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Fixes vdW rmin_half / sigma conversion #808

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merged 6 commits into from
Jan 8, 2021
Merged

Fixes vdW rmin_half / sigma conversion #808

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2f6bc3f
Fixes rmin_half / sigma factor conversion (#807).
Jan 8, 2021
14c963f
Add regression tests comparing energies to v0.8.0
mattwthompson Jan 8, 2021
ce44249
Move a methane in methane_multiconformer*sdf in by [0, 0, 2] angstroms
mattwthompson Jan 8, 2021
129a1eb
Merge remote-tracking branch 'upstream/master' into fix-vdw-sigma
mattwthompson Jan 8, 2021
354838e
Add MDTraj test dependency, make regression tests RDKit-only
mattwthompson Jan 8, 2021
7489780
Update release history
j-wags Jan 8, 2021
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1 change: 1 addition & 0 deletions devtools/conda-envs/openeye.yaml
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Expand Up @@ -31,3 +31,4 @@ dependencies:
- qcelemental
- qcportal
- qcengine
- mdtraj
1 change: 1 addition & 0 deletions devtools/conda-envs/rdkit.yaml
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Expand Up @@ -30,3 +30,4 @@ dependencies:
- qcelemental
- qcportal
- qcengine
- mdtraj
1 change: 1 addition & 0 deletions devtools/conda-envs/test_env.yaml
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Expand Up @@ -32,3 +32,4 @@ dependencies:
- qcelemental
- qcportal
- qcengine
- mdtraj
20 changes: 19 additions & 1 deletion docs/releasehistory.rst
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Expand Up @@ -10,7 +10,9 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
0.8.3 - Current development
---------------------------

This release is a final patch for the ``0.8.X`` series of releases of the toolkit, and also marks the last
This release fixes a critical bug in van der Waals parameter assignment.

This release is also a final patch for the ``0.8.X`` series of releases of the toolkit, and also marks the last
version of the toolkit which will be imported as ``import openforcefield.XXX`` / ``from openforcefield import XXX``.
From version ``0.9.0`` onwards the toolkit will be importable only as ``import openff.toolkit.XXX`` /
``from openff.toolkit import XXX``.
Expand All @@ -19,6 +21,14 @@ From version ``0.9.0`` onwards the toolkit will be importable only as ``import o
so users need not worry about accidentally pulling in a version with changed imports. Users will have to explicitly
choose to install the ``openff-toolkit`` package once released which will contain the breaking import changes.

Bugfixes
""""""""
- `PR #808 <https://github.com/openforcefield/openforcefield/pull/808>`_: Fixes
`Issue #807 <https://github.com/openforcefield/openforcefield/issues/807>`_,
which tracks a major bug in the interconversion between a vdW ``sigma``
and ``rmin_half`` parameter.


New features
""""""""""""
- `PR #794 <https://github.com/openforcefield/openforcefield/pull/794>`_: Adds a decorator
Expand All @@ -29,6 +39,10 @@ New features
0.8.2 - Bugfix release
----------------------

**WARNING: This release was later found to contain a major bug,**
`Issue #807 <https://github.com/openforcefield/openforcefield/issues/807>`_,
**and produces incorrect energies.**

Bugfixes
""""""""
- `PR #786 <https://github.com/openforcefield/openforcefield/pull/xyz>`_: Fixes `Issue #785
Expand All @@ -50,6 +64,10 @@ Bugfixes
0.8.1 - Bugfix and minor feature release
----------------------------------------

**WARNING: This release was later found to contain a major bug,**
`Issue #807 <https://github.com/openforcefield/openforcefield/issues/807>`_,
**and produces incorrect energies.**

