Merge pull request #76 from glotzerlab/update-dependencies

Update Example Dependencies

.github/workflows/test.yml

@@ -31,7 +31,7 @@ jobs:
         python-version: ["3.9", "3.10"]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.0.0
       with:
         path: freud-examples
     # Important! All steps that use the conda environment should define "shell: bash -l {0}".
@@ -52,10 +52,10 @@ jobs:
         # Install testing requirements
         mamba install pytest nbval
     # Build freud from source to test the examples on the latest version
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.0.0
       with:
         path: freud
-        ref: next
+        ref: main
         repository: glotzerlab/freud
         submodules: true
     - name: Install freud
@@ -81,7 +81,7 @@ jobs:
     # notify developers if the scheduled check fails
     - name: Slack notification
       if: ${{ github.event_name == 'schedule' && (failure() || cancelled()) }}
-      uses: 8398a7/action-slack@v3.15.1
+      uses: 8398a7/action-slack@v3.16.2
       with:
         status: ${{ job.status }}
         fields: workflow,job,message,commit

.gitignore

@@ -1,2 +1,3 @@
+examples/gb_lattice.gsd
 *.ipynb_checkpoints
 *__pycache__

.pre-commit-config.yaml

@@ -3,35 +3,35 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.4.0'
+    rev: 'v4.5.0'
     hooks:
       - id: end-of-file-fixer
         exclude: 'setup.cfg'
       - id: trailing-whitespace
         exclude: 'setup.cfg'
       - id: debug-statements
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v3.3.1'
+    rev: 'v3.15.1'
     hooks:
       - id: pyupgrade
         args:
           - --py36-plus
   - repo: https://github.com/PyCQA/isort
-    rev: '5.12.0'
+    rev: '5.13.2'
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '23.3.0'
+    rev: '24.2.0'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: '6.0.0'
+    rev: '7.0.0'
     hooks:
       - id: flake8
         args:
           - --max-line-length=100
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.7.1
     hooks:
       - id: nbqa-pyupgrade
         args:

environment.yml

@@ -4,12 +4,12 @@ dependencies:
   - bokeh
   - fresnel>=0.12
   - freud
-  - gsd<3
-  - hoomd=2.*
+  - gsd
+  - hoomd
   - ipywidgets>=7
   - jupyterlab>=3
   - lammps
-  - matplotlib>=3,<3.7
+  - matplotlib>=3
   - mdanalysis>=2
   - mdtraj
   - nbconvert>=6

examples/HOOMD-MC-W6/.gitignore

@@ -1,2 +1,2 @@
-output.log
 rdf.csv
+w6_data.h5

examples/Smectic.ipynb

@@ -26,6 +26,7 @@
     "import numpy as np\n",
     "import rowan\n",
     "\n",
+    "\n",
     "def randomize_orientations(orientations, perturbation_magnitude):\n",
     "    randomized_orientations = []\n",
     "    for orientation in orientations:\n",
@@ -71,7 +72,7 @@
     "            positions.append(position)\n",
     "            particles_in_layer += 1\n",
     "\n",
-    "    return np.array(positions[:num_particles])\n"
+    "    return np.array(positions[:num_particles])"
    ]
   },
   {

