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
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
9427fc50a5
Update Colvars library to version 2020-01-27
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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
51ba9bd520
Bugfix for Colvars library (update to version 2019-08-05)
...
Bugfix for group2CenterOnly (coordNum option):
https://github.com/Colvars/colvars/pull/278
2019-08-05 14:14:33 -04:00
7e00acce53
Update Colvars library to version 2019-04-26
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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
85a5cab663
Update Colvars library to version 2018-10-16
2018-11-02 17:45:20 -04:00
f479f02589
Fix a Colvars error that was hidden by the previous segfault
2017-10-20 13:41:31 -04:00
3e89b270fd
Update Colvars to version 2017-10-11
...
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics. Also included are several small fixes.
Below is a list of relevant commits in the Colvars repository since the last update.
321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
ee6cac826e
Update Colvars to version 2017-07-15 and support automated builds for it
2017-07-19 14:24:07 -04:00
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
6d200061ca
update colvars library to version 2016-09-30
2016-09-30 08:15:44 -04:00
2fcd26f6c4
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15200 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:07:51 +00:00
212a955285
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14829 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-15 16:07:01 +00:00
067833cf07
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13126 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-02-19 18:20:52 +00:00
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
044084847b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-07 20:30:25 +00:00
4da20dce99
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-06-27 22:48:27 +00:00
1cfdda1f82
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8162 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2012-05-23 16:20:04 +00:00