API-breaking changes
""""""""""""""""""""
- `PR #757 <https://github.com/openforcefield/openforcefield/pull/757>`_: Renames
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1 change: 1 addition & 0 deletions openforcefield/data/README.md
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Expand Up @@ -5,3 +5,4 @@
- `molecules` - contains files for certain molecules used by openforcefield
- `systems` - contains systems consisting of mixtures of molecules
- `proteins` - contains pdb files for example proteins
- `reference_energies` - contains reference energies for regression tests
10 changes: 5 additions & 5 deletions openforcefield/data/molecules/methane_multiconformer.sdf
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Expand Up @@ -18,11 +18,11 @@ $$$$
-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
2.2299 2.2300 2.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 2.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 1.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 2.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 3.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2299 2.2300 4.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 4.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 3.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 4.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 5.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
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10 changes: 5 additions & 5 deletions openforcefield/data/molecules/methane_multiconformer_properties.sdf
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Expand Up @@ -23,11 +23,11 @@ $$$$
-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
2.2299 2.2300 2.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 2.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 1.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 2.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 3.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2299 2.2300 4.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 4.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 3.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 4.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 5.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
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2 changes: 2 additions & 0 deletions openforcefield/data/reference_energies/README.md
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@@ -0,0 +1,2 @@
## Manifest
- `reference_0.8.0.json` - generated by `python /path/to/file.py` with conda environment reference_0.8.0.json.txt
1 change: 1 addition & 0 deletions openforcefield/data/reference_energies/reference_0.8.0.json
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{"ethanol.sdf_constrained": -10.218365198534997, "ethanol.sdf_unconstrained": -10.19846007444734, "methane_multiconformer.sdf_constrained": 2.0119485713874554, "methane_multiconformer.sdf_unconstrained": 2.0175533558944263, "CID20742535_anion.sdf_constrained": 276.16103271162683, "CID20742535_anion.sdf_unconstrained": 276.2305315599303}
180 changes: 180 additions & 0 deletions openforcefield/data/reference_energies/reference_0.8.0.json.txt
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# packages in environment at /Users/mwt/miniconda3/envs/openforcefield-0.8.0:
#
# Name Version Build Channel
amberlite 16.0 pypi_0 pypi
ambertools 20.9 pypi_0 pypi
appnope 0.1.2 py37hf985489_1 conda-forge
argon2-cffi 20.1.0 py37h4b544eb_2 conda-forge
arpack 3.7.0 hff0ca13_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
bleach 3.2.1 pyh9f0ad1d_0 conda-forge
boost 1.74.0 py37h6f8fa6c_2 conda-forge
boost-cpp 1.74.0 hd067f63_1 conda-forge
brotlipy 0.7.0 py37h395d20d_1001 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 hc929b4f_4 conda-forge
c-ares 1.17.1 hc929b4f_0 conda-forge
ca-certificates 2020.12.5 h033912b_0 conda-forge
cairo 1.16.0 h4ec454a_1007 conda-forge
certifi 2020.12.5 py37hf985489_1 conda-forge
cffi 1.14.4 py37hc5b2277_1 conda-forge
chardet 4.0.0 py37hf985489_1 conda-forge
cryptography 3.3.1 py37haf76d9e_0 conda-forge
curl 7.71.1 hcb81553_8 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.21 py37h54c7649_2 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
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fontconfig 2.13.1 h07ff6b0_1003 conda-forge
freetype 2.10.4 h3f75d11_0 conda-forge
gettext 0.19.8.1 h7937167_1005 conda-forge
hdf4 4.2.13 h71d84a9_1004 conda-forge
hdf5 1.10.6 nompi_h34ad4e8_1111 conda-forge
icu 68.1 h74dc148_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 3.3.0 py37hf985489_3 conda-forge
importlib_metadata 3.3.0 hd8ed1ab_3 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 5.4.2 py37he01cfaa_0 conda-forge
ipython 7.19.0 py37he01cfaa_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge
jedi 0.18.0 py37hf985489_1 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
jpeg 9d hbcb3906_0 conda-forge
jsonschema 3.2.0 py_2 conda-forge
jupyter_client 6.1.7 py_0 conda-forge
jupyter_core 4.7.0 py37hf985489_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge
kiwisolver 1.3.1 py37h70f7d40_1 conda-forge
krb5 1.17.2 h60d9502_0 conda-forge
lcms2 2.11 h11f7e16_1 conda-forge
libblas 3.9.0 7_openblas conda-forge
libcblas 3.9.0 7_openblas conda-forge
libcurl 7.71.1 h9bf37e3_8 conda-forge
libcxx 11.0.0 h4c3b8ed_1 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.3 h046ec9c_2 conda-forge
libgfortran 4.0.0 h1a10cd1_15 conda-forge
libgfortran4 7.5.0 h1a10cd1_15 conda-forge
libglib 2.66.4 h7424822_1 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
liblapack 3.9.0 7_openblas conda-forge
libnetcdf 4.7.4 nompi_h9d8a93f_107 conda-forge
libnghttp2 1.41.0 h7580e61_2 conda-forge
libopenblas 0.3.12 openmp_h63d9170_1 conda-forge
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matplotlib-base 3.3.3 py37hdacc966_0 conda-forge
mistune 0.8.4 py37hf967b71_1003 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.2 py37h70f7d40_1 conda-forge
nbclient 0.5.1 py_0 conda-forge
nbconvert 6.0.7 py37hf985489_3 conda-forge
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ncurses 6.2 h2e338ed_4 conda-forge
nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.5.3 nompi_haced683_101 conda-forge
networkx 2.5 py_0 conda-forge
nglview 2.7.7 pyh5ca1d4c_1 conda-forge
notebook 6.1.6 py37hf985489_0 conda-forge
numpy 1.19.5 py37hec87de9_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openforcefield 0.8.0 pyh39e3cac_0 omnia
openforcefields 1.3.0 py_0 omnia
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openssl 1.1.1i h35c211d_0 conda-forge
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parmed at20RC5+54.g5702a232fe.dirty pypi_0 pypi
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py 1.10.0 pyhd3deb0d_0 conda-forge
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python_abi 3.7 1_cp37m conda-forge
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requests 2.25.1 pyhd3deb0d_0 conda-forge
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setuptools 49.6.0 py37hf985489_3 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
smirnoff99frosst 1.1.0 py_2 omnia
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xz 5.2.5 haf1e3a3_1 conda-forge
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zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h7795811_1010 conda-forge
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