SSAGESLabs · pabloferz · Jun 19, 2024 · May 9, 2024 · May 10, 2024 · May 10, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -32,7 +32,7 @@ jobs:
       - name: Install python dependecies
         run: |
           python -m pip install --upgrade pip
-          pip install ase dill "dm-haiku<0.0.11" "e3nn-jax!=0.20.4" "jax<=0.4.15" "jaxlib<=0.4.15" "jax-md>=0.2.7" jaxopt pytest matplotlib
+          pip install ase dill "dm-haiku<0.0.11" "e3nn-jax!=0.20.4" "jax<=0.4.15" "jaxlib<=0.4.15" "jax-md>=0.2.7" jaxopt pytest matplotlib "scipy<1.13"
 
       - name: Install pysages
         run: pip install .

diff --git a/.github/workflows/docker-ci.yml b/.github/workflows/docker-ci.yml
@@ -159,6 +159,38 @@ jobs:
           docker load --input /tmp/pysages.tar
           docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_pucker && python3 ./unbiased.py && python3 ./check_pucker.py"
 
+  cv-ermsd-openmm-unbiased:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Download artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: pysages
+          path: /tmp
+      - name: Load and run test
+        run: |
+          docker load --input /tmp/pysages.tar
+          docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_ermsd/ermsd && python3 ./unbiased.py && python3 ./check_ermsd.py"
+
+  cv-ermsd-cg-openmm-unbiased:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Download artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: pysages
+          path: /tmp
+      - name: Load and run test
+        run: |
+          docker load --input /tmp/pysages.tar
+          docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_ermsd/ermsd_cg && python3 ./unbiased.py && python3 ./check_ermsd.py"
+
   alanine-dipeptide-string:
     runs-on: ubuntu-latest
     needs: build

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/mwouts/jupytext
-    rev: v1.15.2
+    rev: v1.16.2
     hooks:
       - id: jupytext
         args: [--sync]

diff --git a/Dockerfile b/Dockerfile
@@ -3,7 +3,7 @@ FROM ssages/pysages-openmm
 WORKDIR /
 
 RUN python -m pip install --upgrade pip
-RUN python -m pip install ase dill gsd matplotlib "pyparsing<3"
+RUN python -m pip install ase dill "gsd<3.3" matplotlib "pyparsing<3"
 
 # Install JAX and JAX-based libraries
 RUN python -m pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

diff --git a/Dockerfile-base b/Dockerfile-base
@@ -14,7 +14,7 @@ RUN apt-get update && apt-get install -y doxygen swig nvidia-cuda-dev nvidia-cud
 
 # Install python dependencies
 RUN python -m pip install --upgrade pip
-RUN python -m pip install 'numpy==1.22.4'
+RUN python -m pip install "numpy<2"
 RUN env MPICC=$(which mpicc) python -m pip install mpi4py
 
 ENV CC=gcc-8

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,6 +1,7 @@
 furo
 jaxlib
 myst-parser
+scipy<1.13
 setuptools-scm
 sphinx
 sphinx-copybutton

diff --git a/docs/source/module-pysages-colvars-orientation.rst b/docs/source/module-pysages-colvars-orientation.rst
@@ -0,0 +1,16 @@
+Orientation as collective variables
+------------------------------------
+
+.. rubric:: Overview
+
+.. autosummary::
+
+   pysages.colvars.orientation.RMSD
+   pysages.colvars.orientation.ERMSD
+   pysages.colvars.orientation.ERMSDCG
+
+.. rubric:: Details
+
+.. automodule:: pysages.colvars.orientation
+    :synopsis: Python classes Orientation collective variables.
+    :members:
diff --git a/docs/source/module-pysages-colvars.rst b/docs/source/module-pysages-colvars.rst
@@ -19,6 +19,9 @@ Collective Variables available in PySAGES
    pysages.colvars.coordinates.Component
    pysages.colvars.coordinates.Distance
 
+   pysages.colvars.orientation.ERMSD
+   pysages.colvars.orientation.ERMSDCG
+
 Abstract base classes
 
 .. autosummary::
@@ -37,6 +40,7 @@ Abstract base classes
    module-pysages-colvars-shape
    module-pysages-colvars-coordinates
    module-pysages-colvars-core
+   module-pysages-colvars-orientation
 
 .. automodule:: pysages.colvars
     :synopsis: Python classes for collective variables.

diff --git a/docs/source/pysages_wordlist.txt b/docs/source/pysages_wordlist.txt
@@ -83,3 +83,16 @@ workflow
 xy
 xz
 yz
+eRMSD
+RMSD
+Kabsch
+Bottaro
+Palma
+Bussi
+Pyrimidines
+cartesian
+xyz
+unitless
+nm
+nucleotides
+nt
diff --git a/examples/Advanced_Sampling_Introduction.md b/examples/Advanced_Sampling_Introduction.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/Install_PySAGES_Environment.md b/examples/Install_PySAGES_Environment.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/hoomd-blue/ann/Butane_ANN.md b/examples/hoomd-blue/ann/Butane_ANN.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/hoomd-blue/cff/Butane_CFF.md b/examples/hoomd-blue/cff/Butane_CFF.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/hoomd-blue/funn/Butane_FUNN.md b/examples/hoomd-blue/funn/Butane_FUNN.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md b/examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3

diff --git a/examples/hoomd-blue/spectral_abf/Butane-SpectralABF.md b/examples/hoomd-blue/spectral_abf/Butane-SpectralABF.md
@@ -6,7 +6,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     language: python

diff --git a/examples/hoomd-blue/umbrella_integration/Umbrella_Integration.md b/examples/hoomd-blue/umbrella_integration/Umbrella_Integration.md
@@ -7,7 +7,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.15.2
+      jupytext_version: 1.16.2
   kernelspec:
     display_name: Python 3
     name: python3