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Recent Releases of libra-code

libra-code - Libra v5.10.1: Bohmian dynamics, PyTorch DVR, FISH, revised atomistic workflows

Human-added content

Major additions:

  • Bohmian dynamics module in PyTorch - uses multivariate Cauchy-Lorentz trajectory basis functions to represent the probability density, automatic differentiation to compute derivatives needed to construct quantum potential and differentiate it to obtain quantum forces, uses partial vectorization for efficiency; this release comes with the revision of the manuscript "Stable Direct Dynamics with Quantum Potential: Lorentzian Trajectory Basis Function is All You Need" that describes the methodology and shows the method's performance;
  • Highly-efficient DVR solvers via PyTorch - implement exact numerical solution of TD-SE for adiabatic and non-adiabatic dynamics. Way faster than the previous C++ implementation. Very convenient to use as well.
  • NA-MD recipes - a collection of standardized recipes defining various quantum-classical methodologies now comes with Libra. This should minimize the inconsistencies of defining such recipes by different users.
  • FISH (fully-integrated surface hopping) - this method was already available in the previous version, but now it is finalized with few minor fixes. The relevant publication is now available: Han, D.; Shakiba, M.; Akimov, A. V. "Fully-Integrated Surface Hopping as Quantum Decoherence Correction in Nonadiabatic Dynamics" J. Phys. Chem. Lett. 2025, 16, 28, 7168–7176
  • LDR (local diabatic representation) approach for exact quantum dynamics on a grid - a new module written in PyTorch is added and is nearly finalized, the corresponding article in preparation.
  • Interface to ODIN code for correct calculations of time-overlaps with DFTB+ - this is now added, the corresponding DFTB+/Libra interface and workflows are revised. In general, this helps obtain significantly more reasonable results than before, but care should be exercised when using SK files - only correctly-generated ones can be used.
  • Revised atomistic workflows - in particular, the calculations of the overlaps and time-overlaps of Slater determinants is now corrected, the mapping functions are revised, the phase factors previously given in the code are dropped. This does affect the calculations of TD-DFT overlaps and time-overlaps, and helps minimize the presence of "sudden jumps" in population dynamics. At the same time, our tests show that previous workflow still yielded close numerical results in many cases

Minor changes and additions:

  • improved documentation, especially regarding the installation procedures,
  • fixed bugs in Ferretti's model
  • added several model Hamiltonians written with PyTorch
  • fixed CITATION.cff for Zenodo compatibility

Auto-generated content

What's Changed

  • Debug the Ferretti's model by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/254
  • Added the LDR solver with PyTorch by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/255
  • Fix coefficient initialization in LDR by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/256

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.9.0...v5.10.0 Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.10.0...v5.10.1

- Roff
Published by alexvakimov 10 months ago

libra-code - Libra v5.10.0: Bohmian dynamics, PyTorch DVR, FISH, revised atomistic workflows

Human-added content

Major additions:

  • Bohmian dynamics module in PyTorch - uses multivariate Cauchy-Lorentz trajectory basis functions to represent the probability density, automatic differentiation to compute derivatives needed to construct quantum potential and differentiate it to obtain quantum forces, uses partial vectorization for efficiency; this release comes with the revision of the manuscript "Stable Direct Dynamics with Quantum Potential: Lorentzian Trajectory Basis Function is All You Need" that describes the methodology and shows the method's performance;
  • Highly-efficient DVR solvers via PyTorch - implement exact numerical solution of TD-SE for adiabatic and non-adiabatic dynamics. Way faster than the previous C++ implementation. Very convenient to use as well.
  • NA-MD recipes - a collection of standardized recipes defining various quantum-classical methodologies now comes with Libra. This should minimize the inconsistencies of defining such recipes by different users.
  • FISH (fully-integrated surface hopping) - this method was already available in the previous version, but now it is finalized with few minor fixes. The relevant publication is now available: Han, D.; Shakiba, M.; Akimov, A. V. "Fully-Integrated Surface Hopping as Quantum Decoherence Correction in Nonadiabatic Dynamics" J. Phys. Chem. Lett. 2025, 16, 28, 7168–7176
  • LDR (local diabatic representation) approach for exact quantum dynamics on a grid - a new module written in PyTorch is added and is nearly finalized, the corresponding article in preparation.
  • Interface to ODIN code for correct calculations of time-overlaps with DFTB+ - this is now added, the corresponding DFTB+/Libra interface and workflows are revised. In general, this helps obtain significantly more reasonable results than before, but care should be exercised when using SK files - only correctly-generated ones can be used.
  • Revised atomistic workflows - in particular, the calculations of the overlaps and time-overlaps of Slater determinants is now corrected, the mapping functions are revised, the phase factors previously given in the code are dropped. This does affect the calculations of TD-DFT overlaps and time-overlaps, and helps minimize the presence of "sudden jumps" in population dynamics. At the same time, our tests show that previous workflow still yielded close numerical results in many cases

