Merge remote-tracking branch 'upstream/main' into from-openmm-positio…

…ns-warning

.github/workflows/ci.yaml

@@ -80,7 +80,7 @@ jobs:
     - name: Install OpenMM
       if: ${{ matrix.openmm == true }}
       run: |
-        micromamba install openmm "smirnoff-plugins =2024" -c conda-forge
+        micromamba install openmm openmmforcefields "smirnoff-plugins =2024" -c conda-forge
         pip install git+https://github.com/jthorton/de-forcefields.git
 
     - name: Uninstall OpenMM

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/psf/black
-  rev: 24.2.0
+  rev: 24.3.0
   hooks:
   - id: black
     files: ^openff|plugins|stubs
@@ -45,6 +45,11 @@ repos:
     files: ^openff|plugins|stubs
     exclude: openff/interchange/_version.py|setup.py
     args: ["--py39-plus"]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.3.3
+  hooks:
+    - id: ruff
+      args: ["check", "--select", "NPY"]
 - repo: https://github.com/pycqa/pydocstyle
   rev: 6.3.0
   hooks:

devtools/conda-envs/beta_env.yaml

@@ -1,6 +1,5 @@
 name: beta-env
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge/label/openmm_rc
   - conda-forge
   - openeye
@@ -22,6 +21,7 @@ dependencies:
   - foyer >=0.12.1
   # Testing
   - mdtraj
+  - openmmforcefields
   - intermol
   - openeye-toolkits >=2023.2
   - pytest-cov

devtools/conda-envs/dev_env.yaml

@@ -1,14 +1,13 @@
 name: openff-interchange-dev
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
   - openeye
 dependencies:
   # Core
-  - python
+  - python =3.10
   - pip
   - numpy
-  - pydantic
+  - pydantic =2
   - openmm
   # OpenFF stack
   - openff-toolkit =0.15.2
@@ -18,8 +17,9 @@ dependencies:
   # openff-nagl
   # openff-nagl-models
   # Optional features
-  - mbuild
+  - mbuild =0.17
   - foyer >=0.12.1
+  - gmso =0.12
   # Testing
   - mdtraj
   - intermol
@@ -34,6 +34,7 @@ dependencies:
   - gromacs =2023.3=nompi_*_103
   - lammps
   - panedr
+  - openmmforcefields
   # Typing
   - mypy =1.3
   - typing-extensions

devtools/conda-envs/docs_env.yaml

@@ -1,6 +1,5 @@
 name: interchange-docs
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
   # Base depends

devtools/conda-envs/examples_env.yaml

@@ -1,6 +1,5 @@
 name: interchange-examples-env
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
   - openeye
 dependencies:

devtools/conda-envs/test_env.yaml

@@ -1,6 +1,5 @@
 name: openff-interchange-env
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
   # Core
@@ -19,6 +18,7 @@ dependencies:
   - mbuild
   # Testing
   - mdtraj
+  - openmmforcefields
   - intermol
   - jax
   - pytest

docs/releasehistory.md

@@ -15,6 +15,7 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 
 * #933 Fixes #934 in which atom order was sometimes mangled in `Interchange.from_openmm`.
 * #929 A warning is raised when positions are not passed to `Interchange.from_openmm`.
+* #930 Adds `additional_forces` argument to `create_openmm_simulation`.
 
