Start on work on moving calculation of derivatives to apply loop for actions that pass vectors and matrices#1093

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gtribello wants to merge 63 commits intomasterfrom derivatives-from-backpropegation

+33,330-382,173

Commits on Jul 4, 2024

Added flag that forces PLUMED to not use chains when calculating derivatives
Gareth Aneurin Tribello
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Now turning off derivatives on forward pass through task loop when storing values as they are only needed on the backward pass to calculate forces
Gareth Aneurin Tribello
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Commits on Jul 10, 2024

Optimisations in adjacency matrix calculator

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Jul 22, 2024

Removed some if statements that are unecessary

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Jul 25, 2024

Removed parallelism in neightbour lists as it doesn't speed up the code
Gareth Aneurin Tribello
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Reduced the size of the forces array that is manipulated in matrix vector multiplication
Gareth Aneurin Tribello
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Commits on Jul 31, 2024

Changed the code so that values are transferred directly to the Value rather than to the buffer

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 1, 2024

Deleted some code that is not used

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Ran astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 15, 2024

Small fixes that correct the calculation forces when there is a function of a matrix in the apply loop
Gareth Aneurin Tribello
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Commits on Aug 18, 2024

Fixes to ensure that you can calculate local Q6 parameters without using chains

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 19, 2024

Optimisations for running Q6 in backwards loop

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Ran astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 20, 2024

Fixed gathering of Adjacency matrix components to make Steinhardt parameters with forces in backward loop faster
Gareth Aneurin Tribello
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Commits on Aug 24, 2024

Tidy up the way that errors with mask arguments are handled

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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converted mask variable from bool to unsigned

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 25, 2024

Implemented a version of ActionVolume that works when the chains are not used

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 26, 2024

Started implementing code for ensuring that volume selection works with coordination numbers

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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RAn astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Simplified the way that the task list is built

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 28, 2024

Can now calculate Q6 values in a particular volume only

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 29, 2024

Some small optimisations to FunctionOfMatrix
Gareth Aneurin Tribello
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Fixed Q6 implmenentation with volumes by fixing FunctionOfMatrix
Gareth Aneurin Tribello
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Commits on Aug 30, 2024

Replaced checking of derivatives for many regtests with testing of forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixes to ensure that SecondaryStructure variables work with the new scheme for forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Changed the code for generating the graphs to remove everything that outputting information about chains

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Aug 31, 2024

Fixed QuaternionBondProductMatrix so that it works with new apply for forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 1, 2024

This makes rops forces works with new force scheme and also addresses some issues with grids and matrices

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 2, 2024

Fixed treatment of sparse matrices for new force application stuff

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 3, 2024

Fixed rt-pairentropy to work with new scheme for forces in backward chain
Gareth Aneurin Tribello
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Removed doing of spherical integral regtest with new scheme for time being
Gareth Aneurin Tribello
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Commits on Sep 4, 2024

Fixed the way forces are applied for some regtests with new scheme

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Started fixing SMAC stuff so that it works with new force scheme

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 5, 2024

Fixed SMAC so that it works with the new forces backwards

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

The rt-bops regtest was calculating the values of this type of CV incorrectly because the actions have to be a particular order in the input file in that old version. The new reference values that …

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed to ensure that regtests gridtools/rt-spherical-integral-2, symfunc/rt-two-filter and crystdistrib/rt-bops all work with new force scheme

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed code that say regtest adjmat/rt45 works as well

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 8, 2024

Modified tests volumes/rt-q3-insphere and volumes/rt-small-sm to use new scheme for forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed calculation for rt-lq6-vol

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Fixed test volumes/rt-sean-mark to work with new derviative scheme

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Ran astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 10, 2024

Made the code work so that forces are calculated in the backward loop by default.
Gareth Aneurin Tribello
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Reworked secondary structure variables so that they work with forces being calculated during the backwards loop

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 12, 2024

Fixed QUATERNION_BOND_PRODUCT to work with new force propegation scheme. Now everything in the code can run with the new scheme
Gareth Aneurin Tribello
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Ran astyle
Gareth Aneurin Tribello
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First step in removing old implementation of derivatives calculated in forward loop
Gareth Aneurin Tribello
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Removed old style derivatives from MatrixVectorProduct and QuaternionBondProductMatrix
Gareth Aneurin Tribello
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Commits on Sep 15, 2024

FunctionOfMatrix and QuaternionBondProductMatrix are now parallelized over matrix elements rather than over the rows of the matrix

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Ran astyle

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 16, 2024

Removed all old chain stuff from FunctionOfVector
Gareth Aneurin Tribello
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Removed more code that was used for Stream stuff that is not usedd any longer
Gareth Aneurin Tribello
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Commits on Sep 17, 2024

Removed some old chain functionality

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 20, 2024

Removed code that was used for chained version of derivatives that is no longer used for forces

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 22, 2024

Store copies large vectors in ActionWithVector so that we can avoid a lot of malloc and optimise the code

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Sep 24, 2024

Reduced the amount of memory that is used in Q6 so you can now run 4 threads

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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Commits on Nov 9, 2024

Fixed DUMPFORCES command so that you can output forces for vectors, matrices and grids with this command.

Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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