qcscine/utilities: Release 10.0.0

Abstract

Changes: Tests for the QM/MM transition state optimizer In case the atom coordinates given to a GeometryOptimizer are identical to the coordinates of the underlying calculator and a Hessian is requested, it is checked if this result is already present in the calculator to avoid an unnecessary calculation. The Thermochemical Calculator can now be constructed with a PartialHessian. The property PartialGradients is now available. It is intended to signal different contributions to the total gradients, e.g., the QM gradient contribution and the MM gradient contribution in QM/MM. Added a class to store derivatives in a more flexible manner. The Harmonic oscillator, particle-in-a-box, static-rotor free energy for zero Kelvin is now set to the sum of the electronic energy and zero point vibrational energy. Fixed a bug which lead to a crash when extracting thermochemical information from the Orca output for a temperature of zero Kelvin. Relative paths for the point charge file in electrostatic embedding calculations with Orca may now be used. More basis sets supported by Turbomole calculator. Pickle support for ElementType. The DFT grid for calculations with Turbomole is now set to 'm4' if Hessians are requested and the grid was too coarse for reliable Hessians (1 - 3, m3). Added support for lists of lists of integers as generic values. Added support for None in the Python bindings of the extract method of the Settings class. Allow writing pdb trajectory files. Fixes a bug where the coordinates in XYZ trajectory files were no longer separated by white spaces. Fixed a bug where the coordinates in PDB files were wrong if the code was compiled with clang. Added support for QM/QM/MM embedding and QM/QM embedding with Serenity.