52e76502f4
formatting update, correct references
2024-01-20 10:53:04 -05:00
80861fe1ff
New syntax in doc files
2024-01-19 21:24:27 -07:00
fcc85fb223
Revert "revert more general doc changes. those are moved to a separate branch for further edits."
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This reverts commit fb9ae23516
2024-01-18 18:14:41 -05:00
54794a45de
Merge pull request #4030 from alphataubio/alphataubio-charmmfsw-kk
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Kokkos charmmfsw pair and dihedral styles
2024-01-18 18:10:12 -05:00
4b561d5f8e
fix typo
2024-01-18 17:06:58 -05:00
affb879037
Merge branch 'develop' into rheo
2024-01-18 14:52:15 -07:00
fb9ae23516
revert more general doc changes. those are moved to a separate branch for further edits.
2024-01-18 16:46:47 -05:00
01973ddf23
Merge branch 'develop' into alphataubio-charmmfsw-kk
2024-01-18 16:37:27 -05:00
af60285a3f
Merge pull request #4048 from akohlmey/lepton_updates
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Update LEPTON styles for more flexibility
2024-01-18 16:34:38 -05:00
8cf2705d68
Merge branch 'develop' into general-triclinic
2024-01-18 15:01:09 -05:00
fe1b568241
Merge pull request #4046 from akohlmey/molecule-dipole
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Add support for Dipoles section to molecule files
2024-01-18 14:57:01 -05:00
425421c1ca
fix typo, cut-n-paste error, and add clarification
2024-01-18 14:32:40 -05:00
73194764e9
add optional keywords "auto_offset" and "no_offset" to bond/angle style lepton
2024-01-18 11:05:52 -05:00
f78f596d9d
document using enumerator constants in Atom and AtomVec classes
2024-01-17 14:58:09 -05:00
b6d27dfb96
add versionadded tag
2024-01-16 13:06:00 -05:00
9312ce0beb
store and print title line of molecule
2024-01-16 12:20:02 -05:00
f6f7392595
make more user friendly
2024-01-16 12:04:13 -05:00
87297902a3
Add support for "Dipoles" section in molecule file
2024-01-16 12:04:00 -05:00
07876b5d1a
this limitation no longer applies
2024-01-14 07:53:33 -05:00
b6b2c029b6
improve description of testing
2024-01-14 07:33:31 -05:00
faef34a8d4
Merge branch 'develop' into rheo
2024-01-12 13:26:38 -07:00
df5461c27e
Merge pull request #4021 from jtclemm/BPM
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Bug fixes for BPM package
2024-01-12 15:24:24 -05:00
073a72d933
fixing merge conflicts
2024-01-12 11:12:02 -07:00
22c7f0f150
redid plots to not be misleading with y axis not at 0
2024-01-11 10:57:00 -05:00
ad7b5e38ab
Merge branch 'develop' into replicate_periodic_box
2024-01-10 20:01:42 -05:00
60f1233b07
Merge branch 'lammps:develop' into create_atoms-overlap_w_mol
2024-01-10 19:55:18 -05:00
63332eb1b2
Merge branch 'lammps:develop' into fix_reaxff/species-fixes
2024-01-10 19:52:55 -05:00
2643a94f79
minor math formatting changes after phone readability testing, and added note box to use tip3 with charmm
2024-01-06 19:49:43 -05:00
9a97906fe5
fixed Trailing whitespaces in rst
2024-01-06 17:29:37 -05:00
0d431f74d2
fixed latex missing $ error and added little bit of negative spaces
2024-01-06 17:22:28 -05:00
8f0c8592a9
updated charmm docs as requested by @akohlmey
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- gathered all tutorial like discussion, equations, and plot for old charmm and new charmmfsw into howto
- added equations and another plot for charmmfsw
- charmmgui 1HVN and 2CV5 examples
2024-01-06 09:01:22 -05:00
404b579396
integrate into manual and add cross-references for CHARMM styles
2024-01-05 18:17:36 -05:00
aa5a4f5f64
Merge branch 'alphataubio-charmmfsw-kk' of https://github.com/alphataubio/lammps-alphataubio into alphataubio-charmmfsw-kk
2024-01-05 17:25:00 -05:00
c7521c44ef
Revert "updated pair_charmm.rst"
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This reverts commit f113ec84be
2024-01-05 17:23:57 -05:00
ac2c852121
integration into documentation
2024-01-05 13:45:40 -05:00
f113ec84be
updated pair_charmm.rst
2024-01-05 11:17:26 -05:00
8090af5649
Merge branch 'develop' into issue3775_fft_kokkos
2024-01-04 21:11:54 -05:00
c6d1cbef5a
Merge branch 'develop' into general-triclinic
2024-01-04 21:10:50 -05:00
094128dd4d
Merge branch 'develop' into patch-8
2024-01-04 21:10:19 -05:00
0e2a065f6b
Merge pull request #4003 from stanmoore1/kk_half_thread
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Thread over neighbors in addition to atoms when using a half neighlist
2024-01-04 21:04:31 -05:00
fd846d539d
Merge branch 'develop' of github.com:lammps/lammps into issue3775_fft_kokkos
2024-01-03 17:57:41 -07:00
9546fd89e5
adjust heading levels
2023-12-23 12:16:53 -05:00
05bbb94345
add graph to show relation between branches and versions of LAMMPS
2023-12-23 12:06:38 -05:00
5d9f384338
recreate graphvis images with graphviz 8.1
2023-12-23 11:58:40 -05:00
b01065b398
use "neato" layout only for lammps-classes.dot to avoid issues with recent graphviz versions
2023-12-23 11:57:58 -05:00
bdb0fc6b7a
replace non-ASCII character
2023-12-23 11:35:39 -05:00
0515f07172
whitespace
2023-12-23 03:00:11 -05:00
0822a49cfc
Merge branch 'develop' into collected-small-fixes
2023-12-23 02:45:37 -05:00
35214120ad
Merge pull request #4025 from oywg11/ilp-tmd-update
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Add a new potential file for ilp/tmd
2023-12-22 21:06:27 -05:00
4ea40ed2fd
Merge branch 'ilp-tmd-update' of github.com:oywg11/lammps into collected-small-fixes
2023-12-22 14:45:43 -05:00
