0069c4b562
update docs for automatic jpeg/png/zlib library download and build with CMake
2022-05-22 18:10:26 -04:00
7eb926c853
clarify the description of pair style none
...
explain that pair style none is effectively deleting any existing
pair style and that communication and neighbor list cutoff are affected.
update those explanations for changes to LAMMPS that allow adjusting
those not just with the neighbor list skin.
Also add that pair_coeff must not be used.
2022-05-20 07:14:05 -04:00
21c2f8a74b
fix miscalculated example
2022-05-20 01:06:21 -04:00
36d091baeb
fix underline
2022-05-19 23:06:54 -04:00
7b0c7c04ed
address sphinx issues and make command list consistently list all min styles
2022-05-19 12:21:06 -04:00
2138aea01f
Merge branch 'two-command-tables' into collected-small-changes
2022-05-19 12:16:37 -04:00
5990241fbe
refactor min_style spin doc page
2022-05-19 09:13:47 -06:00
898eda794c
minor updates
2022-05-19 00:06:11 -04:00
5ac8e5639a
more information about compiling LAMMPS on windows
2022-05-19 00:06:00 -04:00
fa6c81849b
split Command table into two tables
2022-05-18 16:26:58 -06:00
e94275391c
Merge branch 'develop' into collected-small-changes
2022-05-17 22:10:15 -04:00
72209b0617
Merge pull request #3258 from akohlmey/create-atoms-mesh
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Create atoms from STL mesh
2022-05-17 18:11:41 -04:00
f9efa426a7
Merge pull request #3256 from lammps/delete-atoms-exact
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Delete atoms exactly by fraction or count
2022-05-17 16:25:21 -04:00
ae979aca4e
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
38d7fcee92
correct and update create_atoms mesh documentation
2022-05-17 16:16:32 -04:00
d487ab10e2
doc page and unittest tweaks
2022-05-17 12:00:40 -06:00
dbb3e75f24
change partial to random
2022-05-17 11:02:42 -06:00
f62363516c
streamline the refactored interface for delete_atoms partial some more
2022-05-15 01:56:45 -04:00
55fef9a482
Fixing typos and cleaning up quasirandom comments
2022-05-14 11:39:20 -06:00
9a9bb749fa
Merge remote-tracking branch 'github/develop' into collected-small-changes
2022-05-14 10:39:18 -04:00
9661711a1e
avoid out-of-bounds access in dump style cfg, update docs with simpler semantic
2022-05-14 09:39:50 -04:00
b8a4ddc42a
Merge pull request #3264 from stanmoore1/kk_pace_release
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Add Kokkos version of ML-PACE
2022-05-13 23:36:05 -04:00
c41ad91a9d
add support for reading binary STL files
2022-05-13 12:18:22 -04:00
545cec1785
Fix copy/paste issue
2022-05-13 10:15:25 -06:00
658a89e401
document .lammpsbin suffix for trajectory files
2022-05-13 11:15:06 -04:00
d7bad09d35
Add Kokkos version of ML-PACE
2022-05-12 15:25:07 -06:00
3ea249a576
fix minor documentation issues
2022-05-11 13:23:59 -04:00
4cc3bdd35f
adjust keyword/function names and command line to be simpler to use
2022-05-11 09:25:27 -04:00
442116b305
update
2022-05-11 08:12:59 -04:00
c9d350edc2
Adding quasirandom mesh option
2022-05-10 18:35:36 -06:00
bdbab77286
add note about re-generating optimized meshes for STL files
2022-05-10 15:23:54 -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
b6ee64dc12
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-09 21:58:48 -04:00
eb44cbf848
small updates
2022-05-09 15:22:48 -04:00
23e17363f9
Merge remote-tracking branch 'github/doc-variable-extract-settings' into collected-small-changes
2022-05-09 15:03:13 -04:00
6344c667a0
more doc info for variable extrat_setting() func
2022-05-09 09:33:59 -06:00
24ef021fe0
fix typo
2022-05-09 10:05:12 -04:00
1660bae22a
add examples import one image to manual
2022-05-08 21:15:32 -04:00
9ec35f0235
update docs to match the latest code
2022-05-08 19:14:06 -04:00
e0bb27dbb2
make radscale and radthresh class members
2022-05-07 23:04:34 -04:00
60b9fd2db8
minor tweaks simplify algorithm
2022-05-07 17:08:22 -04:00
6722d3fb00
add simple STL binary to ASCII converter (based on Wikipedia specs)
2022-05-07 16:26:25 -04:00
102b61ae1b
Merge branch 'develop' into create-atoms-mesh
2022-05-07 09:33:40 -04:00
4737b9efb7
Merge pull request #3250 from akohlmey/collected-small-changes
...
Collected small changes and bugfixes
2022-05-07 00:14:32 -04:00
907bc7eaa5
switch to using wall time
2022-05-06 16:58:28 -04:00
905034893c
finished testing of new delete_atoms options
2022-05-06 14:15:41 -06:00
613ef04357
Merge branch 'develop' into timer-variable
2022-05-06 14:27:52 -04:00
78f2907cbb
implement a "make no-installed" command
2022-05-06 13:35:21 -04:00
f3fcd16628
adding of timer-style variables and associated doc pages
2022-05-06 11:21:36 -06:00
2549b86d76
update/correct docs for support of compiling LAMMPS with visual studio on windows
2022-05-06 12:37:28 -04:00
