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
6c375ffade
Update PDF Colvars manual
2022-06-02 11:48:19 -04:00
3a1423dc48
Update Colvars to 2022-05-24 and copy of Lepton library
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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
1220bea011
Update Colvars to version 2022-05-09
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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
19e6a9e0d8
Merge pull request #2924 from ohenrich/cg-dna
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CG-DNA: Documentation Update
2021-09-07 14:12:07 -04:00
b132a7eb3a
Updated docu to new oxdna atom_style
2021-09-06 09:47:46 +01:00
eb52f7c290
Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
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Also include PDF copy of the manual forgotten in previous PR.
2021-08-06 10:32:37 -04:00
4b81802ae8
Created new feature branch for PR as per request
2021-07-05 16:07:40 +01:00
c085e55695
rename USER-SMD package to MACHDYN
2021-06-29 17:19:39 -04:00
efaec31a84
rename USER-CGDNA and USER-CGSDK to CG-DNA and CG-SDK
2021-06-29 15:28:27 -04:00
07c9298558
Fix some broken internal hyperlinks in Colvars PDF
2020-09-18 17:24:12 -04:00
7deb773440
Update Colvars to version 2020-09-17
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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
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
a0d74ca2ae
Bug fix for gay-berne potential when mu != 1.0.
2019-10-27 22:31:00 -07:00
30cff3faf3
Fixing Gay-Berne "extra" documentation to define epsilon parameters consistent with LAMMPS input.
2019-10-18 03:10:31 -07:00
11198e9d29
Merge pull request #1607 from giacomofiorin/colvars-update
...
Update Colvars to version 2019-08-01
2019-08-02 10:43:13 -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
e2a7cdc4f7
Updated extended documentation
2019-07-19 12:20:56 +01:00
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
ef5c327f74
Merge branch 'master' into collected-small-changes
2019-01-31 11:45:15 +01:00
48542f1832
permission update for some bundled PDF files
2019-01-24 04:51:55 -05:00
7ec6e4b262
Merge branch 'master' into user-cgdna
2019-01-22 13:06:42 +00:00
874e4fdafc
Corrected required input angular velocity -> momentum
2019-01-22 13:05:15 +00:00
11de8dafe3
Update Colvars library to version 2018-11-16
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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
5076b6d161
Removed old documentation
2018-05-07 18:25:55 +01:00
722549965e
Added reference to implementation paper
2018-05-07 18:13:18 +01:00
0c005f5cb0
Small fixes to Colvars library
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Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.
6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
2018-05-02 15:03:56 -04:00
f3cf407a21
Collected fixes and updates to Colvars library
...
This commit includes several fixes to moving restraints; also added is support
for runtime integration of 2D and 3D PMFs from ABF.
Mostly changes to existing member functions, with few additions in classes not
directly accessible by LAMMPS. Also removed are calls to std::pow(), replaced
by a copy of MathSpecial::powint().
Relevant commits in Colvars repository:
7307b5c 2017-12-14 Doc improvements [Giacomo Fiorin]
7f86f37 2017-12-14 Allow K-changing restraints computing accumulated work; fix staged-k TI estimator [Giacomo Fiorin]
7c1c175 2017-12-14 Fix 1D ABF trying to do pABF [Jérôme Hénin]
b94aa7e 2017-11-16 Unify PMF output for 1D, 2D and 3D in ABF [Jérôme Hénin]
771a88f 2017-11-15 Poisson integration for all BC in 2d and 3d [Jérôme Hénin]
6af4d60 2017-12-01 Print message when issuing cv delete in VMD [Giacomo Fiorin]
4413972 2017-11-30 Check for homogeneous colvar to set it periodic [Jérôme Hénin]
95fe4b2 2017-11-06 Allow abf_integrate to start in bin with 1 sample [Jérôme Hénin]
06eea27 2017-10-23 Shorten a few constructs by using the power function [Giacomo Fiorin]
3165dfb 2017-10-20 Move includes of colvarproxy.h from headers to files [Giacomo Fiorin]
32a867b 2017-10-20 Add optimized powint function from LAMMPS headers [Giacomo Fiorin]
3ad070a 2017-10-20 Remove some unused includes, isolate calls to std::pow() [Giacomo Fiorin]
0aaf540 2017-10-20 Replace all calls to std::pow() where the exponent is not an integer [Giacomo Fiorin]
2018-02-23 08:34:53 -05:00
f479f02589
Fix a Colvars error that was hidden by the previous segfault
2017-10-20 13:41:31 -04:00
6e7504f153
Import segfault fix in Colvars module
2017-10-19 08:09:44 -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
12fe614ddf
Added sequence-dependent stacking and base-pairing strength
2017-09-05 10:48:38 +01:00
da01be7c18
More robust change from initial to target restraint centers in Colvars
2017-08-10 09:22:53 -04:00
ee6cac826e
Update Colvars to version 2017-07-15 and support automated builds for it
2017-07-19 14:24:07 -04:00
8afed61db1
Upgrade to oxDNA2
2017-03-28 18:16:36 +01:00
7435084375
Verified oxDNA with modified nucleotide layout
2017-03-22 15:59:10 +00:00
7a75cd111c
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
2017-03-14 11:39:09 +00:00
23b8287933
Updated documentation and simple setup tool
2017-03-14 11:36:44 +00:00
f70752c18f
Include PDF of Colvars doc missing in previous commit
2017-03-10 15:58:35 -05:00
5fe6206638
Update Colvars module to version 2017-03-10
2017-03-10 09:16:58 -05:00
149f37e764
Corrected reference to Fig.1
2017-01-26 19:08:59 +00:00
96259ea2d2
Added source code and documentation for USER-CGDNA
2017-01-13 13:36:54 +00:00
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
f8367e3d0f
update documentation pdf for updated colvars lib
2016-10-24 17:49:53 -04:00
6d200061ca
update colvars library to version 2016-09-30
2016-09-30 08:15:44 -04:00
b190abea39
sync with GH
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-08 20:20:32 +00:00