Minor changes and additions:

  • improved documentation, especially regarding the installation procedures,
  • fixed bugs in Ferretti's model
  • added several model Hamiltonians written with PyTorch

Auto-generated content

What's Changed

  • Debug the Ferretti's model by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/254
  • Added the LDR solver with PyTorch by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/255
  • Fix coefficient initialization in LDR by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/256

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.9.0...v5.10.0

- Roff
Published by alexvakimov 10 months ago

libra-code - v5.9.0

What's Changed

Human-generated description

  • this version contains the finalized version of QTSH - see the paper here: Han, D.; Martens, C. C.; Akimov, A. V. "Generalization of Quantum-Trajectory Surface Hopping to Multiple Quantum States" J. Chem. Theory Comput. 2025 20, 5022-5042 https://doi.org/10.1021/acs.jctc.4c01751
  • the restricted path integral (RPI) code and workflow is up - the manuscript is about to be submitted
  • autopep8 tool applied to all of the Pyhon files to cleanup the style
  • ongoing KC-RPMD developments
  • the TRPES ("time-resolved photoelectron spectrogram") plotting script is added
  • active state calculations from the LD - a small but potentially far-going fix
  • added plotting of UV-vis/PDOS/energy vs time and population dynamics
  • added Gu-Franco decoherence scheme
  • added correct GFSH (the prior one conceptually aligns with the GFSH, but may be technically different, which is indeed seen in some tests!)
  • some SQC and MMST variables and functions are added, but they are still in their infancy

Automatically-generated info

  • Debug the phenol model by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/235
  • Add coherence indicator calculating and plotting routines by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/236
  • Update base_matrix for AppleClang by @foxtran in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/234
  • Updated Code: added kcrpmd auxiliary variable variables as double vector by @suarez-va in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/240
  • Update CMakeLists by @foxtran in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/237
  • add fucntion for UV-Vis spectrum by @SpringDabao in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/238
  • added kcrpmdvarsstatus and allocate_kcrpmd() to libdyn.cpp, added placeholders for kcrpmd effective potential by @suarez-va in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/241
  • Add the force options in QTSH by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/243
  • Added new generatemmatrices() function, temporarily just copying children hamiltonian by @suarez-va in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/245
  • added remaining KC-RPMD potential functions, effective potential now working by @suarez-va in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/247
  • step4 plot by @KosarYasin in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/249
  • Add the missing scipy.sparse dependency to trpes.py by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/250
  • Restructured code to minimize number of function calls, added in KCRPMD forces. Created new RPMD file for general RPMD calls by @suarez-va in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/252
  • Add the RPI workflow by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/253

New Contributors

  • @suarez-va made their first contribution in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/240
  • @KosarYasin made their first contribution in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/249

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.8.1...v5.9.0

- Roff
Published by alexvakimov about 1 year ago

libra-code - Libra v5.8.1

What's Changed

Human-generated description:

