Revise README for clarity and community support

Updated README to improve structure and clarity, added community support links, and revised citation instructions.

Author: alexvakimov

README.md

@@ -2,28 +2,26 @@
 
 [![Build Status](https://travis-ci.org/Quantum-Dynamics-Hub/libra-code.svg?branch=master)](https://travis-ci.org/Quantum-Dynamics-Hub/libra-code)
 
-
 This is the main page of the computational chemistry methodology discovery library, Libra
-The program website is [here](https://quantum-dynamics-hub.github.io/libra/index.html)
 
-## Info
+## About
 
-More:
+* [extensive tutorials, example, and documentation](https://github.com/compchem-cybertraining/Tutorials_Libra).
+This resource is actively developed, but the older tutorials may not fully reflect the current stage of the code itself, so the 
+tutorials demonstrating the older features may be failing - please let us know if you need to use any of those and run into problems.
 
-* [Training & Usage](https://github.com/compchem-cybertraining/Tutorials_Libra)
-* [Autogenerated Documentation](https://quantum-dynamics-hub.github.io/libra-code/)
+* [old program website](https://quantum-dynamics-hub.github.io/libra/index.html)
+Not maintained for long time, but may still contain some useful info on some topics
 
+## Community and Support
 
-Due to the increased volume of technical questions about installing and using the 
-Libra, Libra-X, Pyxaid and Pyxaid2 codes, I have decided to create a convenient 
-[public forum](https://groups.google.com/forum/#!forum/quantum-dynamics-hub)
-for all users with the intent:
+* Click below to join our community:
+👉 [Join Slack](https://join.slack.com/t/quantumdynamicshub/shared_invite/zt-mjbhjssx-GGhsbYHxeBMvhmumK_j7LA)
 
- - to share my replies with not only a single user that have a trouble, but also other
-   potential users who may found that information useful;
+* Open an Issue - to ask questions or report a problem
 
- - so that the users/developers who have had some experience with the code would be able to share their
-   knowledge and skills with others;
+* The following [public forum](https://groups.google.com/forum/#!forum/quantum-dynamics-hub) exists, but
+  hasn't been used for a while - use the Slack workspace instead
 
 
 ## Installation Videotutorials (as of 5/16/2022)
@@ -38,8 +36,6 @@ for all users with the intent:
 
 * [Installing Libra](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=7f8dd8c4-9f58-4ca0-a8cb-ae930166b7ec&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
 
-
-
 ## Installation (as of after 3/23/2023)
 
 ### 1. Install miniconda (for Python 3.9) and activate Conda
@@ -326,29 +322,79 @@ installation instructions:
 
 This code is provided in the hope it will be useful. 
 
-  If you use the code in your research, please cite the following paper(s):
-
-  ### Papers that describe Libra or its features 
+  If you use Libra in your research, please cite the following paper:
 
+  ### The "main" Libra papers 
+  * [More recent overview of Libra's capabilities](https://doi.org/10.1016/j.simpa.2022.100445)
+  Shakiba, M.; Smith, B.; Li, W.; Dutra, M.; Jain, A.; Sun, X.; Garashchuk, S.; Akimov, A.V.* "Libra: A modular software library for quantum
+  nonadiabatic dynamics" *Software Impacts* **2022**  14, 100445
+   
   * [The initial implementation](http://onlinelibrary.wiley.com/doi/10.1002/jcc.24367/full)
   Akimov, A. V. "Libra: An open-Source 'methodology discovery' library for quantum and classical dynamics simulations" 
   *J. Comput. Chem.*  **2016**  37, 1626-1649
 
-  * [Phase correction, Ehrenfest dynamics details, basis transformations (see the SI)](https://doi.org/10.1021/acs.jpclett.8b02826)
-  Akimov, A. V.; "A Simple Phase Correction Makes a Big Difference in Nonadiabatic Molecular Dynamics"
-  *J. Phys. Chem. Lett.*  **2018** 9, 6096-6102
+  If you use any of the Libra's methods or implementation, please cite as appropriate:
 
