Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Colvars/colvars issues and pull requests

#666 - Protein-specific coordinates based on index groups

Pull Request - State: open - Opened by jhenin 9 months ago

#664 - Dark mode and VMD - invisible text

Issue - State: closed - Opened by balazsfabian 9 months ago - 1 comment

#661 - Colvars dashboard - colvars do not appear

Issue - State: closed - Opened by balazsfabian 9 months ago - 4 comments

#660 - Dashboard button to load colvars traj

Pull Request - State: closed - Opened by jhenin 9 months ago - 1 comment

#659 - Stop testing GROMACS 2022 patch release

Pull Request - State: closed - Opened by giacomofiorin 9 months ago
Labels: GROMACS, maintenance

#658 - Allow empty string as cvc config

Pull Request - State: closed - Opened by jhenin 10 months ago

#651 - GROMACS - issue continuing a simulation

Issue - State: closed - Opened by fadelm01 10 months ago - 8 comments

#650 - More informative XYZ file reading errors

Pull Request - State: open - Opened by jhenin 10 months ago

#649 - Lambda-ABF implementation for the NAMD interface

Pull Request - State: open - Opened by jhenin 10 months ago

#648 - Allow NumPy-format output for plot_colvars_traj.py

Pull Request - State: closed - Opened by giacomofiorin 10 months ago - 4 comments
Labels: tools

#647 - Remove support for GROMACS 2022 when 2024 is out of beta

Issue - State: closed - Opened by giacomofiorin 11 months ago
Labels: GROMACS, testing

#646 - CI test uses Clang 14 when the action name mentions Clang 16

Issue - State: closed - Opened by jhenin 11 months ago - 1 comment

#644 - Allow reusing computation and data between CVC objects

Pull Request - State: open - Opened by giacomofiorin 11 months ago
Labels: optimization

#643 - Several improvements to colvar component classes

Pull Request - State: open - Opened by giacomofiorin 11 months ago
Labels: stability

#642 - Don't strip input state file in GROMACS (pre-2024)

Pull Request - State: closed - Opened by HubLot 12 months ago

#641 - Removing CI job for NAMD branch no longer maintained

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: NAMD, maintenance

#640 - Use 64bit integers to store prev timestep

Pull Request - State: closed - Opened by jhenin 12 months ago - 4 comments
Labels: bugfix

#639 - ABF histogram overflow shortly after 2 microseconds

Issue - State: closed - Opened by mvondomaros 12 months ago - 10 comments

#638 - Only distribute biases over threads if they don't need I/O

Pull Request - State: closed - Opened by giacomofiorin 12 months ago - 1 comment
Labels: bugfix

#637 - Remove unused includes

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: maintenance

#636 - Push updated documentation through CI jobs

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: documentation

#635 - Delete redundant manual links

Pull Request - State: closed - Opened by jhenin 12 months ago - 1 comment
Labels: documentation

#634 - New keyword format in documentation

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: documentation

#633 - Redundant link to updated doc in manual?

Issue - State: closed - Opened by jhenin 12 months ago - 2 comments

#632 - Fix MSVC 2022 warning

Pull Request - State: closed - Opened by giacomofiorin 12 months ago

#631 - Several CI ccache related fixes and improvements

Pull Request - State: closed - Opened by giacomofiorin 12 months ago - 1 comment
Labels: maintenance

#630 - Limit number of GitHub cache instances

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: maintenance

#629 - Define programmatically the available CVC types, report them in case of errors

Pull Request - State: closed - Opened by giacomofiorin 12 months ago - 2 comments

#628 - Fix OpenMP support in LAMMPS and GROMACS

Pull Request - State: closed - Opened by giacomofiorin 12 months ago
Labels: LAMMPS, GROMACS, bugfix

#627 - Gmx no cv config test

Pull Request - State: open - Opened by jhenin about 1 year ago
Labels: GROMACS, testing

#626 - Remove duplicate symlink creation in CI

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment
Labels: maintenance

#625 - Race condition in CMake symlink creation in CI tests

Issue - State: closed - Opened by jhenin about 1 year ago
Labels: bug, testing

#624 - Fix stalling NAMD jobs in CI

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 2 comments
Labels: maintenance

