Version 3.1 Refactor - #483

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pprcht wants to merge 436 commits into

crest-lab:masterfrom

pprcht:experimental

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Commits on Jan 30, 2026

Fix issues with "natural" zmat setup
pprcht
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274ecb7
Change splitting function to always produce just 2 fragments
pprcht
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f88a8d7

Commits on Feb 2, 2026

Update irmsd routines from irmsd project
pprcht
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cbc6a4d
start building charge distribution for fragment split
pprcht
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9ec2576

Commits on Feb 3, 2026

Working automatic charge distribution
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f044843

Commits on Feb 4, 2026

test
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09a4acb
new bugfix attempt omp hrutils
Lukasrindt
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055df2d
Work on required CREGEN refactor 1
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0495169

Commits on Feb 5, 2026

Commits on Feb 6, 2026

Work on required CREGEN refactor 5
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d0a84fe
Work on required CREGEN refactor 6
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86e2c2a

Commits on Feb 7, 2026

CREGEN refactor (likely) finished. Plus nicer printout
pprcht
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60f2ef6
Some prettier printout for CREGEN
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c9d9de9
Enable internal structure list input for newcregen
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30f446a

Commits on Feb 8, 2026

alkylize rotamerfile for reconstruction
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e7cfae2

Commits on Feb 9, 2026

deform_opt_hess added
Lukasrindt
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9149222

Commits on Feb 10, 2026

double track fixed and deform opt hess changes (still buggy)
Lukasrindt
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e0f99df
smarter pre-sorting in queue reconstruction
pprcht
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bc853a2

Commits on Feb 11, 2026

CREGEN printout changes
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ad16cd6
parallelization in reconstruction, cregen printout changes
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39bbf90
More cregen printout changes
pprcht
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03903e8

Commits on Feb 12, 2026

deform opt hess fixed finally
Lukasrindt
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11267e0
Fix zmat-issue, prettify some printouts
pprcht
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bb81f8c

Commits on Feb 18, 2026

Commits on Feb 19, 2026

optimizers refixed
Lukasrindt
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226f6a9
ancopt alp 1
Lukasrindt
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813eec4

Commits on Feb 21, 2026

Fix io error in cleanup
pprcht
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1fbbef2

Commits on Feb 25, 2026

Moving some thermo/frequency routines around
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b54e119
Start implementing "approxg" with modelhessian thermocontributions
pprcht
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428c4ad
changes to approxg, callable via calculator now. why though?
pprcht
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55c62cb

Commits on Mar 2, 2026

Start implementing RMSD penalty as calculator object
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88b76ff
pass refine_lvl in calculation copy
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bf5904a

Commits on Mar 3, 2026

CREGEN printout fix
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9cbfdb8
RMSD penalty function via calculation.level TOML object
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167f02f

Commits on Mar 4, 2026

ORCA .hess reader for thermo
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8803964

Commits on Mar 5, 2026

allow coord files to be specified in Angström
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a3426b4
Clean up CLI arguments --> map usage, terminate for invalid configs
pprcht
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885b29e

Commits on Mar 9, 2026

Proper final printout for basin-hopping
pprcht
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513ff94

Commits on Mar 10, 2026

Basinhopping on dihedral angles
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bd2135a
Fix optimization tester (sp -> wp)
pprcht
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738e575
fix 1 character readl
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71d73fd
Change asynchronous BH execution
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b73a1bb
drawbox function in iomod
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66ab386

Commits on Mar 11, 2026

Allow "refine" settings for mc quenches
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0319fda

Commits on Mar 12, 2026

Commits on Mar 13, 2026

rename fortbridge -> fmlip_relay
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a83550d
second try at renaming subproject
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1c0a963
Add dftd4 as git submodule (tblite requirement)
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ecf12df
Add mctc-lib as git submodule (tblite dependency)
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47bb33b
Update fmlip_relay update logic
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baeace4
parallel execution of fmlip-relay
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996b42d
thread limitation for parallel MLIPs
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251fc0d
Add charge&spin update from fmlip-relay
pprcht
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c19d5a0
Update git submodule link
pprcht
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7907167
g_sampling fully integrated
Lukasrindt
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2df287f
alternate mlip keyword
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231b456
Add mstore as submodule (tblite dependency)
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9dc0ea4
Add multicharge as submodule (tblite dependency)
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ce898c9
change multicharge version to something dftd4 compliant
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820e3ad
add s-dftd3 submodule (tblite dependency)
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87c8d9e

Commits on Mar 14, 2026

Start another attempt at redoing the meson build system
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48632b3

Commits on Mar 15, 2026

point libpvol to fork with modified meson build
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4f8057c
Update build systems for gfn0 and gfnff locally
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f0d5925
.gitignore update
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5d13f55
meson build configuration updates
pprcht
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5ae0527

Commits on Mar 16, 2026

Thermochem omp protected
Lukasrindt
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65282e7
omp now really protected
Lukasrindt
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74ab584
syntax error fixed
Lukasrindt
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f19f2f8
add fmlip-relay meson build
pprcht
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cc45794
Update gfnff subproject commits
pprcht
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dfb3cef
Add missing meson build srcs, fix weird printout format in ancopt
pprcht
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9d7eecf

Commits on Mar 17, 2026

omp critical for symmetry
Lukasrindt
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157100e
Merge remote-tracking branch 'lukas/hessian_update' into experimental-merge
pprcht
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1898585
Start work on parallel free energy correction calculation
pprcht
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7488285
fix function
pprcht
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9487c3a
serial loop for dG refine implementation
pprcht
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4cd1127
Add (unused) symmetry_i.f90 rewrite of the C code
pprcht
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a70d06b
disable tblite C-api, unneeded for build
pprcht
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3d10912

Commits on Mar 18, 2026

Turn of warnings for default meson build
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25891ef
working STATIC buil with meson, GNU compilers and openblas
pprcht
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a2af9c9
Change to numhess1, enable parallelization
pprcht
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556028d
Merge branch 'experimental' into experimental-meson
pprcht
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6cde111
Refactor symmetry detection C->Fortran
pprcht
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474ce5b
Point groups defined as parameter rather then repeated setup
pprcht
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42bd17a
Fix text-formatting error
pprcht
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2d43d16
formatting
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90e659b
Small refactor, removed getsymmetry2, now only importing symmetry_i
pprcht
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9b75759
Add tests for all relevant point groups
pprcht
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d03bf34
Merge branch 'experimental-meson' into experimental
pprcht
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06fb54b
prepare nicer dry-run printout
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1595bba

Commits on Mar 19, 2026

Commits on Mar 20, 2026

Safeguard some code for intel-llvm builds
pprcht
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d1c7727
fix warning for intel-llvm build
pprcht
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ec04a5f
intel-llvm updates
pprcht
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62f7908
Update metadata printout
pprcht
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bb8e9f3
refactor: move c helpers into src/chelpers/
pprcht
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4c00112
Small refactor of propcalc to remove old code
pprcht
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180efad
refactor to remove legacy readl routine with modern Fortran
pprcht
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676f7e9
Test implementation of a Langevin and a Bussi-Parinello thermostat. The later one still seems bugged
pprcht
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e756c73
Fix Bussi-parinello thermostat
pprcht
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73b2c5d
Clean up thermostat implementations and printouts
pprcht
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e8162ba

Commits on Mar 23, 2026

Start refactor of molecule type and readers
pprcht
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e5547ac
cntd work on molecule type refactor
pprcht
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1af40fb
Re-export types
pprcht
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ae3e346
Some cleanup for molecule type refactor
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e204424

Commits on Mar 24, 2026

Modify the mol%write() function to adapt to file types
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b7c7a75
working on extxyz reader
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a5bf112
extxyz parsing ...
pprcht
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4cea29a
continue on extxyz parsing
pprcht
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2b20668
continue work on extxyz parser
pprcht
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07778c7
Debugging extxyz reader
pprcht
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2f2923e
extxyz printout for crestopt.log.xyz files
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44453d6
extended xyz refactor
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3bbff95
ensemble reader function extended xyz
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fc080e2

Commits on Mar 25, 2026

update dftd4 subproject across builds
pprcht
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6d4d858
Update multicharge subproject to v0.5.0
pprcht
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d459b1e
Update toml-f subproject
pprcht
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8ec2920
Add tblite fixes because of newer version
pprcht
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3610d80
gxtb-tblite calculator setup... still some energy difference compared to the tblite app
pprcht
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96df0f9
Taking care of EEQ-BC aux charges
pprcht
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03527f0

Commits on Mar 30, 2026

fix energy conversion for extxyz ensembles
pprcht
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d83e01b
Fix extxyz energy conversion within sampling workflows
pprcht
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b5ac891

Commits on Apr 7, 2026

Commits on Apr 13, 2026

Remove omp critical statement in orca hessian processor
pprcht
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f9d1b0f

Commits on Apr 24, 2026

new logic for g-xTB usage: WITH_GXTB --> tblite implementation (still confidential), else: xtb syscall with --gxtb
pprcht
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d3e5e68
Deactivate g-xTB tblite build (still confidential, in preparation)
pprcht
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32c663b
Merge remote-tracking branch 'origin/experimental-gxtb' into experimental
pprcht
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4e4df52
Update in preparation for tblite gxtb build
pprcht
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ae8f669
Use the same commits in all of git submodules, Cmake Find* files, and meson wrap files
pprcht
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aa1691e
let refine write in extxyz format
pprcht
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740765d
printout formatting
pprcht
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d04cf04
Avoid starting calculations by itself. require explicit runtype specification now
pprcht
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244b436
rewire --cregen/--sort logic for easier use
pprcht
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919ced4
Nicer --help menu print, plus some man page cleanup
pprcht
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9a8afe7
irmsd test
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526cad7

Commits on Apr 25, 2026

Build updates and tested static builds
pprcht
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453a855
Update commit on meson wrap and cmake find files
pprcht
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6124536
alternative flag '-itmdgc'
pprcht
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2a4d037
workflow rework, part 1
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115d93d

Commits on Apr 26, 2026

workflow rework, part 2
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8de0897

Commits on May 3, 2026

printout update
pprcht
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96f93a0
Perpare for spin-polarized xtb via tblite
pprcht
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c7cbf6e
spin-polarization flags/toml
pprcht
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bbf448e
spin-polarization, some printouts
pprcht
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406aadd
unit test for spin-polarization
pprcht
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023e25f
Repair entropy mode functionality
pprcht
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1a6e936
small modification to extxyz, energy and froces units
pprcht
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0f380e9
prepare global setting for output units in extxyz
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84b85bd

Commits on May 5, 2026

Working on restart logic
pprcht
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29c270a
Update restart logic
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ab02d46

Commits on May 6, 2026

Commits on May 7, 2026

Experimental branch static build test
pprcht
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936e8bd
Update build-upload.yml workflow
pprcht
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aa22218
-rerank and -reopt flags
pprcht
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5807032
multilevel keyword compatibility with --opt
pprcht
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f7e09d0
deprecate -for flag
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5dc2ac3
--ensemblehess and --finalhess keywords
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cc36974

Commits on May 8, 2026

Commits on May 15, 2026

Activate the new protonate/deprotonate protocols by default
pprcht
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d4aac15
Update examples
pprcht
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30eae3e
Add toml keyword for CREGEN
pprcht
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5760b68
update example 10
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0adb694
Update example 12
pprcht
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efa3174
Update file name info protonate/deprotonate/tautomerize
pprcht
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0d3e634
Version bump in preparation of merge
pprcht
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fa99644

Commits on May 22, 2026

cosmetics (adapting term_ui from github.com/pprcht/irmsd)
pprcht
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c5956cc
cosmetics (warning due to temporary array in axis() call)
pprcht
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7598806
cleaner stack handling in queue reconstruction for static build
pprcht
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e373720
cosmetics (avoid ifx warnings in ancopt for static builds)
pprcht
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95729d9
update fermi smearing default for g-xTB, consistent with tblite
pprcht
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58175d9
cosmetics (ir intensities in "vibspectrum" file)
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cda1733

Commits on May 23, 2026

cosmetics (nicer MD/MTD block printout)
pprcht
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12c6caa
cosmetics (remove stale refine part)
pprcht
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5b18166
cosmetics (sdf ensemble rewrite function)
pprcht
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c4688c1
cosmetics (pca clustering as --sort runtype via additonal --cluster arg)
pprcht
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4ca4b50
cosmetics (modernize some ccegen code parts)
pprcht
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e79f12c
cosmetics (update help menue, in particular --help sort)
pprcht
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2e90462
cosmetics (cleanup of ancient ensemblecomp routine --> iRMSD)
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a9778cc

Commits on May 24, 2026

cosmetics (more CCEGEN cleanup)
pprcht
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a8e9467
cosmetics (some source cleanup)
pprcht
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412f416
fmlip-relay example
pprcht
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9813e59
Better handling of parallel fmlip-relay usage
pprcht
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aff0a70
submodule commit update
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a110036

Commits on May 30, 2026

Commits on Jun 1, 2026

Static linkage of subprojects in meson build by default (≠full static build)
pprcht
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a2baea8
allow custom name for optimizer logfile
pprcht
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bee72b8
Simplified orca driver via cli
pprcht
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6be326d

Commits on Jun 4, 2026

Commits on Jun 5, 2026

Commits on Jun 12, 2026

Update tblite version (plus, required for that, dftd3/dftd4)
pprcht
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20b637d

Commits on Jun 13, 2026

Commits on Jun 16, 2026

Fix CMake finder (#487)

awvwgk
authored and
pprcht
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5941442

Commits on Jun 24, 2026

squash merge: callback for fortran engrad calls
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e3c8d25

Commits on Jul 1, 2026

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Set missing return status for numhess
pprcht
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86bb328

Commits on Jul 12, 2026

Commits on Jul 13, 2026

Port tblite to v0.7.0
pprcht
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524470d
"downgrade" mstore to release version v0.3.0
pprcht
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1c8657f
disable jonquil tests in meson
pprcht
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cfc5464
Pin versions of subprojects in subprojects/README.md
pprcht
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066602e

Commits on Jul 14, 2026

Patch Findddx.cmake to add the module output directory to the ddx target's build interface.
pprcht
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904c8b6

Commits on Jul 18, 2026

in restart-mode, source from lowest structure
pprcht
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f726060

Commits on Jul 26, 2026

Pass the per-level threads setting as --max-threads to fmlip-relay servers (bump pin to 1f29707)
pprcht
committed
b2fb77c

Commits on Jul 31, 2026

Delegate ONIOM bookkeeping to the lwONIOM job-table/driver layer (v0.0.2), add ONIOM example and unit tests
pprcht
committed
a5ed646

Commits on Aug 4, 2026

Bugfix: spin polarization setting was missing from deep-copy, so it had no effect.
pprcht
committed
bd27e34