory and add the following line in .bashrc or .bash_profile file,

  export PATH=/root_dir_of_edrixs/edrixs/bin:$PATH

• Install Python parts of edrixs

  Be sure to first make libedrixsfortran.a in src.

  $ python setup.py config_fc --f77exec=mpif90 --f90exec=mpif90 build_ext \
    --libraries=openblas,parpack,arpack --library-dirs=/usr/lib:/usr/local/lib:/opt/local/lib \
    --link-objects=./src/libedrixsfortran.a
  $ pip install .

  where, --library-dirs ares the paths to search --libraries, please set it according to your environments.

Please see our online documentation for more details of installation.