Ecosyste.ms: Issues

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GitHub / Colvars/colvars issues and pull requests

#553 - Fix overflow of exp in arithmetic path CVs

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

#552 - Initialize the list of variables early to restore --list-variables option

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

#551 - Control the update of the .colvars.traj file

Issue - State: closed - Opened by fhh2626 over 1 year ago - 7 comments
Labels: NAMD

#550 - Copilot request

Issue - State: closed - Opened by giacomofiorin over 1 year ago - 2 comments
Labels: question

#549 - Reorganize Colvars repo tree

Issue - State: open - Opened by jhenin over 1 year ago - 1 comment
Labels: documentation, non-urgent, maintenance

#548 - Update required C++ language version to C++11

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

#547 - fix clang12 warnings

Pull Request - State: closed - Opened by HubLot over 1 year ago - 5 comments

#546 - Add minimal .clang-format for library source code

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

#545 - Write the hill trajectory in write_output_files instead of in add_hill and delete_hill

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

#544 - "trying to access an output file/channel from the wrong thread." when using writeHillsTrajectory

Issue - State: closed - Opened by HanatoK over 1 year ago - 2 comments
Labels: bug

#543 - Initialize input string streams alongside input file streams

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

#542 - Support for properly close istringstreams in input_streams_

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

#541 - Optimize the RMSD calculation

Pull Request - State: closed - Opened by HanatoK over 1 year ago - 19 comments

#540 - RMSD is too slow

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

#539 - Full functional test without back-end

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

#538 - Close, but do not delete input streams

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

#537 - Initialize NAMD ID map entry immediately when requesting a new atom

Pull Request - State: closed - Opened by giacomofiorin over 1 year ago - 3 comments
Labels: NAMD, bugfix

#536 - Incorrect RMSD when using "run 0" then "cv configfile" and then "run N" in NAMD

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

#535 - Restarting simulation with colvars

Issue - State: closed - Opened by Praveen-2k21 over 1 year ago - 2 comments
Labels: NAMD

#534 - colvarproxy::post_run() & restart output filename

Issue - State: closed - Opened by HubLot over 1 year ago - 4 comments

#533 - Enable CTest on Windows builds

Pull Request - State: open - Opened by giacomofiorin over 1 year ago

#532 - Add XYZ trajectory reading feature

Pull Request - State: closed - Opened by jhenin over 1 year ago - 6 comments

#531 - Delete objects quietly, unless explicitly requested via script (including VMD)

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

#530 - Append newline to log and error messages if not already present

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

#529 - Log newline

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

#528 - Forward-declare OpenMP lock

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

#527 - Remove unneeded container

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

#526 - Allow collecting configuration files and strings before setting up interface

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

#525 - Meta reflection

Pull Request - State: open - Opened by fabsugar over 1 year ago - 5 comments

#524 - request to include meta_reflection in the master branch

Pull Request - State: closed - Opened by fabsugar over 1 year ago - 1 comment

#523 - Fallback to linearCombination when customFunction is missing in customColvar

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

#522 - Use iostream::fail() to check for I/O error

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

#521 - cv load with non-existent file fails silently

Issue - State: closed - Opened by jhenin over 1 year ago - 10 comments
Labels: bug

#520 - Fix ref count

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

#519 - Update the Colvars bundled in NAMD

Issue - State: closed - Opened by HanatoK over 1 year ago - 7 comments

#518 - Poisson_integrator seems highly inaccurate with 2D path-CV

Issue - State: closed - Opened by gitkol over 1 year ago - 4 comments

#517 - Changing bias temperature during restart in WT-MetaD

Issue - State: closed - Opened by Praveen-2k21 almost 2 years ago - 3 comments

#516 - PMF calculated returned from Colvars module corrects for PBC?

Issue - State: closed - Opened by Praveen-2k21 almost 2 years ago - 2 comments

#515 - request

Pull Request - State: closed - Opened by zwpku almost 2 years ago - 9 comments

#514 - Unusually increased Hill height at a few points in the metadynamics simulation

Issue - State: closed - Opened by Praveen-2k21 almost 2 years ago - 3 comments

#513 - Set target temperature through a common code path

Pull Request - State: closed - Opened by giacomofiorin almost 2 years ago - 5 comments

#512 - fix Uninitialized variables in GROMACS source tree.

Pull Request - State: closed - Opened by HubLot almost 2 years ago
Labels: GROMACS, bugfix

#511 - Allow lowerWall > upperWall for periodic CVs ?

Issue - State: closed - Opened by jhenin almost 2 years ago - 4 comments
Labels: question

#510 - Add support for GROMACS 2022

Pull Request - State: closed - Opened by HubLot almost 2 years ago - 16 comments
Labels: GROMACS, maintenance

#509 - Safer detection of Windows with recent Microsoft Visual Studio versions

Pull Request - State: closed - Opened by akohlmey almost 2 years ago - 1 comment
Labels: maintenance

#508 - Update LAMMPS patching method to reflect Lepton availability

Pull Request - State: closed - Opened by giacomofiorin almost 2 years ago
Labels: LAMMPS, Lepton, maintenance

#507 - BAOA integrator for extended Lagrangian dynamics

Pull Request - State: closed - Opened by jhenin almost 2 years ago - 30 comments

#506 - colvarbias_reweightaMD::write_output_files() has been called in the main thread.

