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…tive-learning test
- get_crest_conformers fix - split_multimolxyzfile title grab - matplotlib: removed deprecated features - thermochemprotocol_single: fix for no SP theory - Added crest_Wigner_TDDFT workflow
- xtBTheory: grab_BOs option and grab_bondorder_matrix function - tweaks to crest_wigner script
- first implementation of interface to Sella, not working yet
…deleted) - some small cleanup in module QM/MM and OpenMMTheory
- MACETheory: adding training keywords(weights, epochs, valid-fraction) to init - Dynamics: ONIOMTheory is now properly supported for MD. Dev Note: creates special OpenMMTheory object for MD regardless of whether ONIOM-object contains an OpenMMTheory object. - ONIOMTheory: Now supporting OpenMMTheory as Theory-level. Creates special OpenMMTheory object for Region1. Only ONIOM-2 for now. Residue limitation, working on. - pyscftheory: platform logic fixed - FairChemTheory: cleanup
…nted differently now (was based E+G calls, which failed for numerical Hessian runs). Now reading geometric-logfile, silly but works.
- fairchem: creating new atoms object if molecule has changed
- get_boundary_atomsm get_linkatom_positions and get_MMboundary (QMMM and ONIOM): now supporting multiple linkatoms
…at the same time as particle masses are set to zero. Fixes the old problem of behaviour of frozen atoms in NPT simulations
spin-density from orbital file using multiwfn
…P models, mace-omol via name - FairChemTHeory: PBC enabled, using platform instead of cpu
…ace_new, old one in module_surface_old. calc_surface and calc_surface_from_XYZ can now handle N-dimensions. - reactionprofile_plot: can now handle if key is tuple instead of float - torchtheory: platform, device fixes - bugfix in cart_to_fract - Periodic_optimizer_cart now writes CIF,XSF or POSCAR files - DFTB: kpoints for case DFTB
- Turbomole : dispersion corrections - Turbomole: PBC via riper (only for HF and pure DFT ) - 3d volume plots in module_plotting - Periodic_optimizer_cart: initial constraints (not well tested)
- openmm: added openMM_cpu_threads also to be safe
- calc_surface: now supports either geometric or dlfind as optimizer. Use of DLFIND required new routines to set geometry - fixes for read and write surfacedict
….py). Globally available. - calc_surface : now can prepare geometry using restraints (set_geometry_via_restraint Boolean). Uses _preset_geometry_restraint and RestraintTHeory
…f.fragment, completely changed interface to allow more easily creating object and then running, separate methods for constraints etc. - fix for Numfreq: accounts for scenarios where no dipole-dictionary, None in dipole-dictionary and actually dipole dictionary with Numpy arrays. - OpenMMTheory.run (qm_elems to allow compatibility with WrapTheory) - calc_surface: now using optimizer objects throughout. optimizer keyword now takes options geometric or dlfind as strings but can also take geomeTRICOptimizerClass and DLFINDOptimizerClass objects. Confirmed to work - calc_surface and optimizers now obey print-levels better. Useful for running really long surface scans with printlevel=0 to prevent outputfiles from becomin too big. - plotting functions: minor improvements - tblite: printlevel obeying - geometric and dlinf: fix for constraints not recognizing torsion (only dihedral)
…updated imports - DL-FIND optimizer: support for PBC - Proper internal-coordinate table - Renamed Periodic_optimizer_cart to Cart_optimizer. Now supports both PBC and non-PBC. - calc_surface: now supporting Cart_optimizer (but not working yet)
- README: ASH citation
- reactionprofile_plot: minor fix
…timizer object - pyscftheory: support for DFT+U Hubbard RKSpU and UKSpU mf types - DL-FIND: support for Cartesian constraints (x,y,x and xy,xz and yz),. Not confirmed to work yet. sigint handling so that DL-FIND actually sends kill signal upon Ctrl-C
…optimizer before each surfacepoint - Nonbondedtheory: minor fixes - Cart_optimizer: cartesian constraints, torsion, bond and angle constraints: soft constraints now work, constrain_method keyword (default soft), hard constraints not yet working
- mace interface: print fix - freezing string interface: preliminary, not ready - dl-find: putting cycles counter at beginning of run - crest: fixes for return, indent issue - cart_optimizer: removed printing lines
…g of constraints, kf values can now be modified, now obeying printlevel
- dlfind: minor fixes, ts-opt job now reporting correct number of cycles - mace: printlevel behaviour - OpenMMTHeory: fix for MD Periodic vs. periodic inconsistency
- MACE: fix for not obeying platform - ORCA: now check for missing ! - subash.sh: now using NTASKS instead to set number of NUM_CORES, used by multiwalker feature
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