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SpinDec2

This project models spinoidal decomposition of a binary alloy system and has the following features:

• Explicit Eulerian approach with either:

  • A constant diffusive mobility field
  • A non-constant diffusive mobility field using the Darkens equation
  • Temperature dependent atomic mobilities

• Pseudo-Spectral solver with constant mobility

For full documentation, please refer to the wiki: https://hetsys.github.io/SpinDec2/

The following is an example end state using the explicit Eulerian solver with an initial concentration range of 0.31 to 0.32:

Dependencies

Prior to installation, please ensure that the following dependencies are installed:

• bash

  • util-linux
  • getopt

• python

  • netCDF4
  • matplotlib
  • numpy
  • scipy
  • argparse

• fortran

  • netCDF
  • fftw

This has been tested on HPC systems, and is known to work with the following dependency versions:

• GCC/7.3.0-2.30 OpenMPI/3.1.1 netCDF-Fortran/4.4.4 FFTW/3.3.8
• GCC/10.3.0 OpenMPI/4.1.1 netCDF-Fortran/4.5.3 FFTW/3.3.9

Download

To download the repository, clone the repository somewhere in your filesystem:

git clone https://github.com/HetSys/SpinDec2

Installation

An installation script is provided with the repository. All options can be viewed by running the script without any flags, or with -h/--help.

All flags have a short and a long version. If using the short option, and the flag supports an additional argument, the argument is called by a single letter immediately after the flag without leaving whitespace. For example, for compilation with debugging:

./install.sh -cd.

When using the long version, additional arguments can be specified like so (also using the compile flag):

./install.sh --compile=debug.

A description of the different flags and their arguments are given below:

Compile

To compile the code, run

./install.sh -c or ./install.sh –-compile.

The compilation argument takes an optional argument d/debug, however this is only for developer use. Running with this argument can cause decreases in performance.

After compilation, you will be prompted to add the binary to your default shell $PATH in $HOME/.bashrc. This feature only works for bash, so if you are using a different shell, you will have to do this manually.

Clean

Using the option will remove all installed binaries, netcdf, and checkpoint files in bin. To do so, run

./install.sh -C or ./install.sh –-clean

The clean argument takes an option argument c/confirm. This will prompt for confirmation before removing binaries.

Testing

Running

Unit tests can be automatically run from the install script. To use this feature, specify the argument

./install.sh -t or ./install.sh --test.

This takes one of several required arguments:

• c/compile to only compile the tests
• r/run to only run the tests
• b/both to both compile and run the tests.

All test binaries are compiled to test/test_bin/, and the main executable is saved as test_spindec.

Cleaning

To clean all unit tests binaries, use

./install.sh -T or ./install.sh --test-clean.

Contributors

Geraldine Anis, Ben Gosling, Dylan Morgan, Matyas Parrag, and Anas Siddiqui

HetSys CDT, University of Warwick

Copyright © 2022, Geraldine Anis, Ben Gosling, Dylan Morgan, Matyas Parrag, and Anas Siddiqui