Decond is a framework to analyze the transport properties in electrolyte solution with various decomposition methods.

Currently, the decomposition by species and by spatial correlation is implemented and is based on J. Chem. Phys. 141, 044126 (2014).

This project consists of two parts:

1. Decomposition of the velocity time correlation functions of ions calculated from the Gromacs MD trajectories. It is done throught the Fortran program fortran/decompose_mpi.
2. Analysis of the decomposed correlation data. It is done through the Python scripts in python/ folder.

Fortran:

• XTC library: Please use the customized version in fortran/lib/xdrfile-1.1.1-d, which has been modified to double precision.
• HDF5: You can use the system built-in HDF5 if available, or download it from the HDF5 group page.

Python:

• Version >= 3.0
• SciPy

Using the Anaconda Python Distribution is the easiest way, which includes many packages useful for scientific calculations including SciPy.

The general idea of the setup process is:

1. Compile and install the customized XTC library fortran/lib/xdrfile-1.1.1-d.
2. Compile and install the HDF5 library, if it is not available on your system already.
3. Manually edit the file fortran/Makefile to suit your environment and then compile with make.
4. Download and install Anaconda Python Distribution. (Rememeber to download the Python 3+ version)

More details can be found on the wiki page.

This project follows semantic versioning