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Merged
RKLindsey merged 189 commits into from
Aug 22, 2025
Merged

Update main from develop: Integrate Lindsey Lab contributions #83

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28c730f
Merge pull request #72 from rk-lindsey/main
rk-lindsey May 30, 2024
961b8a6
Updated module versions for intel and impi
S-A-Almohri Nov 7, 2024
a0b844f
HOTFIX: Fix typos in published_params.liqC.2+3b.cubic.txt
RKLindsey Nov 8, 2024
d522f9e
Add LAMMPS package user-misc to LAMMPS install.sh.
rk-lindsey Nov 16, 2024
3d509b8
Optimize efficiency of chimesFF.{h,cpp}
rk-lindsey Nov 16, 2024
5f38a91
Update ChIMES Carbon 2.0 parameter files:
rk-lindsey Nov 16, 2024
7604083
Merge pull request #31 from S-A-Almohri/main
rk-lindsey Nov 16, 2024
41b1a0f
Merge pull request #32 from LindseyLab-umich/RKLindsey-patch-1
rk-lindsey Nov 16, 2024
4978178
Merge pull request #33 from RKLindsey/develop
rk-lindsey Nov 16, 2024
a63bf28
Merge branch 'main' into develop
rk-lindsey Nov 16, 2024
9229653
Merge pull request #34 from LindseyLab-umich/develop
RKLindsey Nov 16, 2024
1c1de17
Adding integration for 3-Body tabulation for both serial and lammps v…
Nov 22, 2024
dffcd4f
Merge branch 'LindseyLab-umich:main' into tabulation_2b
BTSund Nov 22, 2024
7ede842
Fix bugs in chimesFF.cpp
BTSund Nov 22, 2024
df7092e
Fixed bug in chimesFF.cpp and chimesFF.h placement, along with updati…
Nov 24, 2024
b6af16a
Fixed a bug in the read_parameters function and improves integration …
Nov 24, 2024
af95d35
Merge pull request #35 from BTSund/main
rk-lindsey Nov 25, 2024
897a1a3
Made code more efficient, through streamlining logic and fixed length…
Nov 25, 2024
8729c9d
Updated to include recent efficiency changes
Dec 12, 2024
83b152b
Adding lammps Single point tests
Dec 17, 2024
15ceb84
Merge pull request #36 from BTSund/main
RKLindsey Dec 17, 2024
aed6fd3
Added test cases for Lammps single point calculations
Jan 14, 2025
6c4018f
fix cout bug in chimesff.cpp
Feb 2, 2025
0e92381
Added automatic cluster extraction
Mar 10, 2025
ab5d533
added print atom_id lines to pair_chimes
Mar 13, 2025
6c5d1c6
Corrected list printing
Mar 13, 2025
d586851
Added element tracking to chimesFF.cpp
Mar 13, 2025
a965d1c
added lmp tests
Mar 13, 2025
74cd73a
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Mar 13, 2025
ab2b128
Fixed cluster_combiner.cpp to read 4B
Mar 13, 2025
e31f5e2
added combine.sh and removed atom int print statemtnt
Mar 13, 2025
eb66902
Cleaned directory
Mar 13, 2025
0cb8cd7
Added preliminary calc_histograms.cpp
Mar 13, 2025
0656023
Changed cluster_read function to create adjacency matrices rather tha…
Mar 14, 2025
042d6ed
Added element types to adjacency matrix
Mar 14, 2025
d135440
added read params function and chimesff class
Mar 14, 2025
af4b8c0
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Mar 14, 2025
bfa94af
added chimesFF.h file
Mar 14, 2025
b720169
Added global variables to .cpp file
Mar 14, 2025
af9a292
Added reduced read_parameters function
Mar 14, 2025
ab3d451
Added full read params function
Mar 14, 2025
c8ba964
added necessary read_parameters functions
Mar 14, 2025
3fccc7b
Fixed global variable declaration from params file
Mar 14, 2025
cb5d8e9
Added printing function for global variables
Mar 14, 2025
1a29cdc
Added atom_typ_cnt to global variables
Mar 14, 2025
733d5d3
Added global params to chimesFF.h
Mar 19, 2025
