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[WIP] Convert restraint forces to inherit from CVCustomForce #369

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[WIP] Convert restraint forces to inherit from CVCustomForce #369

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54 changes: 38 additions & 16 deletions docs/releasehistory.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,29 @@
Release History
***************

0.17.0 - Development
====================

New features
------------

- ``RadiallySymmetricRestraintForce`` and all subclasses are now a ``CustomCVForce`` subclass wrapping their
respective ``CustomBondForce`` and ``CustomCentroidBondForce`` objects. This breaks backwards compatibility, but
enables tracking the restraint distances through the new ``SamplerSate`` collective variable features.

Compatibility Warnings
----------------------
- ``RadiallySymmetricRestraintForce``'s conversion to ``CustomCVForce``'s break the backwards compatibility with older
codes which implement subclasses of it. The largest change is how the Energy Function is implemented, and subclass
hierarchy. E.g. All these classes are now ``CustomCVForce``'s instead of ``CustomBondForce`` and
``CustomCentroidBondForce`` objects.

- This affects ``RadiallySymmetricRestraintForce``,
``RadiallySymmetricCentroidRestraintForce``, ``RadiallySymmetricBondRestraintForce``,
``HarmonicRestraintForceMixIn``, ``HarmonicRestraintForce``, ``HarmonicRestraintBondForce``,
``FlatBottomRestraintForceMixIn``, ``FlatBottomRestraintForce``, and ``FlatBottomRestraintBondForce``.


0.16.0 - Py2 deprecated, GlobalParameterState class, SamplerState reads CVs
===========================================================================

Expand Down Expand Up @@ -76,7 +99,6 @@ Enhancements
not work around the NaN's. This is a slow step relative to just resetting positions, but better than simulation
crashing.


0.13.3 - Critical Bugfix to SamplerState Context Manipulation
=============================================================

Expand Down Expand Up @@ -115,8 +137,8 @@ Added bit operators ``and`` and ``or`` to ``math_eval`` (`#301 <https://github.c



0.13.0 - Alternative reaction field models, Langevin splitting MCMCMove
=======================================================================
OpenMMTools 0.13.0
==================

New Features
------------
Expand All @@ -140,6 +162,7 @@ Bug Fixes
0.12.1 - Add virtual sites support in alchemy
=============================================


- Fixed AbsoluteAlchemicalFactory treatment of virtual sites that were previously ignored
(`#259 <https://github.com/choderalab/openmmtools/issues/259>`_).
- Add possibility to add ions to the WaterBox test system
Expand Down Expand Up @@ -169,15 +192,15 @@ Bug fixes
integrator (`#252 <https://github.com/choderalab/openmmtools/issues/252>`_)


0.11.2 - Bugfix release
=======================
Hotfix 0.11.2
=============

- Hotfix in fringe Python2/3 compatibility issue when using old style serialization systems in Python 2
Hotfix in fringe Python2/3 compatibility issue when using old style serialization systems in Python 2



0.11.1 - Optimizations
======================
Release 0.11.1: Optimizations
=============================

- Adds Drew-Dickerson DNA dodecamer test system (`#223 <https://github.com/choderalab/openmmtools/issues/223>`_)
- Bugfix and optimization to ``ContextCache`` (`#235 <https://github.com/choderalab/openmmtools/issues/235>`_)
Expand All @@ -186,11 +209,10 @@ Bug fixes
- Backwards compatible with uncompressed serialized ``ThermodynamicStates``


0.11.0 - Conda forge installation
=================================
0.11.0
======

New Features
------------
New Features:

- ``LangevinIntegrator`` now sets ``measure_heat=False`` by default for increased performance
(`#211 <https://github.com/choderalab/openmmtools/issues/211>`_)
Expand All @@ -202,8 +224,8 @@ New Features



0.10.0 - Optimizations of ThermodynamicState, renamed AlchemicalFactory
=======================================================================
Release 0.10.0 - Optimizations of ThermodynamicState, renamed AlchemicalFactory
===============================================================================

- BREAKS API: Renamed AlchemicalFactory to AbsoluteAlchemicalFactory
(`#206 <https://github.com/choderalab/openmmtools/issues/206>`_)
Expand All @@ -222,8 +244,8 @@ New Features
`#187 <https://github.com/choderalab/openmmtools/issues/187>`_)


0.9.4 - Nonequilibrium integrators overhaul
===========================================
Release 0.9.4 - Nonequilibrium integrators overhaul
===================================================

Major changes
-------------
Expand Down
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