  • Cleaned up and optimized the F-tracking and tNAC phase correction methodologies, added some experimental functions related to it;
  • libint2 wrapper of higher moments in GTO basis (x, y, z, x^2, xy, ... z^3);
  • important bug fixes in the molint implementation of some integrals with Gaussian functions, added the corresponding documentation/derivations;
  • ChatGPT-generated implementation of the Munkres-Kuhn algorithm;
  • Added new model Hamiltonian for phenol molecule;
  • on-going development of the QTSH methodology
  • added a good amount of testing modules for pytest (at the Python level)
  • multiple minor and not-so-minor fixes and language style impovements, adding clang support by @foxtran

Automatically-generated info:

  • Add diabatic hop features to FSSH-2 and FSSH-3 by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/218
  • Skipping the active state computation in the other rep if not necessary by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/219
  • Spin adapted configuration + bug fix for saving sd files by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/221
  • bug fix for CP2K pdos labels returning empty list by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/222
  • Fix the loop in printing 2D wavepackets by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/226
  • Minor fixes by @foxtran in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/224
  • Fix some compilation warnings/error by @foxtran in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/227
  • Fix qtag_potential: two overloads with and without AA-BB-CC by @foxtran in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/228
  • add function for fitting population by @SpringDabao in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/231
  • Add deco time test by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/230
  • New Libint functions for computing the integrals in GTOs with Cartesian moment operators by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/229
  • Bug fix for step 2 file saving and extension of states Slater determinants in step 3 by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/233

New Contributors

  • @foxtran made their first contribution in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/224
  • @SpringDabao made their first contribution in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/231

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.8.0...v5.8.1

- Roff
Published by alexvakimov over 1 year ago

libra-code - Libra v5.8.0: F-tracking and simplified NAC phase correction

The main changes

  • The new F-tracking and simplified NAC phase correction are added and tested (the main reason for this release)

  • Libra/MOPAC interface is developed but is yet to be demonstrated;

  • QTSH is implemented but is yet to be demonstrated

  • A critical bugfix in the step3 of Libra/cp2k interface - to possibly help solve the sudden jump problems we have observed recently

  • The documentation of the main function in libra_py.dynamics.tsh.compute is updated and is now consistent with the parameters of the dyn_control_params class.

  • Surface hopping in diabatic representation is added and is being tested by Daeho Han; within this development, new variable to hold active diabatic state indices for all trajectories are added. Several ways of computing diabatic populations are added: based on counting trajectories and on transformation of adiabatic SE or SH populations.

  • Added auxiliary function to determine the active space selection in step3 of Libra/cp2k interface.

More formal changelog:

  • Update QTSH by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/212
  • Bug fixes for ML workflow, step3, CP2K methods and data reading for BLLZ by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/213
  • Added an auxiliary function to step 3 for generating new active spaces based on the number of occupied and unoccupied orbitals by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/214
  • Reuse the rep_sh param to consider hops in the diabatic representation by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/215
  • Bug fixes for step3 many-body by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/216

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.7.1...v5.8.0

- Roff
Published by alexvakimov almost 2 years ago

libra-code - Libra v5.7.1

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.7.0...v5.7.1

- Roff
Published by alexvakimov almost 2 years ago

libra-code - Libra v5.7.0

The major additions

  • the new FSSH-3 methodology is implemented
  • the FSSH-2 of Araujo et al. is implemented (with slight changes compared to the published version, but likely this is what was intended)
  • added Jasper-Truhlar criterion of velocity reversal on frustrated hops
  • added MD trajectory alignment function/script which processes the MD trajectory to remove the center of mass translation and the overall rotation of the molecule as whole (this is a Python re-interpretation of the Fortran code found in the auxiliary tools of NWChem)
  • added a number of published spin-boson (and their many-state generalization) models withing the GLVC (generalized linear vibronic coupling models)
  • implemented the Ohmic and Drude-Lorentz baths discretizations
  • implemented a correct way of computing SH-based diabatic populations of states
  • revised the way to initialize adiabatic states when the initial conditions are chosen in the diabatic representation
  • added a number of matrix decompositions and linear equations solvers (based on matrix decompositions) from Eigen 3 code
  • fixed bugs in sumcol and sumrow functions of generic matrix class
  • significantly accelerated calculations of the matrix of the SD overlaps but using numpy methods in step3 module of the NBRA workflow (see below)
  • implemented a lot of the functions and workflow for the ML-based prediction of KS Hamiltonians (see below)
  • ongoing work on clarifying the MFSD (see below)