609328f
Added distance transformation of edge lengths
Mar 19, 2025
1d1e5f3
Added broken (but done) code
Mar 19, 2025
edc95f9
Added working calc_histograms file
Mar 20, 2025
d2d3d88
Added swap_c2n.py
Mar 20, 2025
ff3ad87
updated calc_hist and added tests
Mar 20, 2025
6dd743e
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Mar 20, 2025
3aa3b12
Added parallel file analysis in histogram executable
Mar 20, 2025
8ecbada
Calculatates clusters for 3 and 4 bodies even when param file doesn't…
Mar 20, 2025
afa7437
Moved everything for FP to chimesff/src/FP
Mar 20, 2025
8eb69ed
Fixed naming convention in post_process.sh
Mar 21, 2025
92b87f0
Added get_hist.cmd for Ben
Mar 21, 2025
e26af73
Fixed small syntax errors, changed simulation to 500 frames
Mar 21, 2025
27db9a8
Fixed(?) 4b interactions with ghost calls
Mar 21, 2025
f0e64c0
Updated to latest stable LAMMPS
Yanjun-Lyu Apr 8, 2025
40b8a88
Update LAMMPS integration: Add tests, modify installation script, and…
Apr 22, 2025
844b523
Updated multi-element fingerprinting
Apr 29, 2025
c97277b
Added submit script
Apr 29, 2025
58a3b48
Fixed bug when calculating max dissimilarity
Apr 30, 2025
ff7abec
Merge pull request #37 from laubachb/main
RKLindsey May 2, 2025
4a8733a
Fixed overloading of functions
May 7, 2025
92640c2
add CG ChIMES lammps run examples
melodyyzh May 13, 2025
759d812
Merge pull request #42 from melodyyzh/CG_ChIMES_lmp
RKLindsey May 13, 2025
479d462
Made pair_chimes.cpp faster, added lammps test cases for POC
May 15, 2025
6644867
Fixed overloading variables and removed save_files
May 15, 2025
5f2ae1d
Fixed HN3 case
May 16, 2025
c394acd
Added parameter file to TiO2
May 16, 2025
7b4d1cf
Updated files
May 20, 2025
5a460d4
Print penalty values however they are user-specified or default
May 20, 2025
43713a1
Updated fingerprinting, removed ghost implementation
May 21, 2025
5e27249
Added test sets for fingerprinting
May 21, 2025
f2c640e
Fixed histogram exe
May 22, 2025
82e0510
Fixed 4B in chimesFF.cpp
May 22, 2025
ab1aef8
Remove the redundant chimesFF.{cpp, h} files outside src folder
May 29, 2025
0c06ba8
Added a Langeving lammps test with load balancing
May 29, 2025
a1362f0
Added lammps example including explicit D2 dispersion
May 29, 2025
fee1f51
Added files for lammps test
Awwal41 May 29, 2025
e674492
Merge pull request #80 from rk-lindsey/main
rk-lindsey May 30, 2025
9f3f0fe
Removed lmp_test folder, lammps tests located in /etc/lmp/tests/
Jun 3, 2025
9b9b736
Reverted serial_chimes_interface.cpp cluster graph modifications sinc…
Jun 3, 2025
e1a5343
Added test sets for fingerprinting
Jun 4, 2025
3fe090c
Added CO.2.5gcc_6500K.scramble test case
Jun 4, 2025
ba9a90c
Allowed installation on UT-TACC host type
Jun 5, 2025
1e7c85b
Updated install script to work with Stampede3. Tested on scramble dat…
Jun 6, 2025
3088b40
Removed extra LAMMPS fingerprint tests
Jun 11, 2025
a2b2ab5
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Jun 11, 2025
48eae8d
Merge pull request #50 from LindseyLab-umich/main
RKLindsey Jun 13, 2025
9539756
Merge pull request #45 from BTSund/add_lmp_tests
RKLindsey Jun 13, 2025
35130b1
Merge pull request #46 from Awwal41/main
RKLindsey Jun 13, 2025
7345e84
Merge pull request #44 from S-A-Almohri/add_lmp_tests
RKLindsey Jun 13, 2025
2367ca7
Merge pull request #40 from LindseyLab-umich/add_lmp_tests
RKLindsey Jun 19, 2025
47f5c52
