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
2a9be42758
Update Colvars to version 2021-08-03
2021-08-03 18:03:18 -04:00
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
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
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
85a5cab663
Update Colvars library to version 2018-10-16
2018-11-02 17:45:20 -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
5fe6206638
Update Colvars module to version 2017-03-10
2017-03-10 09:16:58 -05:00
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
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
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
20beaccf0f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14703 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-03-01 20:40:25 +00:00
974e1eb022
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13396 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-04-06 15:14:53 +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
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