Pull Request - State: closed - Opened by HanatoK almost 2 years ago
Labels: NAMD, bugfix

#505 - Unable to run GaWTM-eABF simulations due to io issue

Issue - State: closed - Opened by HanatoK almost 2 years ago - 3 comments
Labels: bug, NAMD

#504 - Colvars on Gromacs

Issue - State: closed - Opened by jubilantsundar almost 2 years ago - 2 comments
Labels: question

#503 - Should cvm::log systematically add a newline?

Issue - State: closed - Opened by jhenin about 2 years ago - 2 comments
Labels: question, quick

#502 - Accept multiple config files from NAMD (preliminary work)

Pull Request - State: closed - Opened by jhenin about 2 years ago - 13 comments
Labels: NAMD

#501 - NAMD interface test 003_reinitatoms fails

Issue - State: closed - Opened by jhenin about 2 years ago - 4 comments
Labels: bug, NAMD

#500 - Fix cvm not properly destructed in VMD

Pull Request - State: closed - Opened by jhenin about 2 years ago - 1 comment
Labels: VMD, bugfix

#499 - Cmake debug

Pull Request - State: closed - Opened by jhenin about 2 years ago - 2 comments
Labels: maintenance

#498 - Use Apptainer to manage containers in CI

Pull Request - State: closed - Opened by giacomofiorin about 2 years ago
Labels: maintenance

#497 - Increase the precision of write_multicol

Pull Request - State: closed - Opened by HanatoK about 2 years ago - 15 comments

#496 - Only perform MTS automatic enable/disable for timeStepFactor > 1

Pull Request - State: closed - Opened by giacomofiorin about 2 years ago
Labels: minor bug

#495 - ERMSD

Issue - State: closed - Opened by gsabbih6 about 2 years ago - 5 comments

#494 - Don't track NAMD Makefile, patch it

Pull Request - State: closed - Opened by jhenin about 2 years ago - 1 comment
Labels: NAMD, maintenance

#491 - Is it possible to write grid files using the maximal available precision?

Issue - State: closed - Opened by HanatoK over 2 years ago - 8 comments

#490 - The latest (lepton) version causes compilation error of NAMD

Issue - State: closed - Opened by fhh2626 over 2 years ago - 18 comments

#487 - Use map of output streams, and return references to its elements

Pull Request - State: closed - Opened by giacomofiorin over 2 years ago - 4 comments
Labels: maintenance

#486 - Remember first step of moving restraint

Pull Request - State: closed - Opened by jhenin over 2 years ago - 5 comments

#485 - Add decoupling option for moving restraints

Pull Request - State: closed - Opened by jhenin over 2 years ago - 1 comment

#484 - Finally remove support for appending to files?

Issue - State: closed - Opened by giacomofiorin over 2 years ago - 9 comments
Labels: question, NAMD

#481 - Make file-reading operations of input data abstractable

Pull Request - State: closed - Opened by giacomofiorin over 2 years ago - 5 comments
Labels: maintenance

#477 - Implement minimum image distance RMSD

Issue - State: closed - Opened by jhenin over 2 years ago - 9 comments

#476 - Allowing custom grid definition for each bias instance

Issue - State: open - Opened by giacomofiorin over 2 years ago - 1 comment

#432 - Embedded tcl

Pull Request - State: closed - Opened by jhenin about 3 years ago - 8 comments
Labels: script_API

#418 - Extend support for fix_modify to remaining script API commands

Pull Request - State: closed - Opened by giacomofiorin over 3 years ago - 7 comments
Labels: LAMMPS, documentation, script_API

#412 - Offer some way for parser to deal with spaces in file paths

Issue - State: open - Opened by jhenin over 3 years ago - 2 comments
Labels: non-urgent, parser

#394 - Cannot create object with empty config block on single line

Issue - State: closed - Opened by jhenin over 3 years ago - 9 comments
Labels: non-urgent, parser

#374 - Write NDX index files within the Dashboard

Pull Request - State: closed - Opened by giacomofiorin about 4 years ago - 6 comments

#358 - GPU preparation work

Issue - State: closed - Opened by jvermaas over 4 years ago - 11 comments
Labels: NAMD

#355 - Make ABF inputPrefix accept state files

Issue - State: open - Opened by jhenin over 4 years ago

#353 - More practical smoothing of changing force constant in restraint

Issue - State: closed - Opened by jhenin over 4 years ago - 2 comments

#348 - Smaller variant of multicol files for 3D grids (and beyond)

Issue - State: open - Opened by jhenin over 4 years ago - 10 comments

#342 - More flexible bias-specific grid parameters

Issue - State: closed - Opened by jhenin over 4 years ago - 1 comment

#331 - Should we convert most parse_silent options to parse_echo ?

Issue - State: closed - Opened by jhenin over 4 years ago - 4 comments
Labels: question, parser

#254 - Dependencies between same-level objects

Issue - State: closed - Opened by jhenin over 5 years ago - 6 comments
Labels: maintenance

#187 - "cv load" should not active colvar value check

Issue - State: closed - Opened by fhh2626 about 6 years ago - 21 comments

#61 - Move cvm::atom member data to synchronized vectors within cvm::atom_group

Issue - State: closed - Opened by giacomofiorin over 8 years ago - 11 comments
Labels: important, optimization