final commit

docs/apidoc/classes.rst

@@ -1,6 +1,19 @@
 Classes
 =======
 
+Linear Combination of Atomic Orbitals
+--------------------------------------
+
+.. currentmodule:: qDNA.lcao
+
+.. autoclass:: Base
+   :members:
+
+.. autoclass:: BasePair
+   :members:
+
+.. autoclass:: Dimer
+   :members:
 
 DNA Sequence
 ------------
@@ -9,16 +22,14 @@ DNA Sequence
 
 .. autoclass:: DNA_Seq
    :members:
-   :noindex:
 
-Tight-binding model
+Tight-binding Model
 -------------------
 
 .. currentmodule:: qDNA.model
 
 .. autoclass:: TB_Model
    :members:
-   :noindex:
 
 Tight-binding Hamiltonian
 -------------------------
@@ -27,16 +38,6 @@ Tight-binding Hamiltonian
 
 .. autoclass:: TB_Ham
    :members:
-   :noindex:
-
-Master equation solver
-----------------------
-
-.. currentmodule:: qDNA.dynamics
-
-.. autoclass:: ME_Solver
-    :members:
-    :noindex:
 
 Lindblad Dissipator
 -------------------
@@ -45,4 +46,11 @@ Lindblad Dissipator
 
 .. autoclass:: Lindblad_Diss
    :members:
-   :noindex:
+
+Master Equation Solver
+----------------------
+
+.. currentmodule:: qDNA.dynamics
+
+.. autoclass:: ME_Solver
+    :members:

docs/apidoc/functions.rst

@@ -1,15 +1,21 @@
 Functions
 =========
 
-Linear Combination of Atomic Orbitals (LCAO)
---------------------------------------------
+Calculate Tight-Binding Parameters
+----------------------------------
 
 .. automodule:: qDNA.lcao
    :members: calc_orbital_energy, calc_orbital_overlap, load_xyz, convert_json_to_xyz, convert_pdb_to_xyz, calc_tb_energies_monomers, calc_tb_params_dimer, calc_tb_params
    :show-inheritance: False
 
+Save and Load Tight-Binding Parameters
+--------------------------------------
+
+.. automodule:: qDNA.hamiltonian
+   :members: save_tb_params, load_tb_params, wrap_save_tb_params, wrap_load_tb_params
+   :show-inheritance: False
 
-Tight-binding Basis
+Tight-Binding Basis
 -------------------
 
 There are three relevant bases:
@@ -24,78 +30,67 @@ The first two are refered to as `local` bases, the third as the `global` basis.
    :members: get_tb_basis, get_eh_basis, get_eh_distance, get_particle_eh_states, basis_change, local_to_global, global_to_local
    :show-inheritance: False
 
-Tight-binding Configuration
+Tight-Binding Configuration
 ---------------------------
 
 .. automodule:: qDNA.model
    :members: get_tb_config
    :show-inheritance: False
-   :noindex:
 
-Tight-binding Hamiltonian
+DNA sequences
+-------------
+
+.. automodule:: qDNA
+   :members: create_upper_strands
+   :show-inheritance: False
+
+Tight-Binding Hamiltonian
 -------------------------
 
 .. automodule:: qDNA.hamiltonian
    :members: set_matrix_element, tb_ham_1P, tb_ham_2P, add_groundstate, delete_groundstate, add_interaction
    :show-inheritance: False
-   :noindex:
 
-Save and load tight-binding parameters
---------------------------------------
+Lindblad rates
+--------------
 
-.. automodule:: qDNA.hamiltonian
-   :members: save_tb_params, load_tb_params, wrap_save_tb_params, wrap_load_tb_params
+These functions is adapted from the quantum_HEOM GitHub repository :cite:`Abbott2020`.
+
+.. automodule:: qDNA.environment
+   :members: debye_spectral_density, ohmic_spectral_density, bose_einstein_distrib, dephasing_rate
    :show-inheritance: False
-   :noindex:
 
+Lindblad operators
+------------------
+
+.. automodule:: qDNA.environment
+   :members: get_relax_op, get_glob_therm_op, get_glob_therm_ops, get_loc_therm_op, get_loc_therm_ops, get_loc_deph_ops, get_glob_deph_ops, get_loc_deph_p_ops, get_glob_deph_p_ops
+   :show-inheritance: False
 
-Reduced density matrix
+Master Equation Solver
 ----------------------
 
 .. automodule:: qDNA.dynamics
-   :members: get_reduced_dm, get_reduced_dm_eigs
+   :members: get_me_solver
    :show-inheritance: False
 
-Master equation solver
+Reduced Density Matrix
 ----------------------
 
 .. automodule:: qDNA.dynamics
-   :members: get_me_solver
+   :members: get_reduced_dm, get_reduced_dm_eigs
    :show-inheritance: False
-   :noindex:
 
-
-Exciton Lifetime
-----------------
+Exciton Observables
+-------------------
 
 .. automodule:: qDNA.evaluation
    :members: calc_lifetime, calc_lifetime_dict
    :show-inheritance: False
 
-Average charge separation
--------------------------
-
 .. automodule:: qDNA.evaluation
    :members: calc_dipole, calc_dipole_wrapper, calc_dipole_dict
    :show-inheritance: False
-   :noindex:
-
-Equilibrium states
-------------------
-
-.. automodule:: qDNA.evaluation
-   :members: get_therm_eq_state, get_deph_eq_state
-   :show-inheritance: False
-   :noindex:
-
-
-DNA sequences
--------------
-
-.. automodule:: qDNA
-   :members: create_upper_strands
-   :show-inheritance: False
-
 
