Update main from develop: Integrate Lindsey Lab contributions#83

Merged

RKLindsey merged 189 commits intomainfrom

Aug 22, 2025

Commits on May 30, 2024

Merge pull request #72 from rk-lindsey/main
rk-lindsey
authored

Commits on Nov 7, 2024

Updated module versions for intel and impi
S-A-Almohri
committed

Commits on Nov 8, 2024

HOTFIX: Fix typos in published_params.liqC.2+3b.cubic.txt
RKLindsey
authored

Commits on Nov 16, 2024

Commits on Nov 22, 2024

Commits on Nov 24, 2024

Fixed bug in chimesFF.cpp and chimesFF.h placement, along with updating expected output
btsund
committed
Fixed a bug in the read_parameters function and improves integration with recent updates
btsund
committed

Commits on Nov 25, 2024

Commits on Dec 12, 2024

Updated to include recent efficiency changes
btsund
committed

Commits on Dec 17, 2024

Commits on Jan 14, 2025

Added test cases for Lammps single point calculations
blaubach
committed

Commits on Feb 2, 2025

fix cout bug in chimesff.cpp
Brayden Todd Sundberg
committed

Commits on Mar 10, 2025

Added automatic cluster extraction
Brayden Todd Sundberg
committed

Commits on Mar 13, 2025

added print atom_id lines to pair_chimes
Brayden Todd Sundberg
committed
Corrected list printing
Brayden Todd Sundberg
committed
Added element tracking to chimesFF.cpp
Benjamin Robert Laubach
committed
added lmp tests
Brayden Todd Sundberg
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Brayden Todd Sundberg
committed
Fixed cluster_combiner.cpp to read 4B
Benjamin Robert Laubach
committed
added combine.sh and removed atom int print statemtnt
Brayden Todd Sundberg
committed
Cleaned directory
Benjamin Robert Laubach
committed
Added preliminary calc_histograms.cpp
Benjamin Robert Laubach
committed

Commits on Mar 14, 2025

Changed cluster_read function to create adjacency matrices rather than vectors
Benjamin Robert Laubach
committed
Added element types to adjacency matrix
Benjamin Robert Laubach
committed
added read params function and chimesff class
Brayden Todd Sundberg
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Brayden Todd Sundberg
committed
added chimesFF.h file
Brayden Todd Sundberg
committed
Added global variables to .cpp file
Benjamin Robert Laubach
committed
Added reduced read_parameters function
Brayden Todd Sundberg
committed
Added full read params function
Brayden Todd Sundberg
committed
added necessary read_parameters functions
Brayden Todd Sundberg
committed
Fixed global variable declaration from params file
Benjamin Robert Laubach
committed
Added printing function for global variables
Benjamin Robert Laubach
committed
Added atom_typ_cnt to global variables
Benjamin Robert Laubach
committed

Commits on Mar 19, 2025

Added global params to chimesFF.h
Benjamin Robert Laubach
committed
Added distance transformation of edge lengths
Benjamin Robert Laubach
committed
Added broken (but done) code
Benjamin Robert Laubach
committed

Commits on Mar 20, 2025

Added working calc_histograms file
Brayden Todd Sundberg
committed
Added swap_c2n.py
Benjamin Robert Laubach
committed
updated calc_hist and added tests
Brayden Todd Sundberg
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Brayden Todd Sundberg
committed
Added parallel file analysis in histogram executable
Benjamin Robert Laubach
committed
Calculatates clusters for 3 and 4 bodies even when param file doesn't have interactions
Brayden Todd Sundberg
committed
Moved everything for FP to chimesff/src/FP
Brayden Todd Sundberg
committed

Commits on Mar 21, 2025

Fixed naming convention in post_process.sh
Benjamin Robert Laubach
committed
Added get_hist.cmd for Ben
Benjamin Robert Laubach
committed
Fixed small syntax errors, changed simulation to 500 frames
Benjamin Robert Laubach
committed
Fixed(?) 4b interactions with ghost calls
Benjamin Robert Laubach
committed

Commits on Apr 8, 2025

Updated to latest stable LAMMPS
Yanjun-Lyu
committed

Commits on Apr 22, 2025

Update LAMMPS integration: Add tests, modify installation script, and pair_chimes.cpp to allow unmatched element types between ChIMES models and LAMMPS data files
tg873340
committed

Commits on Apr 29, 2025

Updated multi-element fingerprinting
Benjamin Robert Laubach
committed
Added submit script
Benjamin Robert Laubach
committed

Commits on Apr 30, 2025

Fixed bug when calculating max dissimilarity
Benjamin Robert Laubach
committed

Commits on May 2, 2025

Merge pull request #37 from laubachb/main
RKLindsey
authored

Commits on May 7, 2025

Fixed overloading of functions
Benjamin Robert Laubach
committed

Commits on May 13, 2025

Commits on May 15, 2025

Made pair_chimes.cpp faster, added lammps test cases for POC
Benjamin Robert Laubach
committed
Fixed overloading variables and removed save_files
Brayden Todd Sundberg
committed

Commits on May 16, 2025

Fixed HN3 case
Benjamin Robert Laubach
committed
Added parameter file to TiO2
Benjamin Robert Laubach
committed

Commits on May 20, 2025

Updated files
Benjamin Robert Laubach
committed
Print penalty values however they are user-specified or default
tg873340
committed

