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Merge pull request #920 from openforcefield/virtual-site-split-force-…
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…exceptions-tests

Add tests with virtual sites and split forces
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@mattwthompson
mattwthompson authored Mar 7, 2024
2 parents f70880f + aa23078 commit 7bf0188
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6 changes: 4 additions & 2 deletions .github/workflows/ci.yaml
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Expand Up @@ -79,7 +79,9 @@ jobs:

- name: Install OpenMM
if: ${{ matrix.openmm == true }}
run: micromamba install openmm "smirnoff-plugins =2023" -c conda-forge
run: |
micromamba install openmm "smirnoff-plugins =2024" -c conda-forge
pip install git+https://github.com/jthorton/de-forcefields.git
- name: Uninstall OpenMM
if: ${{ matrix.openmm == false && matrix.openeye == true }}
Expand All @@ -101,7 +103,7 @@ jobs:
if: always()
run: |
python -m pytest $COV openff/interchange/ \
-r fE -nauto --durations=10 \
-r fExs -nauto --durations=10 \
-m "slow or not slow" \
--ignore=openff/interchange/_tests/energy_tests/test_energies.py
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5 changes: 4 additions & 1 deletion devtools/conda-envs/beta_env.yaml
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Expand Up @@ -28,17 +28,20 @@ dependencies:
- pytest-xdist
- pytest-randomly
- mdanalysis
- de-forcefields
# Drivers
- gromacs =2023.3=nompi_*_103
- lammps
# https://github.com/conda-forge/quippy-feedstock/issues/15
- panedr
# Examples
- nglview
- pytest =8.0
- pytest
- nbval
# Typing
- mypy
- typing-extensions
- types-setuptools
- pandas-stubs >=1.2.0.56
- pip:
- git+https://github.com/jthorton/de-forcefields.git
5 changes: 4 additions & 1 deletion devtools/conda-envs/dev_env.yaml
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Expand Up @@ -14,7 +14,7 @@ dependencies:
- openff-toolkit =0.15.2
- openff-interchange-base
- openff-models
- smirnoff-plugins =2023
- smirnoff-plugins =2024
# openff-nagl
# openff-nagl-models
# Optional features
Expand All @@ -30,6 +30,7 @@ dependencies:
- pytest-randomly
- nbval
- mdanalysis
- de-forcefields
# Drivers
- gromacs =2023.3=nompi_*_103
- lammps
Expand All @@ -52,3 +53,5 @@ dependencies:
- flake8
- snakeviz
- tuna
- pip:
- git+https://github.com/jthorton/de-forcefields.git
2 changes: 1 addition & 1 deletion devtools/conda-envs/test_env.yaml
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Expand Up @@ -21,7 +21,7 @@ dependencies:
- mdtraj
- intermol
- jax
- pytest =8.0
- pytest
- pytest-cov
- pytest-xdist
- pytest-randomly
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11 changes: 6 additions & 5 deletions docs/releasehistory.md
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Expand Up @@ -11,32 +11,33 @@ Dates are given in YYYY-MM-DD format.

Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.

## Current development
## 0.3.23 - 2024-03-07

* #923 An error is raised in `Interchange.from_openmm` when the topology and system are incompatible.
* #912 A warning is raised when writing an input/run file (not data file) to an engine that does not implement a switching function described by SMIRNOFF.
* #916 Some internal code paths are re-organized, including removing the `openff.interchange.interop.internal` submodule.
* #916 Improves speed of `Interchange.to_lammps`, particularly for larger systems.
* #920 Fixes a bug in which virtual site exclusions were incorrect when using split non-bonded forces.
* #915 Deprecates `Interchange.__add__` in favor of `Interchange.combine`.
* #897 Improves energy evaluation with LAMMPS when some bonds are constrained.

## 0.3.22 - 2023-02-27
## 0.3.22 - 2024-02-27

* #912 Fixes a bug in which rigid water geometries were incorrectly written to GROMACS files.
* #909 Fixes a bug in which numerical values such as `scale_14` were lost when parsing JSON dumps.

## 0.3.21 - 2023-02-20
## 0.3.21 - 2024-02-20

* #906 Fixes a bug in which intramolecular interactions between virtual sites were not properly excluded with OpenMM.
* #901 `Interchange.from_openmm` now requires the `system` argument.
* #903 The Python API of LAMMPS is now internally used for LAMMPS energy calculations.

## 0.3.20 - 2023-02-12
## 0.3.20 - 2024-02-12

* #891 Adds support for hydrogen mass repartitioning (HMR) in GROMACS export. Note that this implementaiton never modifies masses in waters and requires the system contains no virtual sites.
* #887 Adds support for hydrogen mass repartitioning (HMR) in OpenMM export. Note that this implementaiton never modifies masses in waters and requires the system contains no virtual sites.