examples/Visualization with plato.ipynb

@@ -12,55 +12,62 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "HOOMD-blue v2.6.0-151-gea140cffb DOUBLE HPMC_MIXED MPI TBB SSE SSE2 SSE3 SSE4_1 SSE4_2 AVX AVX2 \n",
-      "Compiled: 09/25/2019\n",
-      "Copyright (c) 2009-2019 The Regents of the University of Michigan.\n",
-      "-----\n",
-      "You are using HOOMD-blue. Please cite the following:\n",
-      "* J A Anderson, C D Lorenz, and A Travesset. \"General purpose molecular dynamics\n",
-      "  simulations fully implemented on graphics processing units\", Journal of\n",
-      "  Computational Physics 227 (2008) 5342--5359\n",
-      "* J Glaser, T D Nguyen, J A Anderson, P Liu, F Spiga, J A Millan, D C Morse, and\n",
-      "  S C Glotzer. \"Strong scaling of general-purpose molecular dynamics simulations\n",
-      "  on GPUs\", Computer Physics Communications 192 (2015) 97--107\n",
-      "-----\n",
-      "HOOMD-blue is running on the CPU\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
+    "import itertools\n",
+    "\n",
     "import hoomd\n",
-    "import hoomd.md\n",
+    "import numpy as np\n",
+    "from hoomd import md\n",
     "\n",
-    "hoomd.context.initialize(\"\")\n",
     "\n",
-    "# Silence the HOOMD output\n",
-    "hoomd.util.quiet_status()\n",
-    "hoomd.option.set_notice_level(0)\n",
+    "def make_simple_cubic_snapshot(a, n):\n",
+    "    \"\"\"Make a snapshot with a simple cubic lattice.\n",
     "\n",
-    "# Create a 10x10x10 simple cubic lattice of particles with type name A\n",
-    "system = hoomd.init.create_lattice(\n",
-    "    unitcell=hoomd.lattice.sc(a=1.5, type_name=\"A\"), n=10\n",
-    ")\n",
+    "    Args:\n",
+    "        a (float): Lattice spacing\n",
+    "        n (int): Number of particles\n",
+    "\n",
+    "    Returns:\n",
+    "        hoomd.Snapshot: The initial system snapshot.\n",
+    "    \"\"\"\n",
+    "    k = int(np.ceil(n ** (1 / 3)))\n",
+    "    L = k * a\n",
+    "    x = np.linspace(-L / 2, L / 2, k, endpoint=False)\n",
+    "    position = list(itertools.product(x, repeat=3))\n",
+    "    position = position[:n]\n",
+    "\n",
+    "    snap = hoomd.Snapshot()\n",
+    "    snap.particles.N = n\n",
+    "    snap.particles.types = [\"A\"]\n",
+    "    snap.particles.typeid[:] = [0] * n\n",
+    "    snap.particles.position[:] = position\n",
+    "    snap.configuration.box = [L, L, L, 0, 0, 0]\n",
+    "\n",
+    "    return snap\n",
+    "\n",
+    "\n",
+    "# Create an 8x8x8 simple cubic lattice\n",
+    "sim = hoomd.Simulation(hoomd.device.CPU())\n",
+    "sim.create_state_from_snapshot(make_simple_cubic_snapshot(a=1.5, n=1000))\n",
+    "sim.seed = 42\n",
     "\n",
     "# Specify Lennard-Jones interactions between particle pairs\n",
-    "nl = hoomd.md.nlist.cell()\n",
-    "lj = hoomd.md.pair.lj(r_cut=3.0, nlist=nl)\n",
-    "lj.pair_coeff.set(\"A\", \"A\", epsilon=1.0, sigma=1.0)\n",
+    "nl = hoomd.md.nlist.Cell(buffer=0.2)\n",
+    "lj = hoomd.md.pair.LJ(default_r_cut=3.0, nlist=nl)\n",
+    "lj.params[(\"A\", \"A\")] = dict(epsilon=1.0, sigma=1.0)\n",
     "\n",
     "# Integrate at constant temperature\n",
-    "hoomd.md.integrate.mode_standard(dt=0.005)\n",
-    "integrator = hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=0.01, tau=0.5)\n",
-    "integrator.randomize_velocities(seed=42)\n",
+    "nvt = md.methods.ConstantVolume(\n",
+    "    filter=hoomd.filter.All(), thermostat=md.methods.thermostats.Bussi(kT=0.01, tau=0.5)\n",
+    ")\n",
+    "integrator = md.Integrator(dt=0.005, methods=[nvt], forces=[lj])\n",
+    "sim.operations.integrator = integrator\n",
+    "sim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=0.01)\n",
     "\n",
     "# Run for 10,000 time steps\n",
-    "hoomd.run(10e3)\n",
-    "snap = system.take_snapshot()"
+    "sim.run(10e3)\n",
+    "snap = sim.state.get_snapshot()"
    ]
   },
   {
@@ -103,7 +110,7 @@
    "outputs": [],
    "source": [
     "positions = snap.particles.position\n",
-    "box = freud.Box.from_box(snap.box)\n",
+    "box = freud.Box.from_box(snap.configuration.box)\n",
     "ld = freud.density.LocalDensity(3.0, 1.0)\n",
     "ld.compute(system=snap)\n",
     "colors = matplotlib.cm.viridis(Normalize()(ld.density))\n",
@@ -130,7 +137,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c8b319501f594ee185999a85a1cdd55d",
+       "model_id": "b07937b725fe49aa9c33ba29650b85ec",
        "version_major": 2,
        "version_minor": 0
       },
@@ -149,7 +156,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -163,7 +170,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.13"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
@@ -2064,5 +2071,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }