CREST Release 3.0.x and older

CREST version 3.0.2 🛡️

Build updates and fixes 🛠️

What’s Changed

• 🪲 Minor bug fixes for MSREACT mode by @gorges97 in https://github.com/crest-lab/crest/pull/309
• 🪲 Circumvent segfault due to optional arg in gcc build in https://github.com/crest-lab/crest/pull/318
• 🪲 Fix for #320 in https://github.com/crest-lab/crest/pull/322
• 🔒 Safer toml input parsing in https://github.com/crest-lab/crest/pull/325 Unrecognized keywords will now throw a warning and stop the program immediately
• 🛠️ Maintenance of submodules in https://github.com/crest-lab/crest/pull/328
• ⚙️ Update of GitHub workflows in https://github.com/crest-lab/crest/pull/335
• 🛠️ Safer (but unfortunately still not fixed) MKL handling for ifort builds in https://github.com/crest-lab/crest/pull/331
• 🌊 Fixing implicit solvation in tblite submodule in https://github.com/crest-lab/crest/pull/331 (most important change, should now be consistent with xtb)
• 📦 Added a GNU/CMake static build for the continuous release, alongside the Intel build:
  

CREST 3.0.1 (CREST 3.0 Hotfixes)

What’s Changed

• Address errors of issues #281
• Restore printout of kpush, mentioned in #284
• Address thread OpenMP handling issues of #284 and #285, see #289
• Fix uninitialized boolean bug in gcc build #287
• Fix axis bug causing #296
• Address QCG issues #297 and #294
• Singlepoint and optimization printout cleanup

Other Additions

• Allow tblite parameter file read-in in #303
• Implement dipole and atomic charges readout for tblite calculators, gfn0 and gfnff
• CMake-based unit tests (run make test after building)

CREST 3.0

CREST 3.0 is a major overhaul of the previous code versions. A large part of the original source code was rewritten to implement calculators, optimization, and molecular dynamics routines directly, rather than relying only on the xtb program as a subprocess. Consequently, there are performance improvements and a significant reduction of I/O operations. Read all about the new program version in the new open access article J. Chem. Phys. 2024, 160, 114110.

Features include:

• New input file reader
• Energy- and gradient-based interface for calculations
• Standalone ANCOPT implementation (RF optimizer with BFGS update step in approximate normal coordinates)
• Standalone MD and metadynamics module
• Standalone implementation of geometrical constraints
• New minimum energy crossing point (MECP) algorithm (see Examples/MECP Calculations)
• Integration of the tblite submodule
• Integration of a GFN0-xTB submodule (see J. Phys. Chem. Lett. 2023, 14, 19, 4440–4448)
• Integration of the TOML-F parser
• Integration of a GFN-FF submodule
• Implementation of a multi-layered multi-center ONIOM calculator (see J. Phys. Chem. B 2024, 128, 13, 3145–3156)
• Proper unit tests for the CMake build

CREST 2.12 and older

2.12

• Finalized QCG implementation consistent with publication JCTC, 2022, 18, 3174- 3189 by @cplett in #94 #104 #103 #116
• Fixes for compiling with GCC by @awvwgk in #92
• Attempt at cleaning up the ‘axis’ routine mess across the code. by @pprcht in #95
• Update of topology check option --notpo by @pprcht in #102
• Modified CREGEN to handle relative energies in ensemble file by @pprcht in #113
• Changes to printouts and some code-cleanup by @pprcht in #118
• Several bugfixes by @cplett, @MtoLStoN, @pprcht in #101 #115 #117

Full Changelog: https://github.com/grimme-lab/crest/compare/v2.11.2…v2.12

2.11.2

• More robust search for MKL in CMake build files by @awvwgk in #71
• Allows compilation of CREST with OpenBLAS by @awvwgk in #78
• Workaround for no convergence in svdcmp error in RMSD module by @pprcht in #89
• QCG implementation by @cplett in #90

2.11.1

• Various small fixes and printout changes (#33, #37, #46, #51, #58, #67)
• Added asciidoc man page (#60)
• Improved memory handling for topology detection (#63)
• Added routine for reading a file with atomic charges for GFN-FF calculations (--charges) (#63)
• Added a simple PDB input format reader (#44)
• New routine for additional XH orientation sampling (--hflip/--noflip). Will be conducted by default after MTD sampling (#63, #70)

2.11

• Moved crest source code to the repository
• Rewritten ensemble sorting routine CREGEN
• Connectivity/topology checks in CREGEN (can be turned off with --notopo)
• Optional PCA and k-Means clustering after sorting (--cluster <number>)
• Multiple smaller tools and improvements implemented
• Updated input reader for Turbomole coord, .xyz and 3D .sdf (V2000,V3000) formats
• Turned off zsort default input sorting of coordinates
• Enabled --alpb usage (new implicit solvation model in xtb)
• Reduced creation of files during optimizations
• Dedicated ensemble entropy (--entropy) mode and iMTD-sMTD workflow (--v4), see preprint

2.10.2

• Code cleanup (pt. 2)
• New flag -gfn2//gfnff, experimental composite mode, structure generation at GFN-FF level, energies at GFN2-xTB level (singlepoint calculations)
• New flag -trev, reverse settings for tautomerization algorithm, i.e., first deprotonation then protonation
• Bugfix: -scratch did not copy back the crest_ensemble.xyz file :beetle:
• New flag -keepscratch to prohibit deletion of a scratch directory
• Some minor printout changes and fixes
• Bugfix: input error for automatic bond constraint (-cbonds) :beetle:

2.10

• Major code cleanup (pt. 1)
• Moved crest from xtb to its own repository
• Proper SIGTERM and SIGINT handling implemented
• Bugfix: Repaired integer overflow in ensemble sorting routine :beetle:
• Reduced memory consumption in ensemble sorting
• Improved efficiency of ensemble sorting (for large ensembles)
• Implemented automatic bond length constraint (-cbonds )