### 0.3.19 - 2023-02-05
### 0.3.19 - 2024-02-05

* #867 Tags `PotentialKey.virtual_site_type` with the associated type provided by SMIRNOFF parameters.
* #857 Tags `PotentialKey.associated_handler` when importing data from OpenMM.
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152 changes: 152 additions & 0 deletions openff/interchange/_tests/data/hexanol-water.pdb
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@@ -0,0 +1,152 @@
REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-03-06
HETATM 1 C1x UNK A 1 1.718 6.917 2.572 1.00 0.00 C
HETATM 2 C2x UNK A 1 0.930 5.618 2.455 1.00 0.00 C
HETATM 3 H1x UNK A 1 2.650 6.760 3.125 1.00 0.00 H
HETATM 4 O1x UNK A 1 2.030 7.415 1.280 1.00 0.00 O
HETATM 5 H2x UNK A 1 1.122 7.670 3.097 1.00 0.00 H
HETATM 6 C3x UNK A 1 1.736 4.511 1.769 1.00 0.00 C
HETATM 7 H3x UNK A 1 0.629 5.291 3.457 1.00 0.00 H
HETATM 8 H4x UNK A 1 0.016 5.799 1.876 1.00 0.00 H
HETATM 9 C4x UNK A 1 0.963 3.191 1.750 1.00 0.00 C
HETATM 10 H5x UNK A 1 1.977 4.808 0.742 1.00 0.00 H
HETATM 11 H6x UNK A 1 2.687 4.369 2.296 1.00 0.00 H
HETATM 12 C5x UNK A 1 1.755 2.093 1.040 1.00 0.00 C
HETATM 13 H7x UNK A 1 0.000 3.334 1.245 1.00 0.00 H
HETATM 14 H8x UNK A 1 0.745 2.880 2.779 1.00 0.00 H
HETATM 15 C6x UNK A 1 1.011 0.767 1.060 1.00 0.00 C
HETATM 16 H9x UNK A 1 1.943 2.385 0.000 1.00 0.00 H
HETATM 17 H10x UNK A 1 2.731 1.964 1.522 1.00 0.00 H
HETATM 18 H11x UNK A 1 0.038 0.855 0.567 1.00 0.00 H
HETATM 19 H12x UNK A 1 1.590 0.000 0.536 1.00 0.00 H
HETATM 20 H13x UNK A 1 0.846 0.426 2.087 1.00 0.00 H
HETATM 21 H14x UNK A 1 2.537 8.235 1.405 1.00 0.00 H
TER 22 UNK A 1
HETATM 23 C1x UNK B 1 4.718 6.917 2.572 1.00 0.00 C
HETATM 24 C2x UNK B 1 3.930 5.618 2.455 1.00 0.00 C
HETATM 25 H1x UNK B 1 5.650 6.760 3.125 1.00 0.00 H
HETATM 26 O1x UNK B 1 5.030 7.415 1.280 1.00 0.00 O
HETATM 27 H2x UNK B 1 4.122 7.670 3.097 1.00 0.00 H
HETATM 28 C3x UNK B 1 4.736 4.511 1.769 1.00 0.00 C
HETATM 29 H3x UNK B 1 3.629 5.291 3.457 1.00 0.00 H
HETATM 30 H4x UNK B 1 3.016 5.799 1.876 1.00 0.00 H
HETATM 31 C4x UNK B 1 3.963 3.191 1.750 1.00 0.00 C
HETATM 32 H5x UNK B 1 4.977 4.808 0.742 1.00 0.00 H
HETATM 33 H6x UNK B 1 5.687 4.369 2.296 1.00 0.00 H
HETATM 34 C5x UNK B 1 4.755 2.093 1.040 1.00 0.00 C
HETATM 35 H7x UNK B 1 3.000 3.334 1.245 1.00 0.00 H
HETATM 36 H8x UNK B 1 3.745 2.880 2.779 1.00 0.00 H
HETATM 37 C6x UNK B 1 4.011 0.767 1.060 1.00 0.00 C
HETATM 38 H9x UNK B 1 4.943 2.385 0.000 1.00 0.00 H
HETATM 39 H10x UNK B 1 5.731 1.964 1.522 1.00 0.00 H
HETATM 40 H11x UNK B 1 3.038 0.855 0.567 1.00 0.00 H
HETATM 41 H12x UNK B 1 4.590 0.000 0.536 1.00 0.00 H
HETATM 42 H13x UNK B 1 3.846 0.426 2.087 1.00 0.00 H
HETATM 43 H14x UNK B 1 5.537 8.235 1.405 1.00 0.00 H
TER 44 UNK B 1