Commits on May 21, 2025

Updated fingerprinting, removed ghost implementation
Benjamin Robert Laubach
committed
Added test sets for fingerprinting
Benjamin Robert Laubach
committed

Commits on May 22, 2025

Fixed histogram exe
Benjamin Robert Laubach
committed
Fixed 4B in chimesFF.cpp
Benjamin Robert Laubach
committed

Commits on May 29, 2025

Remove the redundant chimesFF.{cpp, h} files outside src folder
tg873340
committed
Added a Langeving lammps test with load balancing
aalmohri
committed
Added lammps example including explicit D2 dispersion
Brayden Todd Sundberg
committed
Added files for lammps test
Awwal41
authored

Commits on May 30, 2025

Merge pull request #80 from rk-lindsey/main
rk-lindsey
authored

Commits on Jun 3, 2025

Removed lmp_test folder, lammps tests located in /etc/lmp/tests/
Benjamin Robert Laubach
committed
Reverted serial_chimes_interface.cpp cluster graph modifications since these were untested and out of scope for the pull request
Benjamin Robert Laubach
committed

Commits on Jun 4, 2025

Added test sets for fingerprinting
Benjamin Robert Laubach
committed
Added CO.2.5gcc_6500K.scramble test case
Benjamin Robert Laubach
committed

Commits on Jun 5, 2025

Allowed installation on UT-TACC host type
Benjamin Robert Laubach
committed

Commits on Jun 6, 2025

Updated install script to work with Stampede3. Tested on scramble dataset.
blaubach
committed

Commits on Jun 11, 2025

Removed extra LAMMPS fingerprint tests
Benjamin Robert Laubach
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Benjamin Robert Laubach
committed

Commits on Jun 19, 2025

Merge pull request #40 from LindseyLab-umich/add_lmp_tests
RKLindsey
authored

Commits on Jul 7, 2025

Updated single point files for lammps tests
Benjamin Robert Laubach
committed
File organiziation
Benjamin Robert Laubach
committed

Commits on Jul 22, 2025

Added LAMMPs test suite. 5/6 tests fail - requires further debugging. Possible causes include box sizes, etc.
Benjamin Robert Laubach
committed

Commits on Jul 23, 2025

adds tabulation as an optional flag
btsund
committed
removed the mistaken chimesFF.* files in chimesff
btsund
committed
keeping install.sh formatting
btsund
committed
Updated LAMMPs input files to properly account for conversions. Removed problematic test cases (flagging on GH). Removed use of non standard libraries
Benjamin Robert Laubach
committed
Added CO.9GPa case study
Benjamin Robert Laubach
committed
Added test_suite.log for LAMMPs tests
Benjamin Robert Laubach
committed
Improved clarity in install.sh script and added tabulation documentation
btsund
committed
Fixed documentation wording
btsund
committed
Updated documentation to include fingerprinting
Benjamin Robert Laubach
committed

Commits on Jul 24, 2025

Update utils.rst
RKLindsey
authored
Added link to ChIMES Fingerprint publication to docs.
Benjamin Robert Laubach
committed
Update published_params.liqC.2+3b.cubic.txt.liqC.2.5gcc_6000K.OUTCAR_#000.xyz.dat
laubachb
authored
Updated fingerprint flag to be in any position of the install (not just the first argument).
Benjamin Robert Laubach
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Benjamin Robert Laubach
committed
Updated install script to compile histogram exe when FINGERPRINT flag is enabled.
Benjamin Robert Laubach
committed
Update install.sh
RKLindsey
authored
Pointed expected_output/ and force_fields/ to serial_interface location. Removed tracking of generated_output/ (created when run_*.sh run)
Benjamin Robert Laubach
committed
Merge branch 'FP_Calc' of github.com:BTSund/chimes_calculator-TSFork into FP_Calc
Benjamin Robert Laubach
committed
Updated fingerprint test to have expected output
Benjamin Robert Laubach
committed
Updated example submit job script
Benjamin Robert Laubach
committed
Merge pull request #49 from BTSund/FP_Calc
RKLindsey
authored

Commits on Jul 28, 2025

Combines Fingerprint code and tabulated code
btsund
committed
modifies run_test.sh and test_list.dat
btsund
committed
modifies run_test.sh and test_list.dat
btsund
committed
Updates documentatation to include fingerprinting and tabulation
btsund
committed

Commits on Jul 31, 2025

Fixing double declaration bug
btsund
committed
Fixed bug in install script not allowing for FP or tabulation installation
btsund
committed

Commits on Aug 1, 2025

Fixes serial interface not working due to left over tabulation logic
btsund
committed
Merge pull request #59 from BTSund/develop
RKLindsey
authored
Replaces fix_modify with econserve
Brayden Todd Sundberg
committed
removed fix_modify lines
Brayden Todd Sundberg
committed
Merge pull request #60 from BTSund/develop
RKLindsey
authored

Commits on Aug 4, 2025

Commits on Aug 5, 2025

Commits on Aug 6, 2025

Updated py, C, and Fortran api documentation
Brayden Todd Sundberg
committed
Updated ChIMES Fingerprint documentation. Included example image, increased tool description, tested with sphinx.
Benjamin Robert Laubach
committed
Updated documentation for Fingerprints
Benjamin Robert Laubach
committed
Update etc.rst
PoornimaMMPC
authored

Commits on Aug 7, 2025

Commits on Aug 8, 2025

Commits on Aug 22, 2025