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18 Commits

Author SHA1 Message Date
Giacomo Fiorin
133dee9ac1 Update Colvars library to version 2024-06-04 2024-08-06 01:07:43 +02:00
Giacomo Fiorin
377c652a83 Update Colvars library to version 2023-05-01 
This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
 2023-05-17 13:29:00 -04:00
Giacomo Fiorin
1220bea011 Update Colvars to version 2022-05-09 
This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.

Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).

Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers.  Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.

The following pull requests in the Colvars repository are relevant to LAMMPS:

- 475 Remove fatal error condition
  https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)

- 474 Allow normalizing eigenvector vector components to deal with unit change
  https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)

- 470 Better error handling in the initialization of NeuralNetwork CV
  https://github.com/Colvars/colvars/pull/470 (@HanatoK)

- 468 Add examples of histogram configuration, with and without explicit grid parameters
  https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)

- 464 Fix #463 using more fine-grained features
  https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)

- 447 [RFC] New option "scaledBiasingForce" for colvarbias
  https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)

- 444 [RFC] Implementation of dense neural network as CV
  https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)

- 443 Fix explicit gradient dependency of sub-CVs
  https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)

- 442 Persistent bias count
  https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)

- 437 Return type of bias from scripting interface
  https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)

- 434 More flexible use of boundaries from colvars by grids
  https://github.com/Colvars/colvars/pull/434 (@jhenin)

- 433 Prevent double-free in linearCombination
  https://github.com/Colvars/colvars/pull/433 (@HanatoK)

- 428 More complete documentation for index file format (NDX)
  https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)

- 426 Integrate functional version of backup_file() into base proxy class
  https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)

- 424 Track CVC inheritance when documenting feature usage
  https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)

- 419 Generate citation report while running computations
  https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)

- 415 Rebin metadynamics bias from explicit hills when available
  https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)

- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
  https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)

Authors: @giacomofiorin, @HanatoK, @jhenin
 2022-05-10 11:24:54 -04:00
Giacomo Fiorin
2a9be42758 Update Colvars to version 2021-08-03 2021-08-03 18:03:18 -04:00
Giacomo Fiorin
7deb773440 Update Colvars to version 2020-09-17 
Small changes

Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363

Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361

replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360
 2020-09-18 17:09:18 -04:00
Giacomo Fiorin
85c394453c Update Colvars to version 2020-07-07 
This update contains several fixes and small new features or usability
improvements.  Descriptions and authorship information can be accessed from
the pull requests listed below.

Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357

Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345

Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344

Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341

Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338

Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334

Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333

Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332

Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
 2020-09-09 18:19:21 -04:00
Giacomo Fiorin
9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Giacomo Fiorin
7e00acce53 Update Colvars library to version 2019-04-26 
The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
 2019-04-30 13:46:37 -04:00
Axel Kohlmeyer
ff6507e7b7 convert colvars lib to use c++ style header files 2018-05-08 00:17:57 -04:00
Giacomo Fiorin
f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
Giacomo Fiorin
da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Giacomo Fiorin
f553e230db Update Colvars library to version 2016-12-22 
Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
 2016-12-27 13:17:34 -05:00
sjplimp
17fd5898df git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14900 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-28 14:48:56 +00:00
sjplimp
f539e43b22 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13444 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-04-30 14:09:42 +00:00
sjplimp
5a0a8f1335 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13207 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-03-09 14:50:53 +00:00
sjplimp
c4af1cdbbd git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12811 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-12-02 02:09:53 +00:00
sjplimp
51a148df16 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12650 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-10-28 19:53:17 +00:00
sjplimp
211c12c39e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12613 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-10-07 20:30:53 +00:00