Code

Feature force lever#157

Code

Merged

chryswoods merged 47 commits intodevelOpenBioSim/sire:develfrom feature_force_leverOpenBioSim/sire:feature_force_leverCopy head branch name to clipboardFeb 9, 2024

+12,282-1,706

Commits

Commits on Jan 7, 2024

• Added a sire.v function to make it easier to create Vector and related

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• I've implemented the full suite of -not-perturbed constraints, adding them to the

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Commits on Jan 8, 2024

• Adding ambertools and gromacs to MacOS/ARM64 BioSimSpace dependencies, as these

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  d712200

• Fixed a small bug in indexing atoms from an atoms container. Working on

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• Fixing small bugs uncovered by fuller tests of which constraints are applied

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Commits on Jan 9, 2024

• Added ability to customise the lambda levers by force, and also to have

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Commits on Jan 12, 2024

• Added a unit test that checks an energy scan across lambda for

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Commits on Jan 13, 2024

• Added more to the neopentane tests - these check that things are still correct

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• h-bonds-not-perturbed is the same as h-bonds for neopentane/methane.

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Commits on Jan 14, 2024

• Adding in the somd comparison test for no cutoff

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• Fixed missing copy assigment of cell_matrix_inverse in TriclinicBox that was

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• Added a "kappa" lambda lever to the OpenMM context. This scales the charge correction

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Commits on Jan 15, 2024

• Adding framework for decoupling to LambdaSchedule

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• Exposed the com_reset_frequency to mols.dynamics(com_reset_frequency=X), where

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Commits on Jan 16, 2024

• Added a test that checked that the no-charge energy scan gives the

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  a2a2baf

• Fixed bugs with implementation of h-bonds-not-perturbed constraints

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Commits on Jan 17, 2024

• Added support for dynamic bond constraints. This is exposed via the "dynamic_constraints"

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Commits on Jan 18, 2024

• Fixed bugs with constraint lengths - now always constrain bonds to their r0 lengths

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• Added a test for dynamic constraints

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Commits on Jan 22, 2024

• Allow the user to more easily set the background colour of a 3D view.

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Commits on Jan 23, 2024

• Fixed bug in somd code that accidentally caused some perturbable torsions to be

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  cd807bd

• Added a bugfix where changing the LambdaSchedule would not update any

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Commits on Jan 24, 2024

• The to_alchemlyb function of EnergyTrajectory will now return a dataframe

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• Added the choice of energy unit to the to_alchemlyb functions

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Commits on Jan 25, 2024

• Adding diffs from Lester

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Commits on Jan 27, 2024

• Adding a function that can create a merged molecule from a molecule plus pert file

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• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_force_lever

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• Merge branch 'feature_exception2' of https://github.com/openbiosim/sire into feature_force_lever

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• Merge branch 'feature_exception2' of https://github.com/openbiosim/sire into feature_force_lever

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• Switched SireOpenMM to use auto-generated Python wrappers rather than hand-written ones

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• Working on reporting the perturbations in the molecule

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Commits on Jan 28, 2024

• Working on getting the sr.morph.extract_X, sr.morph.create_from_pertfile and the PerturbableOpenMMMolecule reporting

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• Added code to let you query the parameters that go into a perturbation in the OpenMM context

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Commits on Jan 29, 2024

• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_force_lever

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• Done a lot of work on the new tutorial chapter that describes how to use the

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Commits on Jan 30, 2024

• Remove erroneous warning message about mixed combining rules.

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• I've added in a new constraint type - "X-not-heavy-perturbed". This constraints "X",

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• Added zero_ghost_bond and zero_ghost_angle functions, and also matching (I think) the logic

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Commits on Jan 31, 2024

• Added tests that include a solvated neopentane-methane system

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• Added a section on how to set the lambda lever for specific forces, and also

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Commits on Feb 2, 2024

• Fixed a bug in the streaming of LambdaSchedule that was introduced on

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• I've added a test to check the energy of solvated neopetane-methane

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Commits on Feb 3, 2024

• Added in a shift_coulomb parameter that acts like shift_delta in the softening potential.

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Commits on Feb 4, 2024

• Tests now show excellent agreement between somd1 and sire/openmm energies for

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• Factorised the LJ equation in the sire/openmm custom forces.

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Commits on Feb 8, 2024

• Added more documentation about LambdaSchedule. Also added unit tests.

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• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_force_lever

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