Auto-generated updates

  • Update MFSD by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/207
  • Use act_states for saving the reference state of MFSD by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/208
  • Kohn-Sham Hamiltonian mapping with machine-learning first version by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/209
  • Revision of step3 and high-throughput implementation of KS ML map approach by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/210

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.6.0...v5.7.0

- Roff
Published by alexvakimov about 2 years ago

libra-code - v5.6.0

Final version of the XF-based methods (SHXF, MQCXF, and MFXF), coming along with the manuscript submission.

Major implementation was done already in the previous implementations. The present version ensures the consistency of some underlying transformation.

What's Changed

  • XF propagations for the LD scheme by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/200
  • New functions in dataread and moldenmethods by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/201
  • Update the XF algorithms by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/202
  • Fixing time propagation in XF by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/204
  • Fix the reordering of phase gradients by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/205
  • Elaborate on the comments about the td widths by @DaehoHan in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/206

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.5.0...v5.6.0

- Roff
Published by alexvakimov about 2 years ago

libra-code - Libra with TC-NBRA, MASH, FSSH2, revDISH, revised TSH and Ehrenfest, phase-corrected exact calculations

1. Structural changes and paradigm changes

  • Restructured the libra_py library to set all the package-specific modules into a separate sub-library. Adapted importing libraries based on packages folder

  • Simplified the interface of hop proposal, hop acceptance, and hop handling functions, as well as dish - these all are now taking the dyn_variables input rather than individual variables of all kinds

  • Moved DISH coherence time updates inside dish function, added other decoherence options although they are not doing anything - just for completeness

2. New major capabilities

  • [src/nHamiltonian and src/dyn]: The phase/state-consistency transformations (a.k.a local diabatization transformations) are now applied directly to element of the nHamiltonian object right after the new diabatic-to-adiabatic transformation is computed they are removed right before re-computing the time-overlaps at the next dynamical step. This way, the Hamiltonian properties are well-behaved and can be used both the TSH and Ehrenfest methods. This makes the Ehrenfest method conserve energy even in the adiabatic basis when NACs are used, as well as using the NAC-based integrators in the TD-SE integration of the TSH methods. This is a very critical change that hopefully makes the current implementation more reliable and robust than before.

  • [src/dyn]: added themrally-correct NBRA (TC-NBRA) approach

  • [src/dyn]: initial implementations of the Exact Factorization (XF) and mixed quantum-classical XF (MQCXF) methods

  • [src/dyn]: Implemented MASH scheme

  • [src/dyn]: Implemented FSSH2 scheme of Leonardo Araujo

  • [src/dyn]: A new implementation of the DISH method, it is suitable for NBRA workflow too

  • [src/dyn/wfcgrid2]: Added a phase-consistency correction to the diabatic-to-adiabatic transformation matrices computed at all grid points. This change is important since otherwise the kinetic energy calculations won't converge with dx due to highly-oscillatory behavior of the wavefunction in regions of strong nonadiabaticity. With this correction, the energy conservation is now much more robust and the convergence of kinetic energy w.r.t. the grid's dx is achieved. The wavefunctions are well-behaved too.

  • [src/math_meigen]: Added Cholesky decomposition of real matrices

  • [libra_py.models]: Added Ferretti Hamiltonian

  • [src/dyn]: added Voronoi tesselaiton scheme and initial conditions sampling based on it

  • [libra_py.dynamics.exact]: Added a new capability to the exact propagation function to save the wavefunction snapshots into files for their later plotting and animation. Updated the corresponding functions' documentation.