Update ev_tally_mb function for correct per atom/global virial stress…
Jul 1, 2025
06e6ccf
Fixed file copy and paste mistakes
Jul 1, 2025
0da6ab4
Add example files for running MD in LAMMPS with ChIMES small carbon m…
Jul 1, 2025
791dbed
Update pair.cpp
Yanjun-Lyu Jul 1, 2025
20420e7
Update pair.cpp
Yanjun-Lyu Jul 1, 2025
3041e27
Merge pull request #54 from Yanjun-Lyu/ev_tally_mb_update
RKLindsey Jul 1, 2025
09923e5
Merge pull request #55 from Yanjun-Lyu/add_example_carbon_files
RKLindsey Jul 1, 2025
250205d
Updated single point files for lammps tests
Jul 7, 2025
de224bd
File organiziation
Jul 7, 2025
3a1906a
Added LAMMPs test suite. 5/6 tests fail - requires further debugging.…
Jul 22, 2025
d97cf42
adds tabulation as an optional flag
Jul 23, 2025
febd1a6
removed the mistaken chimesFF.* files in chimesff
Jul 23, 2025
bcb301e
keeping install.sh formatting
Jul 23, 2025
689f787
Updated LAMMPs input files to properly account for conversions. Remov…
Jul 23, 2025
c1dfdbf
Added CO.9GPa case study
Jul 23, 2025
3ccd3fc
Added test_suite.log for LAMMPs tests
Jul 23, 2025
4e838dc
Improved clarity in install.sh script and added tabulation documentation
Jul 23, 2025
09c8c1d
Fixed documentation wording
Jul 23, 2025
e191453
Updated documentation to include fingerprinting
Jul 23, 2025
3bc4d3c
Update utils.rst
RKLindsey Jul 24, 2025
f909013
Added link to ChIMES Fingerprint publication to docs.
Jul 24, 2025
a71eeb1
Update published_params.liqC.2+3b.cubic.txt.liqC.2.5gcc_6000K.OUTCAR_…
laubachb Jul 24, 2025
31529e7
Updated fingerprint flag to be in any position of the install (not ju…
Jul 24, 2025
54a7300
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Jul 24, 2025
45dbb5d
Updated install script to compile histogram exe when FINGERPRINT flag…
Jul 24, 2025
0789cee
Update install.sh
RKLindsey Jul 24, 2025
af3618d
Pointed expected_output/ and force_fields/ to serial_interface locati…
Jul 24, 2025
ddf6778
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork …
Jul 24, 2025
1a77ff4
Updated fingerprint test to have expected output
Jul 24, 2025
bc82905
Updated example submit job script
Jul 24, 2025
d9dfe8f
Merge pull request #49 from BTSund/FP_Calc
RKLindsey Jul 24, 2025
0479928
Combines Fingerprint code and tabulated code
Jul 28, 2025
9a40bce
modifies run_test.sh and test_list.dat
Jul 28, 2025
79cc9cc
modifies run_test.sh and test_list.dat
Jul 28, 2025
da38141
Updates documentatation to include fingerprinting and tabulation
Jul 28, 2025
c2bfdc3
Merge branch 'develop' into tabulation_2b
BTSund Jul 29, 2025
0ad6897
Hotfix: Allow for hybrid overlay pair styles
RKLindsey Jul 29, 2025
9c474bf
Hotfix: Typo
RKLindsey Jul 29, 2025
f6b825d
Merge pull request #43 from BTSund/tabulation_2b
RKLindsey Jul 29, 2025
261fb11
Merge branch 'develop' into develop
RKLindsey Jul 29, 2025
3fc7240
Merge pull request #39 from Yanjun-Lyu/develop: Update LAMMPS version…
RKLindsey Jul 29, 2025
7ccace6
Fixing double declaration bug
Jul 31, 2025
9b65ba0
Fixed bug in install script not allowing for FP or tabulation install…
Jul 31, 2025
b3e908b
Fixes serial interface not working due to left over tabulation logic
Aug 1, 2025
31c559f
Merge pull request #59 from BTSund/develop
RKLindsey Aug 1, 2025
b44d086
Replaces fix_modify with econserve
Aug 1, 2025
f5669b1
removed fix_modify lines
Aug 1, 2025
cf561ec
Merge pull request #60 from BTSund/develop
RKLindsey Aug 1, 2025
b01596e
