Add GeM CV

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, macos-latest]
-        python-version: [3.7, 3.9]
+        python-version: [3.8, 3.9]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
@@ -32,7 +32,7 @@ jobs:
       - name: Install python dependecies
         run: |
           python -m pip install --upgrade pip
-          pip install jaxlib pytest matplotlib
+          pip install dill jaxlib jax-md jaxopt pytest matplotlib
 
       - name: Install pysages
         run: pip install .
@@ -60,7 +60,7 @@ jobs:
       - name: Install python dependecies
         run: |
           python -m pip install --upgrade pip
-          pip install jaxlib pytest pylint flake8
+          pip install dill jaxlib jax-md jaxopt pytest pylint flake8
           pip install -r docs/requirements.txt
       - name: Install pysages
         run: pip install .

Dockerfile

@@ -5,8 +5,9 @@ WORKDIR /
 RUN python -m pip install --upgrade pip
 RUN python -m pip install ase gsd matplotlib "pyparsing<3"
 
-# Install JAX
+# Install JAX and JAX-MD
 RUN python -m pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+RUN python -m pip install --upgrade jax-md jaxopt
 
 COPY . /PySAGES
 RUN pip install /PySAGES/

LICENSE.md

@@ -48,3 +48,36 @@ Whereas the following applies to `pysages/methods/abf.py`:
 
 For a list of contributors to the SSAGES project visit
 <https://github.com/SSAGESproject/SSAGES>.
+
+The code in `pysages/utils/transformations.py` was adapted from
+<https://github.com/cgohlke/transformations/blob/v2022.9.26/transformations/transformations.py>.
+The following applies to the original implementation:
+
+> Copyright (c) 2006-2022, Christoph Gohlke
+> All rights reserved.
+>
+> Redistribution and use in source and binary forms, with or without
+> modification, are permitted provided that the following conditions are met:
+>
+> 1. Redistributions of source code must retain the above copyright notice,
+>    this list of conditions and the following disclaimer.
+>
+> 2. Redistributions in binary form must reproduce the above copyright notice,
+>    this list of conditions and the following disclaimer in the documentation
+>    and/or other materials provided with the distribution.
+>
+> 3. Neither the name of the copyright holder nor the names of its
+>    contributors may be used to endorse or promote products derived from
+>    this software without specific prior written permission.
+>
+> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+> AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+> IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+> ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+> LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+> CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+> SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+> INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+> CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+> ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+> POSSIBILITY OF SUCH DAMAGE.

pysages/colvars/__init__.py

@@ -20,3 +20,12 @@
     ShapeAnisotropy,
 )
 from .utils import get_periods, wrap
+
+# Conditionally export GeM if both `jax_md` and `jaxopt` are available
+try:
+    import jax_md
+    import jaxopt
+
+    from .patterns import GeM
+except ImportError:
+    pass