  • [libra_py.packages.cp2k.methods]: Added analysis function for pdos, exc analysis, energy vs time to CP2K methods

3. Improvements and new minor capabilities

Dynamics

  • Made the velocity rescaling happening only if the initial and final states are different

  • Added the option to save the derivative coupling vectors along the trajectory

CP2K and NBRA

  • Fixed the cp2k input generator script so that the calculations are more robust, correct, and lead to convergences

  • Added new functionality to CP2K input generator for hybrid functionals

  • Updated CP2K input generator

  • Added new functions for computing MO coefficients + description of functions

  • Added "restartfile" parameter for step2. It is useful for big systems to have the initial guess of SCF orbitals

  • Added isUKS implementation of open-shell systems. In Step3 of cp2k interacing-code, modified some functions to account for systems with different numbers of electrons in alpha and beta channels.

QTSH

  • implemented an auxiliary function needed in kinematic momentum calculations for QTSH

GWP

  • added derivatives of the GWP functions, in a somewhat different style

4. Bug fixes and documentation

src/dyn

  • Fixed the bug with the velocity rescaling of only the quantum nuclear DOFs

  • Fixed some bug that was breaking even normal FSSH, modified interface of the hop acceptance function to give a bit more flexibility

src/nHamiltonian

  • Fixed a bug in the copy_content function of the nHamiltonian class where it would copy diabatic time-overlap into the adiabstic one, also added new functions to transform the elements of the nHamiltonian class according to certain transformation matrix, there are several kinds of such transformations with the same matrix - forward,backward, explicit, implicit or normalizing

DISH

  • fixed a bug in the existing implementation of the DISH method

QTAG

  • Adding a careful documentation and somewhat revising the interfaces of the QTAG functions, added new auxiliary ones

Models

  • Fixed a bug in Holstein_gen function that would create an incorrect size of the first derivatives matrix

CP2K

  • Added some documentation in the cp2k input generation module

  • Fixed reading of TDDFT data in CP2K v23 - a very important fix, because it sometimes led to strange energies, especially of the ground state.

MFSD

  • Fixed the implementation of the Shwartz decoherence times, also included the options to account for the local diabatization approximation in computing MF forces, added some documentation on the related functions, fixed some bugs in MFSD - the effective NAC calculations, momentum rescaling. The momentum rescaling and corresponding Hamiltonian update functions are also added in the main dynamics module for MFSD. Fixed more bugs in the mfsd code - the calculations of the Ehrenfest energies was not done correctly. Also, fixed the generic code for computing Ehrenfest energies - need to split by the trajectories

dynamicsplotting and datavisualize

  • updated the decomentation of the dynamics_plotting function that plots surface and fixed a bug of not having the output directory to store figures produced

  • Revised dynamicsplotting and datavisualize modules, added some documentation, added new member functions to the dyn_variables class

step2 of NBRA

  • Fixed the reindexing function for isUKS=True

step3 of NBRA

  • Debugging and revisiting mapping functions for Slater determinant calculations of NACs Added new mapping module with fully revised math and simplified interface

DFTB+

  • Fixed some functions in DFTB+ package for it to be used in current NA-MD procedures, added documentation, got rid of the critical params, replaced them by default onese, fixed a minor bug in the dftb runstep2 function so the overlaps are now correct, changed the number of result objects returned by the dostep function

  • Fixed the DFTB+ methods for reading time-overlap matrices - made them more robust to the known problem of having NaN and wrong values in the off-diagonal blocks of the super-molecule overlap matrix calculations

FT

  • Updated the documentation of the ft2 function in the ft module

5. Cleaning up

  • Removed deprecated dynamics tutorials

  • Removed the DFTB time-overlap calculation tutorials. Moved the tutorial to the Tutorials_Libra repo and revised it

  • Removed excessive output from libint2 code

  • Cleaned up some commented and unnecessary code in the Dynamics.cpp and related files

  • Revised the LZ workflow, removed deprecated or obsolete functionality and keywords

  • Removed the examples of ACF and FT calculations. Now moved to the Tutorials_Libra repository

- Roff
Published by alexvakimov over 2 years ago

libra-code - 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 computedynamics function and reflected that in the Python wrapper function, changed the computeSt 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
    • updateHamiltonian 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, EnergyandForces.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

