Installation

AMP is python-based and is designed to integrate closely with the Atomic Simulation Environment (ASE). In its most basic form, it has few requirements:

  • Python, version 2.7 is recommended (it also supports Python3).
  • ASE.
  • NumPy.
  • SciPy.

To get more features, such as parallelization in training, a few more packages are recommended:

  • Pexpect (or pxssh)
  • ZMQ (or PyZMQ, the python version of ØMQ).

Certain advanced modules may contain dependencies that will be noted when they are used; for example Tensorflow for the tflow module or matplotlib (version > 1.5.0) for the plotting modules.

Basic installation instructions follow.

Install ASE

We always test against the latest version (svn checkout) of ASE, but slightly older versions (>=3.9) are likely to work as well. Follow the instructions at the ASE website. ASE itself depends upon python with the standard numeric and scientific packages. Verify that you have working versions of NumPy and SciPy. We also recommend matplotlib (version > 1.5.0) in order to generate plots.

Get the code

The latest stable release of Amp is version 0.5, which is permanently available at https://doi.org/10.5281/zenodo.322427. If installing version 0.5, you should follow ignore the rest of this page and follow the instructions included with the download (see docs/installation.rst or look for v0.5 on http://amp.readthedocs.io).

We are constantly improving Amp and adding features, so depending on your needs it may be preferable to use the development version rather than “stable” releases. We run daily unit tests to try to make sure that our development code works as intended. We recommend checking out the latest version of the code via the project’s bitbucket page. If you use git, check out the code with:

$ cd ~/path/to/my/codes
$ git clone git@bitbucket.org:andrewpeterson/amp.git

where you should replace ‘~/path/to/my/codes’ with wherever you would like the code to be located on your computer. If you do not use git, just download the code as a zip file from the project’s download page, and extract it into ‘~/path/to/my/codes’. Please make sure that the folder ‘~/path/to/my/codes/amp’ includes subdirectories ‘amp’, ‘docs’, ‘tests’, and ‘tools’.

Set the environment

You need to let your python version know about the existence of the amp module. Add the following line to your ‘.bashrc’ (or other appropriate spot), with the appropriate path substituted for ‘~/path/to/my/codes’:

$ export PYTHONPATH=~/path/to/my/codes/amp:$PYTHONPATH

You can check that this works by starting python and typing the below command, verifying that the location listed from the second command is where you expect:

>>> import amp
>>> print(amp.__file__)

See also the section on parallel processing for any issues that arise in making the environment work with Amp in parallel.