-  * [Belyaev-Lebedev-Landau-Zener Surface Hopping within the Neglect of Back-Reaction Approximation](https://pubs.acs.org/doi/10.1021/acs.jpclett.9b03687)
-  Smith, B.; Akimov, A. V. "Hot Electron Cooling in Silicon Nanoclusters via Landau-Zener Non-Adiabatic Molecular Dynamics: 
-  Size Dependence and Role of Surface Termination" *J. Phys. Chem. Lett.* **2020** 11, 1456-1465
+  ### Papers that describe various developments in Libra
+  * [FISH: Fully-integrated surface hopping](https://doi.org/10.1021/acs.jpclett.5c01509)
+  Han, D.; Shakiba, M.; Akimov, A. V. "Fully-Integrated Surface Hopping as Quantum Decoherence Correction in Nonadiabatic Dynamics"
+  *J. Phys. Chem. Lett.* **2025** 16, 7168-7176
+
+  * [Multiple-state QTSH](https://doi.org/10.1021/acs.jctc.4c01751)
+  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
+
+  * [F-tracking of excited states](https://pubs.acs.org/doi/10.1021/acs.jpclett.4c02909)
+   Akimov, A. V. "State Tracking in Nonadiabatic Molecular Dynamics Using Only Forces and Energies"
+   *J. Phys. Chem. Lett.* **2024** 15, 11944-11953
+    
+  * [FSSH-3, modified FSSH-2, implmenentation of GFSH](https://www.tandfonline.com/doi/full/10.1080/00268976.2024.2376893)
+  Akimov, A. V. "The Fewest Switches Surface Hopping as An Optimization Problem" *Mol. Phys.* **2024** e2376893
+
+  * [Exact Factorization methods: SHXF, MQCXF, MFXF](https://doi.org/10.1021/acs.jctc.4c00343)
+   Han, D.; Akimov, A.V. "Nonadiabatic Dynamics with Exact Factorization: Implementation and Assessment."
+   *J. Chem. Theory Comput.* **2024** 20, 5022–5042
+
+  * [ML Hamiltonian mapping approach](https://doi.org/10.1021/acs.jctc.4c00008)
+  Shakiba, M.; Akimov, A.V. "Machine-Learned Kohn–Sham Hamiltonian Mapping for Nonadiabatic Molecular Dynamics."
+  *J. Chem. Theory Comput.* **2024** 20, 2992–3007
+
+  * [TC-NBRA](https://doi.org/10.1021/acs.jpclett.3c03029)
+  Akimov, A.V. "Energy-Conserving and Thermally Corrected Neglect of Back-Reaction Approximation Method for Nonadiabatic Molecular Dynamics"
+  *J. Phys. Chem. Lett.* **2023** 14, 11673-11683
+
+  * [QTAG](https://doi.org/10.1002/qua.27078)
+  Dutra, M.; Garshchuk, S.; Akimov, A. "The Quantum Trajectory-guided Adaptive Gaussian Methodology in the Libra Software Package"
+  *Int. J. Quntum Chem.* **2023.** 123, e27078
+
+  * [(generalized) Local diabatization](https://doi.org/10.1007/s00214-023-03007-7)
+  Shakiba, M.; Akimov, A.V. "Generalization of the Local Diabatization Approach for Propagating Electronic Degrees of Freedom in Nonadiabatic Dynamics"
+  *Theor. Chem. Acc.* **2023** 142, 68
+
+  * [xTB from cp2k/Libra interface for NA-MD in large-scale systems, k-point formulation, spin-adaptation](https://doi.org/10.1021/acs.jctc.2c00297)
+  Shakiba, M.; Stippel, E.; Li, W.; Akimov, A. V. "Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding:
+  Application to Nanocrystals and Periodic Solids" *J. Chem. Theory Comput.* **2022** 18, 5157-5180
+
+ * [many-body effects, NA-MD with TD-DFT states](https://pubs.acs.org/doi/10.1021/acs.jctc.0c01009)
+  Smith, B.; Shakiba, M.; Akimov, A. V. "Nonadiabatic Dynamics in Si and CdSe Nanoclusters: Many-Body vs. Single-Particle
+  Treatment of Excited States" *J. Chem. Theory. Comput.* **2021** 17, 678-693
 
   * [HEOM implementation](https://pubs.acs.org/doi/10.1002/qua.26373)
   Temen, S.; Jain, A.; Akimov, A. V. "Hierarchical equations of motion in the Libra software package"
-  *Int. J. Quant. Chem.* **2020**
+  *Int. J. Quant. Chem.* **2020** 120, e26373
+
+  * [Belyaev-Lebedev-Landau-Zener Surface Hopping within the Neglect of Back-Reaction Approximation](https://pubs.acs.org/doi/10.1021/acs.jpclett.9b03687)
+  Smith, B.; Akimov, A. V. "Hot Electron Cooling in Silicon Nanoclusters via Landau-Zener Non-Adiabatic Molecular Dynamics: 
+  Size Dependence and Role of Surface Termination" *J. Phys. Chem. Lett.* **2020** 11, 1456-1465 
+
+  * [Phase correction, Ehrenfest dynamics details, basis transformations (see the SI)](https://doi.org/10.1021/acs.jpclett.8b02826)
+  Akimov, A. V.; "A Simple Phase Correction Makes a Big Difference in Nonadiabatic Molecular Dynamics"
+  *J. Phys. Chem. Lett.*  **2018** 9, 6096-6102
+
 
 
   You may find the following papers useful examples
-  ### Parers that utilize Libra
+  ### Papers that utilize Libra
 
   * [Formulation of a fragment-based NA-MD](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00955)
   Akimov, A. V. "Nonadiabatic Molecular Dynamics with Tight-Binding Fragment Molecular Orbitals"