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py_itm

Characterizing local atomic environments using IRA/SOFI. Playing with MPI in python3.

Requirements

  • The following python3 modules:

    • ovito:

      pip3 install ovito

    • mpi4py:

      pip3 install mpi4py

    • cython:

      pip3 install Cython
  • The IRA/SOFI library (provided here as git submodule).

Installation

Clone the repository (SSH/https, you choose):

git clone [email protected]:mgoonde/py_itm.git your/path/to/py_itm

Compile ITM:

cd your/path/to/py_itm
make

Add the python interface directory to PYTHONPATH env variable. Simplest to add in your .bashrc (edit proper path):

export PYTHONPATH=/your/path/to/py_itm/interf:$PYTHONPATH

Compilation errors

In case of errors during compilation, try to figure out in which stage it happened. There are three stages to compile:

  1. IRA library
  2. the src
  3. the cython module py_itm

IRA library is provided as submodule, if the directory IRA is empty, then you need to initialize the submodule manually:

git submodule update --init

The compilation of IRA requires lapack, please see the IRA/src/Makefile in case of problems.

The fortran compiler is set to gfortran in src/Makefile and in IRA/src/Makefile. To use a different compiler, you will need to edit these makefiles. The compilation is currently tested only on gfortran 11.4.0.

There could be missing python modules needed for compilation of the cython module py_itm, this you will have to figure on your own.

Running calculations

See the test directory.