 Observables
 -----------
@@ -104,20 +99,9 @@ Observables
    :members: get_tb_observable, get_eh_observable, get_pop_particle, get_coh_particle
    :show-inheritance: False
 
-Lindblad rates
---------------
-
-This module is adapted from the quantum_HEOM GitHub repository :cite:`Abbott2020`.
-
-.. automodule:: qDNA.environment
-   :members: debye_spectral_density, ohmic_spectral_density, bose_einstein_distrib, dephasing_rate
-   :show-inheritance: False
-   :noindex:
-
-Lindblad operators
+Equilibrium states
 ------------------
 
-.. automodule:: qDNA.environment
-   :members: get_relax_op, get_glob_therm_op, get_glob_therm_ops, get_loc_therm_op, get_loc_therm_ops, get_loc_deph_ops, get_glob_deph_ops, get_loc_deph_p_ops, get_glob_deph_p_ops
+.. automodule:: qDNA.evaluation
+   :members: get_therm_eq_state, get_deph_eq_state
    :show-inheritance: False
-   :noindex:

docs/apidoc/plotting.rst

@@ -14,21 +14,17 @@ Plot Eigenspectrum
 .. automodule:: qDNA.visualization
    :members: plot_eigv, plot_eigs
    :show-inheritance: False
-   :noindex:
 
 Plot Fourier Analysis
 ---------------------
 
 .. automodule:: qDNA.visualization
    :members: plot_fourier, plot_average_pop
    :show-inheritance: False
-   :noindex:
-
 
 Plot Poulations and Coherences
 ------------------------------
 
 .. automodule:: qDNA.visualization
-   :members: plot_pop_fourier, plot_pop, plot_pops, plot_coh, plot_test_fourier
+   :members: plot_pop_fourier, plot_pop, plot_pops,  plot_pops_heatmap, plot_coh, plot_test_fourier
    :show-inheritance: False
-   :noindex:

docs/apidoc/utils.rst

@@ -14,12 +14,10 @@ Hamiltonian Analysis
 .. automodule:: qDNA.utils
    :members: calc_average_pop, calc_amplitudes, calc_frequencies, get_pop_fourier, calc_ipr_hamiltonian
    :show-inheritance: False
-   :noindex:
 
 Density Matrix Analysis
 -----------------------
 
 .. automodule:: qDNA.utils
    :members: calc_trace_distance, calc_purity, calc_coherence, calc_ipr_dm
    :show-inheritance: False
-   :noindex:

docs/guide/guide.rst

@@ -23,21 +23,17 @@ Below is a list of available tutorials. Click on each to access the detailed not
 .. toctree::
    :maxdepth: 1
 
-   PRE_2024 <tutorials/PRE_2024>
    Tight Binding Parameters <tutorials/1_Tight_Binding_Parameters>
    Tight Binding Method <tutorials/2_Tight_Binding_Method>
    Environment Simulation <tutorials/3_Environment_Simulation>
    Visualization <tutorials/4_Visualization>
    Evaluation <tutorials/5_Evaluation>
    Reproduce Papers <tutorials/6_Reproduce_Papers>
+   PRE_2024 <tutorials/PRE_2024>
 
 Descriptions
 ------------
 
-**PRE2024**
-  Reproduces all the figures presented in the reference paper :cite:`Herb2024`.
-  This serves as a comprehensive example of `qDNA`'s visualization and analysis features.
-
 **Tight Binding Parameters**
   Learn the Linear Combination of Atomic Orbitals (LCAO) approach using Slater–Koster two-center
   integrals and Harrison-type expressions. Ideal for tight-binding model parameterization.
@@ -64,11 +60,15 @@ Descriptions
   :cite:`Bittner2007`, :cite:`Simserides2014` and :cite:`Mantela2023` using the `qDNA` package. This tutorial
   demonstrates the package's capabilities in generating results that have already been published elsewhere.
 
+**PRE2024**
+  Reproduces all the figures presented in the reference paper :cite:`Herb2024`.
+  This serves as a comprehensive example of `QuantumDNA`'s visualization and analysis features.
+
 
 Getting Started
 ===============
 
-These tutorials provide hands-on examples designed to guide you through using the `qDNA` package effectively. To get started:
+These tutorials provide hands-on examples designed to guide you through using the `QuantumDNA` package effectively. To get started:
 
 1. Navigate to the `tutorials` folder and open the desired `.ipynb` file in Jupyter Notebook or JupyterLab.
 2. Follow the instructions provided in the notebook to run the cells and explore the package's features interactively.
@@ -79,8 +79,8 @@ Tips for Using the Tutorials
 ----------------------------
 
 - **Run in a Jupyter Environment**: Ensure you have Jupyter Notebook or JupyterLab installed to execute the tutorials interactively.
-- **Dependencies**: Before starting, confirm that all dependencies for `qDNA` are installed. Check the `requirements.txt` file in the repository for details.
+- **Dependencies**: Before starting, confirm that all dependencies for `QuantumDNA` are installed. Check the `requirements.txt` file in the repository for details.
 - **Explore Further**: Modify and experiment with the code to deepen your understanding of the concepts.
 
 
-We hope these tutorials help you leverage the full potential of the `qDNA` package for your quantum biology research!
+We hope these tutorials help you leverage the full potential of the `QuantumDNA` package for your quantum biology research!