Skip to content

Navigation Menu

Appearance settings

- AI CODE CREATION
  GitHub CopilotWrite better code with AI
  GitHub Copilot appDirect agents from issue to merge
  MCP Registry^NewIntegrate external tools
- DEVELOPER WORKFLOWS
  ActionsAutomate any workflow
  CodespacesInstant dev environments
  IssuesPlan and track work
  Code ReviewManage code changes
- APPLICATION SECURITY
  GitHub Advanced SecurityFind and fix vulnerabilities
  Code securitySecure your code as you build
  Secret protectionStop leaks before they start
- EXPLORE
  Why GitHub
  Documentation
  Blog
  Changelog
  Marketplace
View all features
- BY COMPANY SIZE
  Enterprises
  Small and medium teams
  Startups
  Nonprofits
- BY USE CASE
  App Modernization
  DevSecOps
  DevOps
  CI/CD
  View all use cases
- BY INDUSTRY
  Healthcare
  Financial services
  Manufacturing
  Government
  View all industries
View all solutions
- EXPLORE BY TOPIC
  AI
  Software Development
  DevOps
  Security
  View all topics
- EXPLORE BY TYPE
  Customer stories
  Events & webinars
  Ebooks & reports
  Business insights
  GitHub Skills
- SUPPORT & SERVICES
  Documentation
  Customer support
  Community forum
  Trust center
  Partners
View all resources
- COMMUNITY
  GitHub SponsorsFund open source developers
- PROGRAMS
  Security Lab
  Maintainer Community
  Accelerator
  GitHub Stars
  Archive Program
- REPOSITORIES
  Topics
  Trending
  Collections
- ENTERPRISE SOLUTIONS
  Enterprise platformAI-powered developer platform
- AVAILABLE ADD-ONS
  GitHub Advanced SecurityEnterprise-grade security features
  Copilot for BusinessEnterprise-grade AI features
  Premium SupportEnterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

Uh oh!

There was an error while loading. Please reload this page.

Colvars / colvars Public

Notifications You must be signed in to change notification settings
Fork 64
Star 239

Code
Issues 44
Pull requests 22
Discussions
Actions
Projects
Wiki
Security and quality
Insights

Additional navigation options

Code
Issues
Pull requests
Discussions
Actions
Projects
Wiki
Security and quality
Insights

Weighted poisson integration#872

Open

jhenin wants to merge 81 commits into

masterColvars/colvars:masterfrom

weighted_poisson_merged_endedColvars/colvars:weighted_poisson_merged_endedCopy head branch name to clipboard

Conversation Commits81 (81)Checks Files changed

Open

Weighted poisson integration#872
jhenin wants to merge 81 commits into
masterfrom
weighted_poisson_merged_ended

Commits

Commits on Jun 5, 2026

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
Cleanup after PR review

jhenin
authored and
levo-str
committed
prevent div calculation before preparations
levo-str
committed
restore use import of sys/stat.h
levo-str
committed
optimize code thanks to HanatoK's recommendations
levo-str
committed
fix: change the type of nb_averaged_gradients from size_t to int

HanatoK
authored and
levo-str
committed
optimize code thanks to HanatoK's recommendations
levo-str
committed
Fixes after rebase

jhenin
authored and
levo-str
committed
Re-indent two files with inconsistent spaces

jhenin
authored and
levo-str
committed
fix wrong calculations of div "supplement" i.e. boundary handling
levo-str
committed
[fix] fix calculation of eABF gradients with count (for weighted integration)
levo-str
committed
rerun test
levo-str
committed
perf: Avoid calls to std::pow
jhenin
committed
opt: compute_averaged_border_normal_gradient
jhenin
committed

Footer

© 2026 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.