#623 - Several fixes to documentation

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 3 comments
Labels: documentation

#622 - Apply @zwpku's fix to colvargid::get_grad

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment

#621 - issue of integrate_potential::get_grad for non-periodic cv

Issue - State: closed - Opened by zwpku about 1 year ago - 1 comment

#619 - repeat outputting "colvars: The restart output state file will be ..." when using MonteCarloBarostat

Issue - State: closed - Opened by fhh2626 about 1 year ago - 4 comments
Labels: NAMD

#618 - Update GROMACS interface files

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: GROMACS

#617 - Support running LAMMPS tests with partitions

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: LAMMPS, maintenance

#616 - Update multisim test for GMX MdModules

Pull Request - State: closed - Opened by jhenin about 1 year ago - 17 comments
Labels: GROMACS, testing

#615 - Collected ABF improvements

Pull Request - State: open - Opened by jhenin about 1 year ago - 5 comments

#614 - Update doc for Tinker-HP

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment

#613 - CTest coverage reporting

Issue - State: open - Opened by jhenin about 1 year ago - 1 comment

#612 - More flexible control of PBC error handling

Issue - State: open - Opened by giacomofiorin about 1 year ago

#611 - Support external path for Colvars when building GROMACS

Issue - State: open - Opened by giacomofiorin about 1 year ago
Labels: GROMACS

#610 - Allow using a Colvars input state file instead of binary checkpoint in GROMACS

Pull Request - State: open - Opened by giacomofiorin about 1 year ago - 3 comments
Labels: GROMACS

#609 - Unit test for incorrect input

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment

#608 - Enable address sanitizer (via Clang) in CI

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 1 comment
Labels: maintenance

#607 - fix missing patch for cpt for GROMACS 2023

Pull Request - State: closed - Opened by HubLot about 1 year ago - 1 comment

#606 - Build HTML doc from within Colvars worktree

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 5 comments
Labels: documentation

#605 - Formalize code version in online doc URLs and shorten them?

Issue - State: closed - Opened by giacomofiorin about 1 year ago - 1 comment
Labels: question, documentation

#604 - Switch to Sans Serif font for documentation

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: documentation

#603 - Use GitHub-hosted container images for CI workflows

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: maintenance

#602 - Use pre-built Tcl 8.6 library from UIUC

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago

#601 - Add Tcl 8.6 to CentOS 7 container (NAMD 3.x now requires it)

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 2 comments
Labels: maintenance

#600 - Only compute virial when requested in Gromacs

Pull Request - State: closed - Opened by jhenin about 1 year ago

#599 - Cache group definitions that come from PDB files

Issue - State: open - Opened by giacomofiorin about 1 year ago

#598 - NAMD gets stuck when enabling energy minimization with CUDASOAIntegrate and Colvars

Issue - State: closed - Opened by fhh2626 about 1 year ago - 5 comments
Labels: NAMD

#597 - Consolidate backend test runners

Issue - State: open - Opened by giacomofiorin about 1 year ago

#596 - Restore multi-threaded tests for NAMD

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: NAMD, maintenance

#595 - Drop Oracle/Sun compiler from CI tests?

Issue - State: open - Opened by giacomofiorin about 1 year ago - 1 comment
Labels: question, quick

#594 - Silence clang-tidy warnings

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 1 comment
Labels: maintenance

#593 - typos

Issue - State: closed - Opened by zwpku about 1 year ago - 6 comments

#592 - Why is my ABF simulation sampling from a small set of values?

