Amp: Atomistic Machine-learning Potentials#

Developed by Andrew Peterson & Alireza Khorshidi, Brown University School of Engineering. Amp allows for the modular representation of the potential energy surface with descriptor and regression methods of choice for the user.

This project lives at: https://bitbucket.org/andrewpeterson/amp

Documentation lives at: http://amp.readthedocs.org

(This project was formerly known as "Neural". The last stable version of Neural can be found at https://bitbucket.org/andrewpeterson/neural)

License

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Installation

AMP is python-based and is designed to integrate closely with the Atomic Simulation Environment <https://wiki.fysik.dtu.dk/ase/>_ (ASE). In its most basic form, it has few requirements:

• Python, version 2.7 is recommended
• ASE
• NumPy (>= 1.9 for saving data in ".db" database format)
• SciPy

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Install ASE

We always test against the latest version (svn checkout) of ASE, but slightly older versions (>=3.9.0) are likely to work as well. Follow the instructions at the ASE <https://wiki.fysik.dtu.dk/ase/download.html>_ website. ASE itself depends upon python with the standard numeric and scientific packages. Verify that you have working versions of NumPy <http://numpy.org>_ and SciPy <http://scipy.org>. We also recommend matplotlib <http://matplotlib.org> in order to generate plots.

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Check out the code

As a relatively new project, it may be preferable to use the development version rather than "stable" releases, as improvements are constantly being made and features added. We run daily unit tests 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 <https://bitbucket.org/andrewpeterson/amp/>_. If you use git, check out the code with::

$ cd ~/path/to/my/codes $ git clone [email protected]: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 <https://bitbucket.org/andrewpeterson/amp/downloads>_ page, and extract it into '/path/to/my/codes'. Please make sure that the folder '~/path/to/my/codes/amp' includes the script 'init.py' as well as the folders 'descriptor', 'regression', ... At the download page, you can also find historical numbered releases.

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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:$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)

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Recommended step: Fortran modules

The code is designed to work in pure python, which makes it is easier to read, develop, and debug. However, it will be annoyingly slow unless you compile the associated fortran modules which speed up some crucial parts of the code. The compilation of Fortran codes and integration with the python parts is accomplished with the command 'f2py', which is part of NumPy. A Fortran compiler will also be necessary on your system; a reasonable open-source option is GNU Fortran, or gfortran. This complier will generate Fortran modules (.mod). gfortran will also be used by f2py to generate extension module 'fmodules.so' on Linux or 'fmodules.pyd' on Windows. In order to prepare the extension module take the following steps:

• Compile regression Fortran subroutines inside the regression folder by::

  $ cd ~/path/to/my/codes/regression/ $ ifort -c neuralnetwork.f90

• Move the module 'regression.mod' created in the last step, to the parent directory by::

  $ mv regression.mod ../

• Compile the main Fortran subroutines in the parent directory in companian with the descriptor and regression subroutines for Gilgamesh this looks like:

  $ f2py -c -m fmodules main.f90 descriptor/gaussian.f90 regression/neuralnetwork.f90 --fcompiler=intelem

If you update the code and your fmodules extension is not updated, an exception will be raised, telling you to re-compile.

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Recommended step: Run the tests

We include tests in the package to ensure that it still runs as intended as we continue our development; we run these tests on the latest build every night to try to keep bugs out. It is a good idea to run these tests after you install the package to see if your installation is working. The tests are in the folder tests; they are designed to run with nose <https://nose.readthedocs.org/>_. If you have nose installed, run the commands below::

$ mkdir /tmp/amptests $ cd /tmp/amptests $ nosetests ~/path/to/my/codes/amp/tests