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Merged
dwhswenson merged 12 commits into from
Aug 6, 2018
Merged

Direct Engine API Docs #793

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6c35b78
Fix Py2 required statement in install
dwhswenson Jul 21, 2018
1965aec
Fix Alberto's name in acknowledgments
dwhswenson Jul 21, 2018
84ed0b7
fix some sphinx errors
dwhswenson Jul 21, 2018
aa728a1
Docs on direct engines API
dwhswenson Jul 21, 2018
a24dbd6
Start documenting snapshot features
dwhswenson Jul 23, 2018
1264634
better docs on direct API for engines
dwhswenson Jul 23, 2018
f38ba5e
More on snapshot features
dwhswenson Jul 23, 2018
31b2890
Docs. Mostly snapshot features
dwhswenson Jul 24, 2018
5ed09b1
more updates to snapshot features docs
dwhswenson Jul 24, 2018
0429273
More docs on snapshot features
dwhswenson Jul 26, 2018
9c86b69
SnapshotDescriptor docs; more on features
dwhswenson Jul 28, 2018
1d4aa05
Finish up direct engine API dev docs
dwhswenson Jul 28, 2018
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More docs on snapshot features
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@dwhswenson
dwhswenson committed Jul 26, 2018
commit 0429273df1cd061f8ec267887ed47c16035cc55e
19 changes: 14 additions & 5 deletions docs/developers/snapshot_features.rst
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Expand Up @@ -137,7 +137,7 @@ Features that contain information that should be stored are a bit more
complicated. First, such objects should be registered as "variables" by
including their names in the list of strings in ``variables``.

TODO: finish this documentation
.. TODO: finish this documentation

Creating Proxy (Container) Snapshot Features
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -189,13 +189,22 @@ OpenMM engine.
| | :mod:`.engines.features.kinetics`. |
+---------------------+----------------------------------------------------+
| ``box_vectors`` | Unit cell vectors for the periodic box. Unitted. |
| | Stored. |
| | As stored feature in |
| | :mod:`.engines.features.box_vectors` As property |
| | feature in :mod:`.engines.features.statics`. |
+---------------------+----------------------------------------------------+
| ``statics`` | |
| ``statics`` | Combination of coordinates and box vectors. As |
| | container feature in |
| | :mod:`.engines.features.statics` and |
| | :mod:`.engines.features.shared`. |
+---------------------+----------------------------------------------------+
| ``kinetics`` | |
| ``kinetics`` | Container for velocities. As container feature in |
| | :mod:`.engines.features.kinetics` and |
| | :mod:`.engines.features.shared`. |
+---------------------+----------------------------------------------------+
| ``xyz`` | Particle positions, without units. Property. |
| ``xyz`` | Particle positions, without units. As property |
| | feature in :mod:`.engines.features.coordinates`, |
| | :mod:`.engines.features.statics`. |
+---------------------+----------------------------------------------------+
| ``masses`` | Particle masses (in actual mass units, not mass |
| | per mole, as used in some engines). Unitted. |
Expand Down