 ## 0.3.23 - 2024-03-07
 

examples/ligand_in_water/ligand_in_water.ipynb

@@ -23,17 +23,11 @@
     "import openmm\n",
     "import openmm.app\n",
     "import openmm.unit\n",
-    "from openff.toolkit import ForceField, Molecule, Topology\n",
-    "from openff.units import unit\n",
+    "from openff.toolkit import ForceField, Molecule, unit\n",
     "from rich.pretty import pprint\n",
     "\n",
     "from openff.interchange import Interchange\n",
-    "from openff.interchange.components._packmol import (\n",
-    "    RHOMBIC_DODECAHEDRON,\n",
-    "    UNIT_CUBE,\n",
-    "    pack_box,\n",
-    ")\n",
-    "from openff.interchange.interop.openmm import to_openmm_positions"
+    "from openff.interchange.components._packmol import RHOMBIC_DODECAHEDRON, pack_box"
    ]
   },
   {
@@ -168,19 +162,17 @@
     "    )\n",
     "\n",
     "    barostat = openmm.MonteCarloBarostat(\n",
-    "        1.0 * openmm.unit.bar, 293.15 * openmm.unit.kelvin, 25\n",
+    "        1.0 * openmm.unit.bar,\n",
+    "        293.15 * openmm.unit.kelvin,\n",
+    "        25,\n",
     "    )\n",
     "\n",
     "    simulation = interchange.to_openmm_simulation(\n",
     "        combine_nonbonded_forces=True,\n",
     "        integrator=integrator,\n",
+    "        additional_forces=[barostat],\n",
     "    )\n",
     "\n",
-    "    simulation.system.addForce(barostat)\n",
-    "\n",
-    "    # https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#why-does-it-ignore-changes-i-make-to-a-system-or-force\n",
-    "    simulation.context.reinitialize(preserveState=True)\n",
-    "\n",
     "    # https://github.com/openmm/openmm/issues/3736#issuecomment-1217250635\n",
     "    simulation.minimizeEnergy()\n",
     "\n",
@@ -245,10 +237,18 @@
     "    print(f\"Elapsed time: {(end_time - start_time):.2f} seconds\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "15",
+   "metadata": {},
+   "source": [
+    "We should observe (small) fluctuations in the density of the simulation, which is running under the NPT ensemble. If the initial density was a good guess, there shouldn't be significant changes from the initial value around $30 nm^3$."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -257,7 +257,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "17",
    "metadata": {},
    "source": [
     "## Appendix A: visualizing the trajectory\n",
@@ -268,7 +268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "18",
    "metadata": {
     "tags": [
      "nbval-skip"
@@ -283,7 +283,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "18",
+   "id": "19",
    "metadata": {},
    "source": [
     "## Appendix B: Using the OPC water model\n",
@@ -294,7 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -304,7 +304,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "20",
+   "id": "21",
    "metadata": {},
    "source": [
     "We can also get a rough visualization of a single water molecule including the virtual site."
@@ -313,7 +313,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -328,7 +328,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "22",
+   "id": "23",
    "metadata": {},
    "source": [
     "Since we want to use a different force field with the same chemical topology - a ligand in a box of water - we can re-use the same `Topology` object we prepared earlier, re-using the same functions we defined above!"
@@ -337,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -350,7 +350,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -360,7 +360,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -372,7 +372,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "27",
    "metadata": {
     "tags": [
      "nbval-skip"
@@ -406,7 +406,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27",
+   "id": "28",
    "metadata": {},
    "source": [
     "## Appendix C: Using the TIP4P-FB water model with GROMACS\n",
@@ -417,7 +417,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -433,7 +433,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "29",
+   "id": "30",
    "metadata": {},
    "source": [
     "To use a different force field, such as [TIP4P-FB](https://pubs.acs.org/doi/10.1021/jz500737m), simply point the `ForceField` constructor at a different file:"
@@ -442,7 +442,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -451,7 +451,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "31",
+   "id": "32",
    "metadata": {},
    "source": [
     "From here we can create a new `Interchange` object - necessary since we're using a different force field - and use the `Interchange.to_gromacs` method to write GROMACS files."
@@ -460,7 +460,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -473,7 +473,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -484,7 +484,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34",
+   "id": "35",
    "metadata": {},
    "source": [
     "Now, with GROMACS files written, we can use the bundled `run.mdp` file to compile and run a GROMACS simulation!"
@@ -493,7 +493,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -504,7 +504,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "37",
    "metadata": {
     "tags": [
      "nbval-skip"
@@ -535,7 +535,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

openff/interchange/_tests/__init__.py

@@ -4,6 +4,7 @@
 import sys
 from typing import Optional
 
+import numpy
 import pytest
 from openff.toolkit import Molecule
 from openff.toolkit.utils import (
@@ -42,6 +43,9 @@
 )
 
 
+_rng = numpy.random.default_rng(12345)
+
+
 def get_test_file_path(test_file: str) -> pathlib.Path:
     """Given a filename in the collection of data files, return its full path."""
     test_dir_path = get_test_files_dir_path()