Libra with the ANN; new xTB/CP2k workflows; generalized and simplified workflows; libint2 and pickling support;

Major additions and changes:

• ANN functionality is revised and extended, now fully-functional
• Eigen3 is removed from the codebase, build instructions are now set to use the external package
• Added the libint2 support, Libra is linked to the external libint2 libraries and can use them
• Added the MOLDEN-file procedures: constructing the molecular integrals using these files
• Added the CP2k workflow with libint2 support
• Added the xTB (in CP2k) workflow
• Pickling support for various Libra classes
• Simplified and generalized the multithreading calculations and made the workflows more user-friendly
• Added more efficient methods for SD overlap and time-overlap calculations
• Added user-friendly general NA-MD workflows, with a set of new recipes for common types of calculations
• Less memory-demanding saving in the files
• Fixed a memory leak in the NA-MD workflows
• Moved some examples to the CyberTraining repository

Libra goes black box

Major:

• added "Libra executable" scripts to conduct workflow (black box) calculations with Libra via taking simple input files. This feature enables the execution of Libra on the computational science gateways with restricted scripting support such as SEAGrid.

Minor:
Numerous changes and fixes to the previous state of the code

• functions for NBRA workflow calculations
• new capabilities for DVR (numerically exact) calculations
• revitalized the artificial neural networks capabilities of Libra
• removed a fraction of tutorials and redeveloped them in the compchem-cybertraining

Hotfix for the TD-DFT/NAMD with Libra

Major:

• the use of the signs of the CI amplitudes of the excited Slater determinats in contrast to their absolute values, which was incorrect

Other:

• the single-particle and many-body (MB) basis are now both constructed in a post-process fashion, allowing the user greater control;
• introduced a new parameter in the step2 calculations called "completion_level". This parameter allows users to only complete specific tiers of the calculations, such as only overlaps and energies in the KS basis, without explicitly computing overlaps in the MB basis. The construction of the MB basis can now be done in a post-process fashion, which allows for greater user control;
• added a function in Libra to apply orthonormalization procedure to a matrix of dimensions NxN, where N is the number of electronic states. Previously in Libra, the apply orthonormalization procedure was only applicable to matrices of dimensions 2Nx2N in spin-block notation. The MB basis is orthonormalized before the application of state reordering and phase corrections, respectively.
• revised the format of the user-defined excited Slater determinants used in the NA-MD calculations to be able to setup correct spin-adapted states
• fixed a hidden problem (infrequent bug) in the hop function
• added more general Holstein-like Hamiltonians, with the position-dependent electronic couplings

NA-MD workflow with TD-DFT states, CP2K/Libra, stochastic state tracking

• added a big new workflow based for doing NA-MD with TD-DFT states,
  using CP2K, DFTB+ (TD-DFTB), or Gaussian codes that can now play with Libra.
  one can use many-body (TD-DFT) or single-particle (individual Slater determinants)
  wavefunctions. This workflow is to be documented in paper to come out soon.
  This workflow relies heavily on the use of the "cube" files to compute time-overlaps.
• added a new stochastic state tracking/reordering algorithm, the details will be
  reported in another paper to come out soon
• the DISH is re-implemented correctly, but still needs to be tested and benchmarked
• revised, extended, and made consistent the set of the dynamics control parameters
  for the dynamics controlled by the C++-level Dynamics module.
• fixed bugs with the thermostat
• allow thermostatting of arbitrary DOFs
• allow arbitrary partitioning of quantum and classical nuclear DOFs
• allow constraining nuclear DOFs
• improved and generalized the plotting functions for TSH and PES scan results
• generalized calculations of the matrix elements with Hellers GWPs
• added new model Hamiltonians: generalization of the "Holstein"/spin-boson Hamiltonian,
  multi-dimensional Parandekar-Tully-like models

HEOM in Libra

• tsh, heom, and exact dynamics (on the grid) module are systematically organized in the libra_py/dyn
• the clean and tested HEOM module
• significantly improved the functionality of the exact quantum dynamics module
• Colbert-Miller DVR
• NBRA-LZ for TD-DFTB+ codes
• adopted MolSSI cookiecutter strategies for documenting and maintaining the code

Although this release has added many features, we consider it a snapshot for the first official release of the HEOM module.

First official indexed release

v4.4.0

Pre-deposition to the code ocean