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

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

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2982b55
Added flag that forces PLUMED to not use chains when calculating deri…
Jul 4, 2024
b9b8969
Now turning off derivatives on forward pass through task loop when st…
Jul 4, 2024
d15c12f
Optimisations in adjacency matrix calculator
Jul 10, 2024
10da9a4
Merge branch 'master' into derivatives-from-backpropegation
Jul 16, 2024
ead56cd
Merge branch 'master' into derivatives-from-backpropegation
Jul 16, 2024
cd6f553
Added faster version of matrix vector multiply that is used when not …
Jul 16, 2024
94d33a9
Added some optimisations in AdjacencyMatrixBase
Jul 18, 2024
033d957
Added optimisation for matrix times vector to avoid allocating large …
Jul 19, 2024
2115528
Optimisations of derivatives by back propegation
Jul 19, 2024
7e0f435
Optimised adding of forces in AdjacencyMatrixBase by using the fact t…
Jul 19, 2024
cb37323
Removed some if statements that are unecessary
Jul 22, 2024
1889cf1
Removed parallelism in neightbour lists as it doesn't speed up the code
Jul 25, 2024
e0f5606
Reduced the size of the forces array that is manipulated in matrix ve…
Jul 25, 2024
e23214d
Changed the code so that values are transferred directly to the Value…
Jul 30, 2024
fd50ad4
Deleted some code that is not used
Aug 1, 2024
6492e55
Ran astyle
Aug 1, 2024
05389b7
Small fixes that correct the calculation forces when there is a funct…
Aug 15, 2024
b3bc765
Fixes to ensure that you can calculate local Q6 parameters without us…
Aug 18, 2024
8be05b8
Optimisations for running Q6 in backwards loop
Aug 19, 2024
daa3a83
Ran astyle
Aug 19, 2024
12a0ecf
Fixed gathering of Adjacency matrix components to make Steinhardt par…
Aug 20, 2024
98647c6
Tidy up the way that errors with mask arguments are handled
Aug 24, 2024
4607ff5
converted mask variable from bool to unsigned
Aug 24, 2024
c65a33d
Implemented a version of ActionVolume that works when the chains are …
Aug 25, 2024
b978c66
Started implementing code for ensuring that volume selection works wi…
Aug 26, 2024
59b2212
RAn astyle
Aug 26, 2024
d207200
Simplified the way that the task list is built
Aug 26, 2024
67c9ab0
Can now calculate Q6 values in a particular volume only
Aug 28, 2024
15cb43e
Some small optimisations to FunctionOfMatrix
Aug 29, 2024
95369e7
Fixed Q6 implmenentation with volumes by fixing FunctionOfMatrix
Aug 29, 2024
7c58054
Replaced checking of derivatives for many regtests with testing of fo…
Aug 30, 2024
f36f670
Fixes to ensure that SecondaryStructure variables work with the new s…
Aug 30, 2024
dfe4aaf
Changed the code for generating the graphs to remove everything that …
Aug 30, 2024
06b6235
Fixed QuaternionBondProductMatrix so that it works with new apply for…
Aug 31, 2024
30519d8
This makes rops forces works with new force scheme and also addresses…
Sep 1, 2024
a490eef
Fixed treatment of sparse matrices for new force application stuff
Sep 2, 2024
938d5a8
Fixed rt-pairentropy to work with new scheme for forces in backward c…
Sep 3, 2024
da73f0e
Removed doing of spherical integral regtest with new scheme for time …
Sep 3, 2024
b15bb38
Fixed the way forces are applied for some regtests with new scheme
Sep 4, 2024
b77402e
Started fixing SMAC stuff so that it works with new force scheme
Sep 4, 2024
f46ca43
Fixed SMAC so that it works with the new forces backwards
Sep 5, 2024
cd81a35
The rt-bops regtest was calculating the values of this type of CV inc…
Sep 6, 2024
8080dcb
Fixed to ensure that regtests gridtools/rt-spherical-integral-2, symf…
Sep 6, 2024
aaa48f6
Fixed code that say regtest adjmat/rt45 works as well
Sep 6, 2024
e632be0
Modified tests volumes/rt-q3-insphere and volumes/rt-small-sm to use …
Sep 8, 2024
9675fb7
Fixed calculation for rt-lq6-vol
Sep 8, 2024
85bd330
Fixed test volumes/rt-sean-mark to work with new derviative scheme
Sep 8, 2024
14c8511
Ran astyle
Sep 8, 2024
fef88fb
Made the code work so that forces are calculated in the backward loop…
Sep 10, 2024
35802bd
Reworked secondary structure variables so that they work with forces …
Sep 10, 2024
570827a
Fixed QUATERNION_BOND_PRODUCT to work with new force propegation sche…
Sep 12, 2024
9d4c4e5
Ran astyle
Sep 12, 2024
6ca7a9a
First step in removing old implementation of derivatives calculated i…
Sep 12, 2024
f8e4519
Removed old style derivatives from MatrixVectorProduct and Quaternion…
Sep 12, 2024
5bc572d
FunctionOfMatrix and QuaternionBondProductMatrix are now parallelized…
Sep 13, 2024
5e562d7
Ran astyle
Sep 15, 2024
a88ff36
Removed all old chain stuff from FunctionOfVector
Sep 16, 2024
374d19f
Removed more code that was used for Stream stuff that is not usedd an…
Sep 16, 2024
03e8500
Removed some old chain functionality
Sep 17, 2024
46f53ba
Removed code that was used for chained version of derivatives that is…
Sep 17, 2024
8628615
Store copies large vectors in ActionWithVector so that we can avoid a…
Sep 22, 2024
636898f
Reduced the amount of memory that is used in Q6 so you can now run 4 …
Sep 24, 2024
c9df402
Fixed DUMPFORCES command so that you can output forces for vectors, m…
Nov 9, 2024
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630 changes: 0 additions & 630 deletions regtest/adjmat/rt-basic-matrix/deriv.reference
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This file was deleted.

2 changes: 1 addition & 1 deletion regtest/adjmat/rt-basic-matrix3/config
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
type=driver
plumed_modules=adjmat
# this is to test a different name
arg="--plumed plumed.dat --ixyz gas-one.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num"
arg="--plumed plumed.dat --ixyz gas-one.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num"
0 regtest/symfunc/rt-q6-lowmem/Makefile → regtest/adjmat/rt-basic-matrix4/Makefile
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4 changes: 4 additions & 0 deletions regtest/adjmat/rt-basic-matrix4/config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
type=driver
plumed_modules=adjmat
# this is to test a different name
arg="--plumed plumed.dat --ixyz gas-one.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num"
3 changes: 3 additions & 0 deletions regtest/adjmat/rt-basic-matrix4/fcolvar.reference
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
#! FIELDS time mts
0.000000 20.46772
1.000000 20.46772
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