133dee9ac1
Update Colvars library to version 2024-06-04
2024-08-06 01:07:43 +02:00
c3cc4974d1
silence uninitialized access valgrind warning
2023-09-21 07:33:03 -04:00
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
3f496905d6
Merge branch 'develop' into lepton-package
2023-01-06 00:44:28 -05:00
6e60131f14
Windows portability changes
2022-12-28 20:53:53 -05:00
efc2e96a9e
explicitly share Lepton settings between lepton and colvars folders
2022-12-27 17:42:59 -05:00
2a3d1a1ba5
import JIT settings to colvars library makefile
2022-12-27 15:16:58 -05:00
4f4f7be9c8
must provide list of object for colvars lib
2022-12-27 14:04:54 -05:00
faa2a9ffeb
remove Lepton source from lib/colvars folder
2022-12-27 13:59:34 -05:00
7e984bfa2c
update traditional make build support for shaking Lepton between LEPTON and COLVARS
2022-12-27 11:16:09 -05:00
04586e634e
Remove trailing whitespace from Lepton per suggestion from @akohlmey
2022-06-02 11:52:39 -04:00
3a1423dc48
Update Colvars to 2022-05-24 and copy of Lepton library
...
One bugfix for the Colvars library in the ABF method, and update of the copy
of the Lepton library as per the OpenMM repository.
List of relevant PR.
- 483 Update Lepton via patching procedure
https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)
- 482 Fix integer overflow in log_gradient_finite_diff and gradient_finite_diff
https://github.com/Colvars/colvars/pull/482 (@HanatoK)
2022-06-02 11:24:04 -04:00
7e75b7bff5
whitespace
2022-05-19 12:16:31 -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
7601001632
Fix Colvars output files not written with "run 0"
...
See:
https://github.com/Colvars/colvars/commit/ff2f0d39ee5
which fixes a bug introduced in:
https://github.com/Colvars/colvars/commit/1e964a542b
The message applies to NAMD, but the logic used in LAMMPS when handling "run 0" is very similar.
The Colvars version string is also updated, however this commit does not
include other changes, such as the following:
https://github.com/Colvars/colvars/pull/419
which were not fully completed before the LAMMPS Summer 2021 finalization.
2021-09-27 13:38:30 -04:00
92b5b159e5
replace tabs and remove trailing whitespace in lib folder with updated script
2021-08-22 20:45:24 -04:00
eb52f7c290
Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
...
Also include PDF copy of the manual forgotten in previous PR.
2021-08-06 10:32:37 -04:00
2a9be42758
Update Colvars to version 2021-08-03
2021-08-03 18:03:18 -04:00
878795e64a
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
9cdacbdebd
apply cast to first variable in sequence of multiplications
2021-02-07 21:18:54 -05:00
5573d01079
Use typecast to silence CodeQL warnings
2021-02-06 18:18:52 -05:00
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
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
2bb5c53a47
remove/replace extended ASCII characters from comments
2020-07-27 17:15:29 -04:00
634f274a04
whitespace cleanup: replace tabs and remove trailing whitespace
2020-07-27 17:14:53 -04:00
4042b836c2
enable full c++11 in colvars, same as LAMMPS
2020-06-14 12:18:51 -04:00
be1f307384
Add defines to build Lepton with MSVC and traditional make
2020-04-14 16:57:04 -04:00
209a3fde71
use MY_PI everywhere, not M_PI.
2020-04-13 12:02:53 -04:00
5d2ec73c5d
re-enable cross-compilation with mingw64
2020-04-13 11:22:19 -04:00
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
8af9d40392
Update DOI resolver
...
https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
2020-03-12 16:53:24 +09:00
7be004512f
Update Colvars to version 2020-02-27
...
This update contains several small new features or usability improvements.
Descriptions and authorship information can be accessed from the pull
requests listed below.
Allow setting sigma parameter directly for metadynamics
https://github.com/Colvars/colvars/pull/325
Remove default values for lowerWall and upperWall legacy keywords
https://github.com/Colvars/colvars/pull/324
biasActualColvar option to bypass extended-Lagragian for a bias
https://github.com/Colvars/colvars/pull/321
Flexible restart-reading
https://github.com/Colvars/colvars/pull/320
2020-02-27 19:55:31 -05:00
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
693e34b587
Print parsed compiler flags, some cosmetic changes for added consistency
2019-10-17 22:53:13 -04:00
c578e4e7fc
Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS
2019-10-17 22:48:57 -04:00
b6af3c7ad0
Conventional make tweaks to handle Lepton C++11 requirement
2019-10-14 16:05:45 -04:00
e04a18fc4f
Upgrade Lepton library to version 2019-06-02
2019-10-14 16:05:45 -04:00
97501f0946
Fix typo
2019-08-05 14:59:40 -04:00
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
52e2db44a1
Update Colvars to version 2019-08-01
...
One new feature (geometric path variables) and bugfixes.
Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276
Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272
Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261
Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259
Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
2019-08-01 15:15:58 -04:00
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
3aacea671e
use argparse in colvars lib build
2019-01-14 12:52:21 -05:00
d603d084c4
Fix typo, whitespace cleanup
2018-12-03 18:12:10 -05:00
46c0be57de
Restore deleted deps file (if deletion is intentional, please delete again)
2018-12-03 18:08:27 -05:00
e5c555fa7d
consolidate shared code from various Install.py files into install_helpers.py
2018-12-03 17:50:20 -05:00
11de8dafe3
Update Colvars library to version 2018-11-16
...
Fixes several issues with running averages and time correlation function
computations. Details are in:
https://github.com/Colvars/colvars/issues/143
https://github.com/Colvars/colvars/issues/193
https://github.com/Colvars/colvars/pull/194
2018-11-16 09:57:07 -05:00
85a5cab663
Update Colvars library to version 2018-10-16
2018-11-02 17:45:20 -04:00
ff6507e7b7
convert colvars lib to use c++ style header files
2018-05-08 00:17:57 -04:00
1888b616c4
remove some extra semicolons
2018-05-07 18:04:25 -04:00
88dca11b3c
update colvars dependencies
2018-05-05 02:36:02 -04:00