Issue - State: closed - Opened by wisecashew about 1 year ago - 2 comments

#591 - Allow redefining outputPrefix in NAMD

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: NAMD

#590 - Initialize integer and floating point members of colvar class

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: bugfix

#589 - Reset error code when invoking colvarmodule::reset()

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 1 comment

#588 - Program segfaulting after simulation runs

Issue - State: closed - Opened by wisecashew about 1 year ago - 4 comments
Labels: bug

#587 - Improve the NeuralNetwork CV

Pull Request - State: closed - Opened by HanatoK about 1 year ago - 1 comment

#586 - Track date-based CV dashboard versions

Pull Request - State: closed - Opened by jhenin about 1 year ago

#585 - Improve rotation

Pull Request - State: closed - Opened by HanatoK about 1 year ago

#584 - Merge GROMACS MDModules interface

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 1 comment
Labels: GROMACS

#583 - Droplets Coalescence

Issue - State: closed - Opened by nguyen2504to about 1 year ago - 6 comments

#582 - Silence Clang static analyzer warnings

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 3 comments
Labels: maintenance

#581 - Warning from Clang static analyser

Issue - State: closed - Opened by HubLot about 1 year ago

#580 - Which OS to build documentation on?

Issue - State: closed - Opened by giacomofiorin about 1 year ago - 4 comments
Labels: question, documentation

#579 - Fix several issues preventing reading state from LAMMPS restart file

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago - 2 comments
Labels: LAMMPS, bugfix

#578 - Use Ninja when available to build CMake targets

Pull Request - State: closed - Opened by giacomofiorin about 1 year ago
Labels: maintenance

#573 - Default param for set_unit_system

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment

#572 - Move Python, C_fortran, stubs to misc_interfaces/

Pull Request - State: closed - Opened by jhenin about 1 year ago - 1 comment

#571 - Fix #569 and allow mixing scalar and vector CVCs

Pull Request - State: closed - Opened by HanatoK about 1 year ago - 7 comments

#570 - enable use of CVs defined by PyTorch neural network models

Pull Request - State: open - Opened by zwpku about 1 year ago - 18 comments

#569 - memory not allocated when customColvar is used as a cvc with vector-valued sub-cvcs?

Issue - State: closed - Opened by zwpku about 1 year ago - 2 comments
Labels: minor bug

#568 - Set CVC description consistently

Pull Request - State: closed - Opened by jhenin over 1 year ago - 3 comments

#567 - Projecting PMF along a new collective variable?

Issue - State: closed - Opened by Praveen-2k21 over 1 year ago - 1 comment

#566 - Better handling of faulty configs in Dashboard

Pull Request - State: open - Opened by EzryStIago over 1 year ago - 1 comment
Labels: VMD

#565 - Writing Custom Function in NAMD Colvar Configuration

Issue - State: closed - Opened by naliio over 1 year ago - 2 comments

#564 - Major updates of the arithmetic PCV code

Pull Request - State: closed - Opened by HanatoK over 1 year ago - 3 comments

#563 - Description of a cvc is not updated after set_function_type

Issue - State: closed - Opened by HanatoK over 1 year ago - 1 comment

#562 - Support for GROMACS 2023

Pull Request - State: closed - Opened by HubLot over 1 year ago - 3 comments

#561 - Change of output prefix by NAMD script is ignored by Colvars

Issue - State: closed - Opened by jhenin over 1 year ago - 1 comment
Labels: NAMD, minor bug

#560 - RFC: Further optimize the optimal rotation code path

Issue - State: open - Opened by HanatoK over 1 year ago - 6 comments
Labels: optimization, non-urgent

#559 - Option to run NAMD regtests in GPU-resident mode

Pull Request - State: closed - Opened by jhenin over 1 year ago - 4 comments

#558 - Unformatted (binary) checkpointing

Pull Request - State: closed - Opened by giacomofiorin over 1 year ago - 13 comments

#557 - Disable Sun compiler +w, use Clang -Wshadow-field when available

Pull Request - State: closed - Opened by giacomofiorin over 1 year ago
Labels: maintenance

#556 - Separate checking the name of the bias from reading its state data

Pull Request - State: closed - Opened by giacomofiorin over 1 year ago
Labels: bugfix

#555 - Fix gpath simulations after PR #541

Pull Request - State: closed - Opened by HanatoK over 1 year ago - 2 comments

#554 - Update containers for Linux CI builds

Pull Request - State: closed - Opened by giacomofiorin over 1 year ago - 1 comment
Labels: maintenance