Updated the index, quicl start, citing, contribution and legal portio…
S-A-Almohri Aug 4, 2025
ed70f71
fixed documentation on serial interface
melodyyzh Aug 4, 2025
c0ef563
undo mentioning the expert mode
melodyyzh Aug 4, 2025
4d92358
Updated documentation for tabulation and chimesff.cpp notation
Aug 4, 2025
ceb35a7
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
f59c790
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
b3b73a9
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
b56c837
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
78a355b
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
33b90df
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
f002102
Update getting_started.rst
PoornimaMMPC Aug 4, 2025
235e332
Update pair_chimes.cpp to better deal with element type unmatch betwe…
Aug 5, 2025
e22d08b
Update getting_started.rst
PoornimaMMPC Aug 5, 2025
20434c4
Merge pull request #1 from PoornimaMMPC/PoornimaMMPC-develop-1
PoornimaMMPC Aug 5, 2025
2dd0bbc
Updated py, C, and Fortran api documentation
Aug 6, 2025
f4a9d8f
Updated ChIMES Fingerprint documentation. Included example image, inc…
Aug 6, 2025
44d85a7
Updated documentation for Fingerprints
Aug 6, 2025
e0bdd09
Update etc.rst
PoornimaMMPC Aug 6, 2025
0c161d6
Update getting_started.rst
PoornimaMMPC Aug 7, 2025
72f56d5
edited the rst file based on Dr. Lindsey's comments
melodyyzh Aug 7, 2025
3c87655
Fix I/O: Several instances in MPI code where printing needed to be co…
RKLindsey Aug 7, 2025
83ad0c9
Update/organize test suite and examples
RKLindsey Aug 7, 2025
7201ed9
Update documentation for ChIMES in LAMMPS
RKLindsey Aug 7, 2025
e846c58
Update etc.rst
Yanjun-Lyu Aug 7, 2025
7bb91e2
Merge pull request #66 from PoornimaMMPC/develop
RKLindsey Aug 7, 2025
9740409
Merge pull request #62 from melodyyzh/dev
RKLindsey Aug 7, 2025
fc13ea3
Merge pull request #65 from Yanjun-Lyu/develop
RKLindsey Aug 7, 2025
aa5b86c
Update quick_start.rst
S-A-Almohri Aug 7, 2025
4b469b8
Merge branch 'develop' into develop
RKLindsey Aug 8, 2025
354264b
Merge pull request #67 from laubachb/develop
RKLindsey Aug 8, 2025
a851c4d
Removed all references to quadtypes or 4-body interactions and exppla…
Aug 8, 2025
6bca7d8
Merge pull request #70 from prat2001/develop
RKLindsey Aug 11, 2025
67eae55
Merge branch 'develop' into develop
RKLindsey Aug 11, 2025
73e3994
Merge pull request #68 from RKLindsey/develop
RKLindsey Aug 11, 2025
991c006
Updated contributing.rst to include LAMMPS instructions
S-A-Almohri Aug 11, 2025
ffd1e64
Added a missed 's' in contributing.rst
S-A-Almohri Aug 11, 2025
424a8a7
Merge pull request #61 from S-A-Almohri/develop
RKLindsey Aug 11, 2025
9432202
Updated tabulation documentation with a speed comparison
Aug 13, 2025
91da3d7
Merge branch 'develop' into develop
BTSund Aug 13, 2025
ade00a6
Update utils.rst to include atom count for tabulated speed test.
BTSund Aug 13, 2025
15233ee
Merge pull request #64 from BTSund/develop
RKLindsey Aug 13, 2025
3e14a3c
Update expected output for serial interface; files not updated in pre…
RKLindsey Aug 13, 2025
a1b212b
Merge pull request #72 from RKLindsey/develop
RKLindsey Aug 13, 2025
cde992b
Merge pull request #81 from LindseyLab-umich/develop
rk-lindsey Aug 22, 2025
9b03577
Update run_job.sh
rk-lindsey Aug 22, 2025
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etc/lmp/tests/*/correct_output/*
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