Start of transfer of functionality from hack-the-tree to maser #933

Merged

gtribello merged 43 commits intomasterfrom htt-new-interface-only

Jan 25, 2024

+3,281-2,881

Commits on Apr 30, 2023

Started adding vector/matrix/grid stuff into Value from hack-the-tree

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 1, 2023

Using basic/rt-make-extracv to test passing values from plumed to code

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Added functionality for passing data to and from PLUMED from hack-the-tree

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 5, 2023

Passing cell vectors through PUT action

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Changes to pass timestep from MD code to PLUMED through a PUT action

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Passing kBT through a PUT action

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 6, 2023

Ran astyle and fixed some codecheck issues

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed ccpcheck issues and issues with DEBUG mode

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 7, 2023

Fixed bug in last commit

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 12, 2023

Functionality for passing atoms moved from Atoms to DOMAIN_DECOMPOSITION

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 15, 2023

Fixed mechanism for passing energy between MD code and PLUMED

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed dates for copyright in header in these files

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Getting group from Group class rather than storing groups in Atoms
Gareth Aneurin Tribello
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Added getKBoltzmann, getUnits and usingNaturalUnits methods to Action

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 16, 2023

Moved duplicated functionality for getting forces from Values in Function and Colvar to ActionWithValue
Gareth Aneurin Tribello
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Commits on May 18, 2023

Virtual atom positions are now passed in three PLMD::Value

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Moved code for storing real precision to DataPassingTools and out of Atoms

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on May 19, 2023

Moved passing of units from MD code into PlumedMain and out of Atoms
Gareth Aneurin Tribello
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Removed Atoms and MDAtoms classes as they are no longer used and ran astyle to fix formatting
Gareth Aneurin Tribello
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Fixed bug for ccpcheck with extra docs adding in header file for DomainDecomposition
Gareth Aneurin Tribello
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Fixed bug due to unintialised variable "resetable" in constructor for ActionToPutData

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
committed

Commits on May 22, 2023

This test doesn't really use mpi so removed need for it
Gareth Aneurin Tribello
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Fixed a couple of unitialised variables
Gareth Aneurin Tribello
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Changed a couple of unsigned variables to size_t variables to stop some complaints
Gareth Aneurin Tribello
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Merge remote-tracking branch 'origin/master' into htt-atom-interface
Gareth Aneurin Tribello
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Ran asyle and fixed some warnings that the compiler gave
Gareth Aneurin Tribello
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Commits on May 24, 2023

Added virtual destructors in DataPassingObject and DataPassingTools
Gareth Aneurin Tribello
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Commits on May 25, 2023

Fixed code quality issues that were flagged by github
Gareth Aneurin Tribello
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Commits on Jun 19, 2023

Changes to make clearInputForces faster when you pass small number of atoms
Gareth Aneurin Tribello
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Commits on Jun 20, 2023

Some small optiisations of the code for retrieving atoms that mean we don't have to regularly call functions
Gareth Aneurin Tribello
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Commits on Jun 27, 2023

Optimisation of code for passing data from MD code to PLUMED

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Dec 8, 2023

Merge branch 'master' into htt-new-interface-only

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Changes to improve performance of CENTER

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Dec 25, 2023

Changes to the way forces are determined in the apply loop to make this code faster

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Dec 26, 2023

Used unique_serial flag to speed up apply

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Adjusted way forces on atoms are set to make apply loop faster

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Dec 29, 2023

Further small things to increase the speed of applying forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Jan 4, 2024

Small change to ActionWithValue::checkForForces that speeds up the code very slightly

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Jan 6, 2024

Changes to speed up the apply part of ActionWithVirtualAtom as well as WholeMolecules and WrapAround

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Jan 11, 2024

Ran astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Added some basic documentation to new actions for PLUMED interface

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed EMMIVox to reflect changes in Atoms class due to htt branch

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed a typo in previous commit

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
committed