Significant refactoring of the code, Local diabatization and more

• Code restructuring:

  • significantly restructured the code (via the tsh_revision branch). Now, the dynamics code
    is much more compact, clean, and consistent. New functions are added in a modular way to
    enable more compact coding of the may computational workflow.

  • reducing the nesting levels and making it more modular: the hamiltonian library and namespaces
    are broken into atomistic (for MM and QM) and models (collection Hamiltonians) modules

  • the nhamiltonian library and namespace is made top-level, to avoid unnecessary dependencies

  • all the dynamical variables are now held in the dyn_variables class. Functions are coded to
    take this data class. Withing it, the amplitudes or density matrix variables can be used, the conversion
    functions (including from-to different representations are available)

  • Added cctor and memory status check functions to the nHamiltonian class - now it all works fine, removed the
    implementation of the propagators that dependend on the projectors, added auxiliary Hamiltonian as an input parameter
    to the compute_dynamics function and reflected that in the Python wrapper function, changed the compute_St functions
    to take two nHamiltonian objects as input, removed the use of Uprev variable in the compute_dynamics function,
    since it is now deprecated

• New methods and variables:

  • the local diabatization approach and multiple electronic integrators are added: There are algorithms based on
    matrix exponential, rotation, and others (e.g. QTAG-like). The integrators are available for diabatic and adiabatic
    representations.

  • the propagation in terms of density matrix is now available (solving the QCLE). The QCLE integrators are coded.

  • added Shenvi-Subotnik-Yang (SSY) phase correction algorithm (to fix the decoherence-induced phase effects)

  • added Zhu's Liouvillian-based phase correction method (developed as an alternative to the SSY method)

  • added Zhu-Nakamura (ZN) hop attempt probability.

  • new dynamical control variables added to provide a more convenient definition of the computing recipes

  • added new electronic integrator in the diabatic basis - according to the qtag approach

  • added new control variables for various schemes of variables updates, added new functions for computing hopping probabilities in a more efficent way

  • added generalized Holstein Hamiltonian

  • reactivated BCSH and DISH methods

  • added packages.cp2k module that implements an input generator for cp2k

  • added Morse model Hamiltonians and the parameterization of Coronado-Xing-Miller

• Deprecations and removals:

  • the external_hamiltonian class/namespace is deprecated

  • the Ensemble class is deprecated

  • update_Hamiltonian_ functions are deprecated in favor of the new general version

  • removed a lot of unnecessary (commented or not) C++ code in files in the dyn module (e.g. Dynamics.cpp, Energy_and_Forces.cpp, etc.)

  • the state tracking and phase correction approaches are deprecated in lieu of the local diabatization-based
    approaches: the original one of Granucci, Persico, and Toniolo + a number of other interators derived in the
    TCA paper (to be published)

  • Many old nearly duplicate or confusing functions for electronic integration are removed to clean up the code, yet to keep
    the essential functionality.

  • moved tutorial on plotting model Hamiltonians to the CyberTraining repo

  • removed outdated QTAG examples

• Fixes:

  • fixed a minor but important bug in GFSH; the algorithm is now working

  • fixed the false fail of the SDM (mSDM) method which could happen under certain conditions when the populations
    on a given state is close to 1.0

• Misc:

  • revised and simplified the installation instructions (including building a suitable Conda environment)

  • simplified and optimized build/compillation scripts, started using precompiled headers (PCH)

  • made the C++ code compatible with the C++11 stnadard

• Other notable changes:

  • improved quality of dynamics_plotting plots and added new options for plotting

  • Added plotting of the time-resolved Hamiltonians, time-overlaps and projections

  • changed NULL to nullptr