- Roff
Published by alexvakimov about 3 years ago

libra-code - Libra with the QTAG method

The major changes/additions include: * added and validated the quantum trajectory adaptable Gaussian (QTAG) methodology, including scripts and functions at both C++ and Python levels;

Other significant changes: * added new functions in the GWP library, needed for more convenient implementation of the QTAG; * implemented Meek-Levine's norm-preserving interpolation (NPI) algorithms to compute scalar NACs; * added new functions to the wfcgrid2 class - e.g. for finding the hyperplanes, adding complex absorbing potential, and more; * removed many tutorials/examples that have been moved to the Tutorials_Libra repository; * changes to the auxiliary functions for the TD-DFT excitation analysis, to reflect changes in cp2k software v9.1; * updated build instructions (cmake files) to correctly compile/build the code with the new libint2 library; * important bug fix of the NAC calculation workflow in the case of spin-polarized DFT calculations; * added new functions for computing the time-overlaps with ORCA and OpenMolcas;

- Roff
Published by alexvakimov over 3 years ago

libra-code - Revised xTB/Libra workflow

Major Changes

  • Revised the installation instructions and CMakeLists to work with the newer version of Libint2. Added links to the installation videotutorials.
  • Added the option to conduct the NBRA calculations without explicitly running many trajectories. In this case, one Hamiltonian is computed for each nuclear trajectory and re-used by many stochastic trajectories.
  • Fixed the bug in the step2 of the NBRA methodology with xTB/Libra, where S AO matrices were used instead of St AO matrices.
  • Fixed model Hamiltonians of Zhu in the models collection to correctly work in multi-trajectory settings
  • in the QTAG: added new LHAe and BATe routines.

What's Changed

  • Devel by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/153
  • Bug fixes + NBRA type calculations for step4 by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/154

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.2.0...v5.2.1

- Roff
Published by alexvakimov almost 4 years ago

libra-code - Libra with the xTB/NA-MD workflow

Major changes

  • Finalized and tested the xTB/NA-MD workflow:
    • used to conduct studies of Si QDs and C3N4 monolayer;
    • can now handle periodic systems
    • file storage optimizations
    • Improving the general NA-MD workflows
    • adding new recipes
    • new methods (e.g. MF-SD, BCSH, various decoherence times options)
    • new control parameters
  • QTAG
    • the key elements are implemented and working, but need more work on the user interface and better integration into C++ layer

What's Changed

  • Modified CP2K/Libra/Libint interface for DFT and xTB calculations by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/129
  • A new working version for step2 and step3 of the Libra/Libint interface by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/130
  • QTAG by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/132
  • Libra/CP2K workflow completed by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/133
  • bug fixes for single-particle SDs by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/134
  • Retry of qtag_ham.py changes by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/137
  • Devel by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/138
  • Devel by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/140
  • Nested dicts and getattr calls in Python QTAG by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/142
  • txt2 Saver Update + Dict Update by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/144
  • qtagmom, qtagprop updates by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/145
  • QTAG Docs Updates by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/146
  • Updated qtag/save.py by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/148
  • QTAG LHA Fix by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/149
  • qtag/save updates by @mdutra21 in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/150
  • Added cube visualizatio to step2 by @MohammadShakiba in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/151

New Contributors

  • @mdutra21 made their first contribution in https://github.com/Quantum-Dynamics-Hub/libra-code/pull/132

Full Changelog: https://github.com/Quantum-Dynamics-Hub/libra-code/compare/v5.1.0...v5.2.0

- Roff
Published by alexvakimov about 4 years ago

libra-code - 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

- Roff
Published by alexvakimov over 4 years ago

libra-code - 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

- Roff
Published by alexvakimov about 5 years ago

libra-code - 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

- Roff
Published by alexvakimov over 5 years ago

libra-code - 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

- Roff
Published by alexvakimov over 5 years ago

libra-code - 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.

- Roff
Published by alexvakimov about 6 years ago

libra-code - First official indexed release

- Roff
Published by alexvakimov over 6 years ago