Merge branch 'cmelab:main' into main

.github/workflows/pytest.yml

@@ -14,12 +14,25 @@ on:
       - flowermd/**
       - environment-dev.yml
       - .github/workflows/pytest.yml
-  # Allows workflow to be manually triggered
+  issue_comment:
+    types: [created]
+    branches: [ main ]
+    paths:
+      - flowermd/**
+      - environment-dev.yml
+      - .github/workflows/pytest.yml
+
   workflow_dispatch:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, macOS-13, ubuntu-latest]
+        python-version: ['3.10', '3.11']
+
+    runs-on: ${{ matrix.os }}
 
     steps:
     - name: Check out repository
@@ -29,6 +42,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         environment-file: environment-dev.yml
+        python-version: ${{ matrix.python-version }}
         miniforge-variant: Mambaforge
         miniforge-version: 4.9.2-4
         use-mamba: true
@@ -46,3 +60,56 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
+
+  test-tutorials:
+    if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Put a reaction to the comment
+      run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        NODE_ID: ${{ github.event.comment.node_id }}
+    - name: Check if PR is open
+      run: |
+          STATE=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json state --jq .state)
+          if [ "$STATE" != "OPEN" ]; then
+            echo "Cannot build for closed PRs"
+            (
+              echo "**${{ github.workflow }}**"
+              echo "Cannot build Kuby for a closed PR. Use the `latest` version (built for the `master` branch) or create a new PR."
+            ) | \
+            gh pr comment "${PR_NUMBER}" --repo ${{ github.repository }} -F -
+            gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:THUMBS_DOWN}){reaction{content}subject{id}}}"
+            gh api graphql --silent --raw-field query="mutation RemoveReaction {removeReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
+            exit 1
+          fi
+      env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.issue.number }}
+          NODE_ID: ${{ github.event.comment.node_id }}
+    - name: Get PR HEAD Ref
+      id: getRef
+      run: echo "pr_ref=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json headRefOid | jq -r '.headRefOid')" >> $GITHUB_OUTPUT
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        PR_NUMBER: ${{ github.event.issue.number }}
+
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Build environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment-dev.yml
+        miniforge-variant: Mambaforge
+        miniforge-version: 4.9.2-4
+        use-mamba: true
+
+    - name: Install package
+      shell: bash -l {0}
+      run: pip install .
+
+    - name: Run pytest on tutorials
+      shell: bash -l {0}
+      run: python -m pytest -rs -v --nbmake tutorials/

.pre-commit-config.yaml

@@ -11,14 +11,14 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.4.2
     hooks:
       - id: black
         args: [ --line-length=80 ]
@@ -37,6 +37,7 @@ repos:
       - id: flake8
         args:
           - --max-line-length=80
+          - --extend-ignore=E203
         exclude: '__init__.py'
 
   - repo: https://github.com/pycqa/pydocstyle

README.md

@@ -16,6 +16,11 @@ This is bolstered by a library-based approach to system initialization, making
 flowerMD agnostic to system identity, forcefield, and thermodynamic
 ensemble, and allowing for growth on an as-needed basis.
 
+flowerMD's design allows for creation of modules where an end-to-end interface is designed with a complex task in mind, such as fusion welding of polymers and surface wetting:
+
+<img src='docs/images/interface.png' width='250' height='160'> <img src='docs/images/adhesion.png' width='250' height='160'> <img src='docs/images/tensile2.png' width='320' height='160'>
+
+<img src='docs/images/surface-wetting.png' width='410' height='180'> <img src='docs/images/surface-wetting2.png' width='410' height='180'>
 
 Installing flowermd
 ===================

environment-dev.yml

@@ -7,16 +7,17 @@ dependencies:
   - freud >=2.13.1
   - gmso >=0.11.2
   - gsd >=3.0
+  - grits=0.4.1
   - hoomd=4.3
-  - mbuild >=0.16.4
+  - mbuild >=0.17.0
   - numpy
   - openbabel >=3
   - pip
   - pre-commit
   - py3Dmol
   - pytest
   - pytest-cov
-  - python >=3.10
+  - nbmake
+  - python >=3.10, <3.12
   - fresnel >=0.13.5
   - cmeutils >=1.1.1
-  - grits >=0.3.0

environment.yml

@@ -8,12 +8,12 @@ dependencies:
   - gmso >=0.11.2
   - gsd >=3.0
   - hoomd=4.3
-  - mbuild >=0.16.4
+  - mbuild >=0.17.0
   - numpy
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10
+  - python >=3.10, <3.12
   - fresnel >=0.13.5
   - cmeutils >=1.1.1
-  - grits >=0.3.0
+  - grits =0.4.1

flowermd/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (1, 2, 0)
+VERSION = (1, 3, 0)
 
