dehe1011 · dehe1011 · Jun 23, 2026 · Jun 23, 2026 · Jun 23, 2026
diff --git a/docs/apidoc/apidoc.rst b/docs/apidoc/apidoc.rst
@@ -1,14 +1,22 @@
 .. _apidoc:
 
 *****************
-API documentation
+API Documentation
 *****************
 
-This chapter contains automatically generated API documentation, including a
-list of TensorHEOM's public classes and functions.
+This chapter contains automatically generated API documentation for all public
+classes and functions in TensorHEOM.
+
+The API is organised into two files:
+
+- **Classes & Module Functions** (:doc:`classes`) — the internal building blocks:
+  bath decomposition, pulse types, tensor-train classes, circuit compilation,
+  dynamics, and HPC utilities.
+- **Top-level Functions** (:doc:`functions`) — the functions you use most often,
+  importable directly via ``from ttheom import ...``.
 
 .. toctree::
    :maxdepth: 3
 
-   classes.rst
-   functions.rst
+   functions
+   classes
diff --git a/docs/apidoc/classes.rst b/docs/apidoc/classes.rst
@@ -1,30 +1,23 @@
-Classes & Functions
-===================
+Classes & Module Functions
+==========================
 
-This section provides an overview of the available classes and functions contained in the `TensorHEOM` package.
+This section documents TensorHEOM's internal classes and module-level
+functions, grouped by subsystem.
 
-Decomposition of bath auto-correlation functions
-------------------------------------------------
-
-.. currentmodule:: ttheom.bath
-
-.. autofunction:: getBathParams
-.. autofunction:: broadbandNoise
-
-Connection of quantum gates and pulse sequences
------------------------------------------------
+Pulse types and gate specifications
+-------------------------------------
 
 .. currentmodule:: ttheom.pulse
 
 .. autofunction:: setGates
 .. autofunction:: getGate
-.. autoclass:: directCplStepVarJ
-.. autoclass:: iSwapDPulse
 .. autoclass:: rxyStep
 .. autoclass:: U3Pulse
+.. autoclass:: iSwapDPulse
+.. autoclass:: directCplStepVarJ
 
-Tensor Train representation
----------------------------
+Tensor-train representation
+----------------------------
 
 .. currentmodule:: ttheom.tt
 
@@ -34,8 +27,8 @@ Tensor Train representation
 .. autoclass:: TTs2QId
 .. autoclass:: TTsMQChainId
 
-Compilation of Qiskit circuits to pulse sequences
--------------------------------------------------
+Circuit compilation
+-------------------
 
 .. currentmodule:: ttheom.circuit
 
@@ -54,15 +47,15 @@ Time evolution
 .. autofunction:: outputCurrentStates
 .. autofunction:: getRotatingRDO
 
-Running Simulations on HPC
---------------------------
+HPC cluster support
+--------------------
 
 .. currentmodule:: ttheom.ssh
 
-.. autofunction:: slurmShell
-.. autofunction:: slurmStatus
+.. autofunction:: submitJob
+.. autofunction:: downloadResult
+.. autofunction:: getClient
 .. autofunction:: commandsForSubmission
 .. autofunction:: getStatus
-.. autofunction:: getClient
-.. autofunction:: submitJob
-.. autofunction:: downloadResult
+.. autofunction:: slurmShell
+.. autofunction:: slurmStatus
diff --git a/docs/apidoc/functions.rst b/docs/apidoc/functions.rst
@@ -1,4 +1,41 @@
-Main Function
-=============
+Top-level Functions
+===================
 
-.. autofunction:: ttheom.main.main
+This section documents the public functions available at the top level of the
+``ttheom`` namespace (i.e., importable directly via ``from ttheom import ...``).
+
+High-level simulation interface
+--------------------------------
+
+.. currentmodule:: ttheom.main
+
+.. autofunction:: calcTimeEvo
+.. autofunction:: main
+
+Physical-unit helpers
+----------------------
+
+.. currentmodule:: ttheom.main
+
+.. autofunction:: prepareSystemArgs
+.. autofunction:: prepareBathArgs
+.. autofunction:: prepareGateArgs
+
+Bath decomposition
+------------------
+
+.. currentmodule:: ttheom.bath
+
+.. autofunction:: getBathParams
+.. autofunction:: broadbandNoise
+
+Evaluation and analysis
+-----------------------
+
+.. currentmodule:: ttheom.evaluation
+
+.. autofunction:: loadResult
+.. autofunction:: getFidelity
+.. autofunction:: getConcurrence
+.. autofunction:: getLogarithmicNegativity
+.. autofunction:: plotPulseSeq
diff --git a/docs/conf.py b/docs/conf.py
@@ -79,15 +79,25 @@
 
