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Colvars / colvars Public

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Pull requests 27
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ABF using kernelized gradient grid#905

Draft

jhenin wants to merge 124 commits intoweighted_poisson_merged_endedColvars/colvars:weighted_poisson_merged_endedfrom

kernel_gridColvars/colvars:kernel_gridCopy head branch name to clipboard

Conversation Commits124 (124)Checks Files changed

Draft

ABF using kernelized gradient grid#905
jhenin wants to merge 124 commits intoweighted_poisson_merged_endedfrom
kernel_grid

Commits

Commits on Dec 19, 2025

Weighted Poisson integration (squashed changes)

jhenin
authored and
levo-str
committed
cache the laplacian coefficients and integrate calculate weight sum in the laplacian loop to make the programme faster
levo-str
committed
precompute laplacian coefficient and parallelize code
levo-str
committed
implement data extrapolation
levo-str
committed
fix print of convergence
levo-str
committed
uses the conjugate gradient optimizer for unweighted poisson resolution
levo-str
committed
implement as minimization of error on data's estimation of the gradient
levo-str
committed
fix unweighted boundary conditions handling and change laplacian calculation when there is no precomputation of the coefficients
levo-str
committed
fix segmentation error in div calculation when handling periodic boundary condition and implement choice between on the fly laplacian computation or precompute coefficients
levo-str
committed
clean code
levo-str
committed
use optimal parameter
levo-str
committed
Don't include omp header

jhenin
authored and
levo-str
committed
delete unused code
levo-str
committed
parallel for loop over signed int and force thresholds as floats
levo-str
committed
fix type incoherence
levo-str
committed
remove excess variable
levo-str
committed
reformat code as normal
levo-str
committed
[MUST BE CHECKED] add flag for weighted integration
levo-str
committed
comment code
levo-str
committed
chore: remove unused code in poisson_integrator

jhenin
authored and
levo-str
committed
chore: remove unused code

jhenin
authored and
levo-str
committed
chore: undo formatting changes

jhenin
authored and
levo-str
committed
chore: more cleanup of weighted Poisson

jhenin
authored and
levo-str
committed
fix: Adapt weighted Poisson for ABF

jhenin
authored and
levo-str
committed
test: Update NAMD regression tests output

jhenin
authored and
levo-str
committed
allow eABF weighted Poisson integration
levo-str
committed
fix reading for eABF
levo-str
committed
fix: smart pointer to fix memory leak

jhenin
authored and
levo-str
committed
test: add functional test for 2D eABF

jhenin
authored and
levo-str
committed
:fix: fix pointer issue, computation size issue and divergence stencil calculation
levo-str
committed
fix the memory leakage by correcting border gradients calculation for potential extrapolation
levo-str
committed
fix the memory leakage by correcting border gradients calculation for potential extrapolation
levo-str
committed
add deletion of computation grid pointer
levo-str
committed
fix extrapolation (again)
levo-str
committed
fix: add missing test inputs

jhenin
authored and
levo-str
committed
delete unused logs
levo-str
committed
update test and delete unused testing variable
levo-str
committed
add new test eabf test with weighted integration
levo-str
committed
add new test abf2d_euler_weighted.in
levo-str
committed
:fix: correct test's colvar file name
levo-str
committed
update tests [Needs to be checked]
levo-str
committed
fix: test for empty count grid before integrating

jhenin
authored and
levo-str
committed
test: reduce grid size in ext abf2d test

jhenin
authored and
levo-str
committed
add documentation
levo-str
committed
add missing argument
levo-str
committed
allow sample grid to be added later
levo-str
committed
add 2D eABF with weighted integration test
levo-str
committed
allow sample grid to be added later
levo-str
committed
format code
levo-str
committed
check if this passes the test
levo-str
committed
delete unused import
levo-str
committed
error catching to handle 1D cases
levo-str
committed
fix: more robust colvargrid_gradient constructor