 __version__ = ".".join(map(str, VERSION))

flowermd/base/molecule.py

@@ -3,6 +3,7 @@
 import itertools
 import os.path
 import random
+import warnings
 from typing import List
 
 import mbuild as mb
@@ -211,13 +212,20 @@ def _align_backbones_z_axis(self, heavy_atoms_only=False):
         backbone_direction = np.array([0, 0, 1])
         for mol in self.molecules:
             if heavy_atoms_only:
-                positions = np.array(
-                    [
-                        p.xyz[0]
-                        for p in mol.particles()
-                        if p.element.symbol != "H"
-                    ]
-                )
+                try:
+                    positions = np.array(
+                        [
+                            p.xyz[0]
+                            for p in mol.particles()
+                            if p.element.symbol != "H"
+                        ]
+                    )
+                except AttributeError:
+                    positions = mol.xyz
+                    warnings.warn(
+                        "No element information found."
+                        "Using all particle positions to fit backbone axis."
+                    )
             else:
                 positions = mol.xyz
             backbone = get_backbone_vector(positions)

flowermd/base/simulation.py

@@ -67,6 +67,7 @@ def __init__(
         log_write_freq=1e3,
         log_file_name="sim_data.txt",
         thermostat=HOOMDThermostats.MTTK,
+        rigid_constraint=None,
     ):
         if not isinstance(forcefield, Iterable) or isinstance(forcefield, str):
             raise ValueError(
@@ -104,7 +105,17 @@ def __init__(
         self._kT = None
         self._reference_values = dict()
         self._reference_values = reference_values
-        self._integrate_group = hoomd.filter.All()
+        if rigid_constraint and not isinstance(
+            rigid_constraint, hoomd.md.constrain.Rigid
+        ):
+            raise ValueError(
+                "Invalid rigid constraint. Please provide a "
+                "hoomd.md.constrain.Rigid object."
+            )
+        self._rigid_constraint = rigid_constraint
+        self._integrate_group = self._create_integrate_group(
+            rigid=True if rigid_constraint else False
+        )
         self._wall_forces = dict()
         self._create_state(self.initial_state)
         # Add a gsd and thermo props logger to sim operations
@@ -290,7 +301,16 @@ def volume(self):
     def mass_reduced(self):
         """The total mass of the system in reduced units."""
         with self.state.cpu_local_snapshot as snap:
-            return sum(snap.particles.mass)
+            if self._rigid_constraint:
+                last_body_tag = -1
+                for body_tag in snap.particles.body:
+                    if body_tag > last_body_tag:
+                        last_body_tag += 1
+                    else:
+                        break
+                return sum(snap.particles.mass[last_body_tag + 1 :])
+            else:
+                return sum(snap.particles.mass)
 
     @property
     def mass(self):
@@ -603,7 +623,14 @@ def set_integrator_method(self, integrator_method, method_kwargs):
 
         """
         if not self.integrator:  # Integrator and method not yet created
-            self.integrator = hoomd.md.Integrator(dt=self.dt)
+            self.integrator = hoomd.md.Integrator(
+                dt=self.dt,
+                integrate_rotational_dof=(
+                    True if self._rigid_constraint else False
+                ),
+            )
+            if self._rigid_constraint:
+                self.integrator.rigid = self._rigid_constraint
             self.integrator.forces = self._forcefield
             self.operations.add(self.integrator)
             new_method = integrator_method(**method_kwargs)
@@ -1286,6 +1313,11 @@ def _lj_force(self):
             ][0]
         return lj_force
 
+    def _create_integrate_group(self, rigid):
+        if rigid:
+            return hoomd.filter.Rigid(("center", "free"))
+        return hoomd.filter.All()
+
     def _create_state(self, initial_state):
         """Create the simulation state.
 

flowermd/base/system.py

@@ -641,6 +641,8 @@ class Pack(System):
         The factor by which to expand the box for packing.
     edge : float, default 0.2
         The space (nm) between the edge of the box and the molecules.
+    overlap : float, default 0.2
+        Minimum separation (nm) between particles of different molecules.
 
 
     .. warning::
@@ -670,6 +672,7 @@ def __init__(
         packing_expand_factor=5,
         edge=0.2,
         overlap=0.2,
+        fix_orientation=False,
     ):
         if not isinstance(density, u.array.unyt_quantity):
             self.density = density * u.Unit("g") / u.Unit("cm**3")
@@ -682,6 +685,7 @@ def __init__(
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
+        self.fix_orientation = fix_orientation
         super(Pack, self).__init__(molecules=molecules, base_units=base_units)
 
     def _build_system(self):
@@ -709,6 +713,7 @@ def _build_system(self):
             box=list(target_box * self.packing_expand_factor),
             overlap=self.overlap,
             edge=self.edge,
+            fix_orientation=self.fix_orientation,
         )
         return system
 
@@ -729,6 +734,13 @@ class Lattice(System):
     basis_vector : array-like, default [0.5, 0.5, 0]
         The vector between points in the unit cell.
 
+    Notes
+    -----
+    The system is built in a way that the long axis of the
+    molecules is aligned with the z direction, and the
+    lattice is made by repeating and translating in the
+    x and y directions.
+
     """
 
     def __init__(

flowermd/library/__init__.py

@@ -9,6 +9,7 @@
     BaseHOOMDForcefield,
     BaseXMLForcefield,
     BeadSpring,
+    EllipsoidForcefield,
     FF_from_file,
     KremerGrestBeadSpring,
     TableForcefield,
@@ -17,6 +18,7 @@
     PEEK,
     PEKK,
     PPS,
+    EllipsoidChain,
     LJChain,
     PEKK_meta,
     PEKK_para,