 # Options for HTML output
 html_theme = "sphinx_rtd_theme"
-html_static_path = []
+html_static_path = ["_static"]
+html_logo = "figures/logo.png"
+html_theme_options = {
+    "logo_only": False,
+    "prev_next_buttons_location": "bottom",
+    "collapse_navigation": False,
+    "sticky_navigation": True,
+    "navigation_depth": 3,
+}
 
-exclude_patterns = [
-    "_build",
-    "Thumbs.db",
-    ".DS_Store",
-]
+html_context = {
+    "display_github": True,
+    "github_user": "dehe1011",
+    "github_repo": "TensorHEOM",
+    "github_version": "main",
+    "conf_py_path": "/docs/",
+}
 
-# Syntax highlighing for code blocks in the documentation
+# Syntax highlighting for code blocks in the documentation
 pygments_style = "sphinx"
 
 # Do not add parentheses to function names in cross-references like :func:

diff --git a/docs/copyright.rst b/docs/copyright.rst
@@ -5,10 +5,10 @@ Copyright and Licensing
 ***********************
 
 The text of this documentation is licensed under the `Creative Commons Attribution 3.0 Unported License <https://creativecommons.org/licenses/by/3.0/>`_.
-Unless specifically indicated otherwise, all code samples, the source code of qDNA, and its reproductions in this documentation, are licensed under the terms of the 3-clause BSD license, reproduced below.
+Unless specifically indicated otherwise, all code samples, the source code of TensorHEOM, and its reproductions in this documentation, are licensed under the terms of the 3-clause BSD license, reproduced below.
 
 License Terms for Documentation Text
-====================================
+=====================================
 
 The canonical form of this license is available at `https://creativecommons.org/licenses/by/3.0/ <https://creativecommons.org/licenses/by/3.0/>`_, which should be considered the binding version of this license.
 It is reproduced here for convenience.
@@ -19,9 +19,9 @@ It is reproduced here for convenience.
 .. include:: LICENSE_cc-by-3.0.txt
 
 
-License Terms for Source Code of QuantumDNA and Code Samples
-============================================================
+License Terms for Source Code of TensorHEOM and Code Samples
+=============================================================
 
 ..
-    BSD-3-Clause/ MIT license
+    BSD-3-Clause license
 .. include:: ../LICENSE.txt
diff --git a/docs/gui/gui.rst b/docs/gui/gui.rst
@@ -1,30 +1,63 @@
 .. _guidoc:
 
-*****************
-GUI documentation
-*****************
+*******************************
+Graphical User Interface (GUI)
+*******************************
 
-This chapter contains documentation for the graphical user interface (GUI) which is designed to provide an user-friendly way to interact with the `TensorHEOM` package.
+TensorHEOM provides an optional graphical user interface built with
+`CustomTkinter <https://github.com/TomSchimansky/CustomTkinter>`_.
+The GUI is designed for users who prefer an interactive, form-based workflow
+without writing code.
+
+Launching the GUI
+=================
+
+.. code-block:: python
+
+   from ttheom import TensorHeomApp
+
+   TensorHeomApp().mainloop()
+
+Or from the command line after installing the package:
+
+.. code-block:: bash
+
+   python -c "from ttheom import TensorHeomApp; TensorHeomApp().mainloop()"
+
+Main window
+===========
+
+The main window provides input fields for all simulation parameters:
+qubit frequencies, initial state, bath parameters, numerical settings, and the
+output file name.
 
 .. figure:: ../figures/GUI1.png
    :align: center
-   :width: 3in
+   :width: 5in
 
-*Figure 1: Main window of the GUI.*
+   Main window showing system, bath, and simulation parameter fields.
 
----
+Quantum circuit editor
+======================
+
+The circuit editor window integrates with Qiskit to let you build and visualise
+quantum circuits graphically.  Gates can be added via drop-down menus and the
+resulting Qiskit circuit is passed directly to the simulation engine.
 
 .. figure:: ../figures/GUI2.png
    :align: center
-   :width: 3in
+   :width: 5in
+
+   Quantum circuit editor with Qiskit circuit visualization.
 
-*Figure 2: Quantum circuit editor window with qiskit integration.*
+Results viewer
+==============
 
----
+Once a simulation completes, the results viewer displays the time-evolved
+reduced density matrix elements and derived quantities such as concurrence.
 
 .. figure:: ../figures/GUI3.png
    :align: center
-   :width: 3in
-
-*Figure 3: Visualization of results (here: concurrence).*
+   :width: 5in
 
+   Results viewer showing the concurrence as a function of time.