3b38145d91
Update compute_stress_mop.cpp
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Fixing sign issues because I was considering the theta angle to be formed by vectors x[atom2] - x[atom1] & x[atom3] - x[atom2] instead of x[atom1] - x[atom2] & x[atom3] - x[atom2] as done in lammps
2023-05-29 16:34:44 +03:00
86743bc0a6
Update compute_stress_mop.cpp
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The angle was computed using the dot product of the vectors x[atom2] - x[atom1] and x[atom3] - x[atom2]. This is not consistent with the lammps convention where the angle is computed using the dot product between x[atom1]-x[atom2] and x[atom3]-x[atom2].
2023-05-29 10:59:18 +03:00
b28ee36f00
update documentation for compute stress/mop
2023-05-27 14:50:31 +03:00
458cce7699
Updating unit test for mop to reflect the contribution from bonds
2023-05-27 14:33:46 +03:00
f26f397e08
avoid crashing when there are no bonds or no angles
2023-05-25 14:47:20 +03:00
8e6615918b
avoid crashing when no bonds or no angles exist
2023-05-25 14:39:03 +03:00
9ee40cceef
fixing indexing issue and more sign problems for angle contributions
2023-05-24 17:01:13 +03:00
c7c8b065a2
fixing bug with sign issue for bond contribution in compute_stress_mop.cpp
2023-05-24 16:49:35 +03:00
25bff3e4ed
fixing bug with sign for angle contribution in compute_stress_mop.cpp
2023-05-24 16:24:33 +03:00
df708a67a5
Code for angle contribution to stress/mop
2023-05-24 11:55:08 +03:00
0692ed3bd7
@evoyiatzis Include method for angle contribution & variables to compute_stress_mop.h
2023-05-24 11:47:15 +03:00
1d7a6f813b
Update compute_stress_mop.cpp
2023-05-20 15:14:47 +03:00
90427c8750
Update compute_stress_mop.cpp
2023-05-20 15:12:42 +03:00
5da65bbd0a
Code for bond contribution to stress/mop
2023-05-20 13:06:19 +03:00
36eb11f499
Include method for bond contribution & variables to compute_stress_mop.h
2023-05-20 12:59:34 +03:00
ed03d04a70
Merge pull request #3779 from lammps/fix-ttm-mod-arrays
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Reorder fix ttm/mod 3d arrays to be consistent with fix ttm and fix ttm/grid
2023-05-18 18:33:25 -04:00
c73b7483b2
swtich loop order back to be consistent with rest of file
2023-05-18 11:47:20 -06:00
af71279df1
Merge branch 'fix-ttm-mod-arrays' of github.com:lammps/lammps into fix-ttm-mod-arrays
2023-05-18 11:44:31 -06:00
50858205f6
refresh log files for fix ttm/mod example
2023-05-18 11:43:54 -06:00
6585151ce1
reorder loops to compute properties vector
2023-05-17 22:04:32 -04:00
d206f583c4
whitespace
2023-05-17 21:57:14 -04:00
f1aca8b71a
formatting tweaks
2023-05-17 16:39:14 -06:00
10880332ed
Merge pull request #3783 from Colvars/colvars-update
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Update Colvars library to version 2023-05-01
2023-05-17 18:26:41 -04:00
5be9eda905
Merge pull request #3780 from srtee/patch-3
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Bugfix fix_efield.cpp for atom-style energy
2023-05-17 16:33:37 -04:00
377c652a83
Update Colvars library to version 2023-05-01
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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
88d9d39bab
Merge branch 'fix-ttm-mod-arrays' of github.com:lammps/lammps into fix-ttm-mod-arrays
2023-05-17 08:17:11 -06:00
d98b1e9f04
fix left/right indices
2023-05-17 08:15:42 -06:00
166301180b
Merge pull request #3769 from stanmoore1/kk_optimize
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Kokkos package optimizations
2023-05-17 07:13:04 -04:00
e044ccbbb3
Bugfix fix_efield.cpp for atom-style energy
2023-05-17 16:41:21 +10:00
4f57026dc0
whitespace
2023-05-16 21:15:01 -04:00
2e58a9ecf8
whitespace
2023-05-16 21:13:48 -04:00
05b8082e3c
code cleanup
2023-05-16 17:03:34 -06:00
0d31ab9c88
one more change
2023-05-16 16:51:00 -06:00
2b9c65855a
swap 3d array indices in fix ttm/mod
2023-05-16 16:38:12 -06:00
858fd4cc2c
Small optimization
2023-05-16 15:23:31 -06:00
b1ee177c0a
Must use local variable for lambda capture
2023-05-16 12:43:19 -06:00
b9256fa492
Reduce memory allocations
2023-05-16 11:09:37 -06:00
a84470383b
Merge pull request #3777 from ilia-nikiforov-umn/kim_adapt
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Add "scale" attribute to pair_kim to be used with fix adapt
2023-05-16 07:08:40 -04:00
2328cae55f
Merge branch 'develop' of https://github.com/lammps/lammps into kk_optimize
2023-05-15 10:48:51 -06:00
91e0d0411b
one more programming style tweak
2023-05-15 02:04:17 -04:00
cf51c94be0
update unit test for presence of Pair::extract() function in pair style kim
2023-05-15 02:02:36 -04:00
ed958d8aed
Merge branch 'develop' into kim_adapt
2023-05-15 02:01:01 -04:00
d584f2fe50
follow LAMMMPS' programming style more closely
2023-05-15 01:58:45 -04:00
17747a3c58
moved scaling to immediately after compute and removed virial scaling
2023-05-14 15:07:31 -05:00
2d18883e8b
Merge pull request #3755 from jtclemm/doc-edits
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Reorganization of the programming guide
2023-05-13 17:22:41 -04:00
c76e85c445
Merge pull request #3770 from akohlmey/collected-small-fixes
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Collected small fixes and updates
2023-05-13 15:19:13 -04:00
d6d825258e
Merge pull request #3771 from lammps/variable-current
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Change how variables check if computes are current
2023-05-12 19:26:36 -04:00
8414d23c2b
use symbolic constants
2023-05-12 18:04:37 -04:00
ac4cf2dc99
Merge pull request #3776 from inflowencer/develop
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Fixed read-in of initial electron temperature file
2023-05-12 18:03:50 -04:00
96af466f4a
as a few details to the discussion of programming languages and their standards
2023-05-12 15:45:55 -04:00
