Tutorials_Libra

Tutorials showcasing various capabilities of Libra

Working with version v4.8.1

TOC

1. Rigid body

• 1.1. Construct & describe properties of rigid bodies

2. Integrators

• 2.1. Runge-Kutta 4-th order

3. Linear Algebra

• 3.1. operations with VECTOR, MATRIX, and CMATRIX data types

4. Optimization

• 4.1. Gradient descent optimizer
• 4.2. line search using DIIS

5. Electronic Structure Calculations in Libra

• 5.1. Extended Huckel Theory, EHT

  • 5.1.1. Compact version
  • 5.1.2. Detailed version

• 5.2. Incomplete Neglect of Differential Overlap, INDO

  • 5.2.1. Compact version

6. Dynamics with Libra

• 6.1. Quantum-classical, trajectory methods

  • 6.1.1. Model, adiabatic MD
    • 6.1.1.1. NVE ensemble
    • 6.1.1.2. NVT ensemble
      • 6.1.1.2.1 1 electronic state
  • 6.1.2. Model, common approach to adiabatic, Ehrenfest, and TSH
  • 6.1.3. Model, Ehrenfest recipes

• 6.2. Quantum-classical, neglect-of-back-reaction trajectory workflows

  • 6.2.1. step 1 with DFTB+
  • 6.2.2. step 1 with QE
  • 6.2.3. step 2 with QE
  • 6.2.4. step 3
    • 6.2.4.1 build_SD_basis

• 6.3. Hierarchical equations of motion, HEOM

• 6.4. DVR, on-the-grid wavepackets

• 6.5. Fermi Golden Rule rates, FGR

7. Special Functions

• 7.1. Sorting, matrix statistics

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Use cases

1. Create a chemical system

• 5.1.1.

2. EHT calculations with Libra

• 5.1.1.

3. INDO calculations with Libra

• 5.2.1.

4. Compute .cube files from orbitals computed with Libra

• 5.1.1.
• 5.2.1.

5. Visualize the MOs from .cube files

• 5.1.1.
• 5.2.1.

6. Compute pDOS from built-in electronic structure calculations in Libra

• 5.1.1.

7. Plot pDOS computed with Libra

• 5.1.1.

8. Visualize MD trajectory with py3Dmol:

• 6.2.1.

9. Constructing the vibronic Hamiltonian from the QE MD calculations:

• 6.2.3.

10. Reading the vibronic Hamiltonian data files to obtain its properties:

• 6.2.3.
• 6.2.4.1.

11. Compute the time-averaged nonadiabatic couplings of the vibronic Hamiltonian:

• 6.2.3.
• 6.2.4.1.

12. Manually construct a Slater Determinant basis:

• 6.2.4.1.

13. Using Libra to auto-generate a Slater Determinant basis:

• 6.2.4.1.

14. Compute the energies and nonadiabatic couplings in the SD basis:

• 6.2.4.1.

15. Calculate population and coherence dynamics of a quantum system embedded in a bath

• 6.3.1.

16. Calculate absorbance spectral lineshapes of a quantum system embedded in a bath

• 6.3.1.

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Functions

• liblibra::libqm_tools

  • charge_density 5.1.1.
  • compute_dos 5.1.1.

• libra_py

  • LoadMolecule

    • Load_Molecule 5.1.1.

  • LoadPT

    • Load_PT 5.1.1.

  • pdos

    • libra_pdos 5.1.1.

  • workflows

    • nbra
      • step2
        • run 6.2.3.
      • step3
        • build_SD_basis 6.2.4.1.
        • run 6.2.4.1.

  • QE_methods

    • out2inp 6.2.3.

  • hpc_utils

    • distribute 6.2.3.

  • data_read

    • get_data_sets 6.2.3.

  • data_stat

    • cmat_stat2 6.2.3.

  • dynamics

    • heom
      • compute
        • run_dynamics6.3.1.

  • ft

    • ft26.3.1.

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Classes and class members

• liblibra::libcontrol_parameters::Control_Parameters 5.1.1.

• liblibra::libchemobjects

  • libchemsys::System

    • Number_of_atoms 5.1.1.
    • get_xyz 5.1.1.

  • libuniverse::Universe 5.1.1.

• liblibra::libhamiltonian::libhamiltonian_atomistic::libhamiltonian_qm

  • listHamiltonian_QM

    • compute_scf 5.1.1.
    • get_electronic_structure 5.1.1.
    • basis_ao 5.1.1.
    • atom_to_ao_map 5.1.1.

  • Electronic_Structure

    • Nelec 5.1.1.
    • Norb 5.1.1.
    • get_bands_alp 5.1.1.
    • get_bands_bet 5.1.1.
    • get_occ_alp 5.1.1.
    • get_occ_bet 5.1.1.