HETATM 45 C1x UNK C 1 1.718 6.917 5.572 1.00 0.00 C
HETATM 46 C2x UNK C 1 0.930 5.618 5.455 1.00 0.00 C
HETATM 47 H1x UNK C 1 2.650 6.760 6.125 1.00 0.00 H
HETATM 48 O1x UNK C 1 2.030 7.415 4.280 1.00 0.00 O
HETATM 49 H2x UNK C 1 1.122 7.670 6.097 1.00 0.00 H
HETATM 50 C3x UNK C 1 1.736 4.511 4.769 1.00 0.00 C
HETATM 51 H3x UNK C 1 0.629 5.291 6.457 1.00 0.00 H
HETATM 52 H4x UNK C 1 0.016 5.799 4.876 1.00 0.00 H
HETATM 53 C4x UNK C 1 0.963 3.191 4.750 1.00 0.00 C
HETATM 54 H5x UNK C 1 1.977 4.808 3.742 1.00 0.00 H
HETATM 55 H6x UNK C 1 2.687 4.369 5.296 1.00 0.00 H
HETATM 56 C5x UNK C 1 1.755 2.093 4.040 1.00 0.00 C
HETATM 57 H7x UNK C 1 0.000 3.334 4.245 1.00 0.00 H
HETATM 58 H8x UNK C 1 0.745 2.880 5.779 1.00 0.00 H
HETATM 59 C6x UNK C 1 1.011 0.767 4.060 1.00 0.00 C
HETATM 60 H9x UNK C 1 1.943 2.385 3.000 1.00 0.00 H
HETATM 61 H10x UNK C 1 2.731 1.964 4.522 1.00 0.00 H
HETATM 62 H11x UNK C 1 0.038 0.855 3.567 1.00 0.00 H
HETATM 63 H12x UNK C 1 1.590 0.000 3.536 1.00 0.00 H
HETATM 64 H13x UNK C 1 0.846 0.426 5.087 1.00 0.00 H
HETATM 65 H14x UNK C 1 2.537 8.235 4.405 1.00 0.00 H
TER 66 UNK C 1
HETATM 67 O1x UNK D 1 3.061 10.389 0.059 1.00 0.00 O
HETATM 68 H1x UNK D 1 3.724 9.688 -0.038 1.00 0.00 H
HETATM 69 H2x UNK D 1 2.215 9.923 -0.021 1.00 0.00 H
TER 70 UNK D 1
HETATM 71 O1x UNK E 1 8.061 10.389 3.059 1.00 0.00 O
HETATM 72 H1x UNK E 1 8.724 9.688 2.962 1.00 0.00 H
HETATM 73 H2x UNK E 1 7.215 9.923 2.979 1.00 0.00 H
TER 74 UNK E 1
HETATM 75 O1x UNK F 1 3.061 10.389 3.059 1.00 0.00 O
HETATM 76 H1x UNK F 1 3.724 9.688 2.962 1.00 0.00 H
HETATM 77 H2x UNK F 1 2.215 9.923 2.979 1.00 0.00 H
TER 78 UNK F 1
CONECT 1 2 3 4 5
CONECT 2 1 6 7 8
CONECT 3 1
CONECT 4 1 21
CONECT 5 1
CONECT 6 2 9 10 11
CONECT 7 2
CONECT 8 2
CONECT 9 6 12 13 14
CONECT 10 6
CONECT 11 6
CONECT 12 9 15 16 17
CONECT 13 9
CONECT 14 9
CONECT 15 12 18 19 20
CONECT 16 12
CONECT 17 12
CONECT 18 15
CONECT 19 15
CONECT 20 15
CONECT 21 4
CONECT 23 24 25 26 27
CONECT 24 23 28 29 30
CONECT 25 23
CONECT 26 23 43
CONECT 27 23
CONECT 28 24 31 32 33
CONECT 29 24
CONECT 30 24
CONECT 31 28 34 35 36
CONECT 32 28
CONECT 33 28
CONECT 34 31 37 38 39
CONECT 35 31
CONECT 36 31
CONECT 37 34 40 41 42
CONECT 38 34
CONECT 39 34
CONECT 40 37
CONECT 41 37
CONECT 42 37
CONECT 43 26
CONECT 45 46 47 48 49
CONECT 46 45 50 51 52
CONECT 47 45
CONECT 48 45 65
CONECT 49 45
CONECT 50 46 53 54 55
CONECT 51 46
CONECT 52 46
CONECT 53 50 56 57 58
CONECT 54 50
CONECT 55 50
CONECT 56 53 59 60 61
CONECT 57 53
CONECT 58 53
CONECT 59 56 62 63 64
CONECT 60 56
CONECT 61 56
CONECT 62 59
CONECT 63 59
CONECT 64 59
CONECT 65 48
CONECT 67 68 69
CONECT 68 67
CONECT 69 67
CONECT 71 72 73
CONECT 72 71
CONECT 73 71
CONECT 75 76 77
CONECT 76 75
CONECT 77 75
END
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