jhenin
authored and
levo-str
committed
fix: grid handling in ABF, limit header scope

jhenin
authored and
levo-str
committed
test: fix output for custom grid metadata in ABF

jhenin
authored and
levo-str
committed
put back integrate weighted argument
levo-str
committed
improve test with custom grid of different size to the original one
levo-str
committed
update eABF weighted test reference value
levo-str
committed
delete solved comments and unused log
levo-str
committed
create ABF with weighted integration NAMD test
levo-str
committed
create NAMD test for eABF
levo-str
committed
update tests
levo-str
committed
Make total_forces_same_step consistent

jhenin
authored and
levo-str
committed
Remove redundant gradient tests

jhenin
authored and
levo-str
committed
Improve poisson_integrator by adding CLI flags

jhenin
authored and
levo-str
committed
Cast integers to cvm::real before division

jhenin
authored and
levo-str
committed
delete useless imports
levo-str
committed
add more details to the documentation
levo-str
committed
update tests
levo-str
committed
delete unused member 'samples'
levo-str
committed
delete duplicate code by creating a colvar_grid_scalar_function
levo-str
committed
try to pass the CI
levo-str
committed
[WIP] implement kernel grid
levo-str
committed
update file with new implementation
levo-str
committed
change argument value so it doesn't shadow class attribute
levo-str
committed
[WIP] continue implementing kernel grid
levo-str
committed
[WIP] continue implementing kernel grid
levo-str
committed
[WIP] :fix: add positions size assignment
levo-str
committed
[WIP] use bins for acc_abf_force
levo-str
committed
[WIP] :fix: fix acc_value
levo-str
committed
[WIP] add log
levo-str
committed
fix initialization for czar gradients with weights kernel grid
levo-str
committed
fix conversion to int of scalar weights and add smooth abf possibilities
levo-str
committed
clean debugging lines
levo-str
committed
handle use of scalar weights
levo-str
committed
make sure pointers out are initialized
levo-str
committed
make sure pointers out are initialized
levo-str
committed
[WIP] comment debugging log that may be useful until implementation
levo-str
committed
[WIP] comment debugging log that may be useful until implementation
levo-str
committed
fix: cut and paste error

jhenin
authored and
levo-str
committed
delete useless logs
levo-str
committed
allow weighted integration with scalar weights
levo-str
committed
disable divergence calculation without having done preparation first
levo-str
committed
finish implementation of kernel grid and clean unused logs
levo-str
committed
fix miscalculation of kernel support
levo-str
committed
add unit test
levo-str
committed
fix implementation
levo-str
committed
use the whole kernel support
levo-str
committed
try fixing floating point exceptions test error
levo-str
committed
try fixing floating point exceptions test error
levo-str
committed
add smoothing argument in file
levo-str
committed
add namd tests for kernel grid abf
levo-str
committed
add helper function to loop properly on the kernel support
levo-str
committed
update tests
levo-str
committed
precompute kernel parameters
levo-str
committed
precompute kernel parameters
levo-str
committed
finish kernel grid implementation
levo-str
committed
add smoothing to the test
levo-str
committed
update test
levo-str
committed
delete unused helper function
levo-str
committed
fix copy and paste error
levo-str
committed
update test
levo-str
committed
make sure pointers are not null
levo-str
committed
delete unused logs
levo-str
committed

Commits on Jan 22, 2026

implement adaptative kernel size
levo-str
committed
implement adaptative kernel size
levo-str
committed

Commits on Jan 26, 2026

improve code performance by using the kernel's separability
levo-str
committed
comment unused dim_sum
levo-str
committed
make the weight of each data point mean force estimate equal to 1
levo-str
committed
make kernel support more symmetric
levo-str
committed
make kernel more adaptive
levo-str
committed
clean useless comment
levo-str
committed

Commits on Feb 3, 2026

fix appearance of kernels of size 0
levo-str
committed
fix appearance of kernels of size 0
levo-str
committed

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