87a9695c64
Merge remote-tracking branch 'github/develop' into collected-small-changes
2023-03-01 20:37:50 -05:00
c2fe2b4360
Merge pull request #3661 from bathmatt/hippy-fixes
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Hippy fixes
2023-03-01 20:36:37 -05:00
d44ba14030
Merge pull request #3657 from akohlmey/custom-wall-fixes
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Add fix wall/table and fix wall/lepton for customizable wall fixes
2023-03-01 20:16:56 -05:00
bc4da2afef
roll back change causing unittest failures
2023-02-28 19:26:18 -05:00
103e63eca5
more careful checks and print error messages to global root.
2023-02-28 18:58:57 -05:00
2507e414d9
fix broken link
2023-02-28 18:11:05 -05:00
a98c497dbb
redesign the Howto pages on water models and add inputs and molecule files
2023-02-28 18:10:45 -05:00
202a22ea68
Merge branch 'develop' into collected-small-changes
2023-02-28 11:27:26 -05:00
02190b82c2
link pair style hybrid/scaled to fix adapt and fix alchemy
2023-02-28 11:22:28 -05:00
a6eac92cd5
update list of pair styles that support fix adapt
2023-02-28 11:20:33 -05:00
a67d82c183
Merge pull request #3662 from akohlmey/fix-alchemy
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New fix command for alchemical transformations using multiple partitions
2023-02-27 21:07:21 -05:00
81a2d47c16
print warning about not checking lambda variable
2023-02-27 16:50:17 -05:00
446913f2f3
make ramp more flexible by defining lambda through a variable
2023-02-27 16:01:17 -05:00
83f936f31b
Update fix_alchemy.rst
2023-02-27 11:00:11 -07:00
095f1d328e
make non-polymorph functions and all data members protected.
2023-02-27 12:12:39 -05:00
8368b78f23
document the change in mass handling
2023-02-26 13:52:31 -05:00
0b5acdca51
convert hard error about invalid atom masses from EAM potentials to warning
2023-02-26 13:47:11 -05:00
2bd6cde4e8
add reference output
2023-02-26 00:19:39 -05:00
76c879c388
make sure that output variables are initialized
2023-02-26 00:16:03 -05:00
3e2b5dd9d3
small cleanup
2023-02-25 23:47:46 -05:00
666be5c3d9
add log files for example run
2023-02-25 23:47:34 -05:00
c9b22ba04f
mention pair style hybrid/scaled as alternative
2023-02-25 17:17:41 -05:00
bb17541c30
add simple example for transforming a pure metal into an alloy
2023-02-25 16:01:26 -05:00
2bad63c68e
add documentation
2023-02-25 14:09:14 -05:00
828b70fbfa
silence warning
2023-02-25 13:58:58 -05:00
60129958c8
refactor how properties computed by the fix are accessed
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lambda is no an (intensive) scalar property
and the vector property only has the potential energies.
pressure is accessed via compute pressure/alchemy.
2023-02-25 12:47:49 -05:00
d691d1db78
synchronize box dimensions at the beginning and when needed
2023-02-25 12:42:10 -05:00
81b0bb47be
allow dynamic groups with fix oneway
2023-02-25 12:03:05 -05:00
c288a20077
add progress information to screen or universe logfile
2023-02-25 11:14:56 -05:00
7242186045
add compute pressure/alchemy so it can be used with fix npt
2023-02-25 10:43:49 -05:00
fdf5148238
don't store topology information with ghost atoms. they will be ignored.
2023-02-24 22:55:23 -05:00
6d12f7925b
first working implementation of fix alchemy. still w/o support for pressure and variable cell.
2023-02-24 19:02:11 -05:00
7a4b23938e
update example so we can use the simpler communication pattern
2023-02-24 19:00:12 -05:00
ed822f8002
WIP
2023-02-24 15:41:04 -05:00
c5f29dee39
Merge pull request #3658 from akohlmey/collected-small-changes
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Collected small changes and bug fixes
2023-02-23 23:10:52 -05:00
6b9911dd74
update unit test for correct fix wall/morse
2023-02-23 15:28:21 -05:00
d3ac4a728d
fix bug in fix wall/morse that was computing the force incorrectly
2023-02-23 15:22:38 -05:00
6ae177f37e
rename fix pimd to fix pimd/nvt (with backward compatibility)
2023-02-23 12:26:42 -05:00
cad3c5ba95
Fixed code to run with hippynn
2023-02-23 15:53:43 +01:00
fc0efd43fc
added kokkos functinos to the list of functions registered for ML-IAP
2023-02-23 15:53:43 +01:00
e422ae9477
improve error messages and make them consistent across variants
2023-02-23 09:40:51 -05:00
2e5bc2f6b7
add test example for validating custom potentials
2023-02-23 01:09:44 -05:00
34430c1047
add unit tests for fix wall/lepton and fix wall/table
2023-02-23 00:57:41 -05:00
b314f73ef4
update .gitignore and fix typo in doc makefile
2023-02-23 00:40:07 -05:00
ec87c71064
add documentation for fix wall/lepton, fix wall/table and WallTabulate()
2023-02-23 00:35:25 -05:00
0dcb591ee8
add support to create tables for fix wall/table
2023-02-22 23:31:04 -05:00
a3ff40ccf0
fixes to avoid uninitialized or out-of-bounds memory accesses
2023-02-22 23:29:46 -05:00
b12facbd54
add fix wall/table
2023-02-22 19:06:07 -05:00
36ec4a098b
add fix wall/lepton
2023-02-22 19:06:07 -05:00
f4d8b2a57a
remove unused namespace import
2023-02-22 19:06:07 -05:00
