Fix documentation

tempoCollaboration · Jun 22, 2024 · a719eaf · a719eaf
1 parent 3049416
commit a719eaf
Show file tree

Hide file tree

Showing 17 changed files with 2,275 additions and 133 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 
 # OQuPy: Open Quantum Systems in Python
 
-**A Python 3 package to efficiently compute non-Markovian open quantum systems.**
+**A Python package to efficiently simulate non-Markovian open quantum systems
+with process tensors.**
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/tempoCollaboration/OQuPy/main?filepath=tutorials%2Fquickstart.ipynb)
 [![Tests status](https://github.com/tempoCollaboration/OQuPy/actions/workflows/python-package-tests.yml/badge.svg)](https://github.com/tempoCollaboration/OQuPy/actions/workflows/python-package-tests.yml)
@@ -18,12 +19,12 @@ OQuPy includes numerically exact methods (i.e. employing only numerically well c
 - quantum systems coupled to a single environment [2-4],
 - quantum systems coupled to multiple environments [5],
 - interacting chains of non-Markovian open quantum systems [6], and
-- ensembles of open many-body systems with many-to-one coupling to some common central system [7].
+- ensembles of open many-body systems with many-to-one coupling [7].
 
 Furthermore, OQuPy implements methods to ...
 - optimize control protocols for non-Markovian open quantum systems [8,9],
 - compute the dynamics of an non-Markovian environment [10], and
-- obtain the thermal state of a quantum system strongly coupled to a structured environment [11].
+- obtain the thermal state of a strongly couled quantum system [11].
 
 ![OQuPy - overview](docs/graphics/overview.png)
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'OQuPy'
-copyright = '2022, TEMPO Collaboration'
+copyright = '2024, TEMPO Collaboration'
 author = 'TEMPO Collaboration'
 
 # The full version, including alpha/beta/rc tags

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,62 +1,62 @@
 OQuPy - Open Quantum Systems in Python
 ======================================
 
-**A Python 3 package to efficiently compute non-Markovian open quantum
-systems.**
+**A Python package to efficiently simulate non-Markovian open quantum systems
+with process tensors.**
 
 .. image:: https://img.shields.io/badge/Supported%20By-UNITARY%20FUND-brightgreen.svg?style=for-the-badge
  :target: http://unitary.fund
 
 
 This open source project aims to facilitate versatile numerical tools to
-efficiently compute the dynamics of quantum systems that are possibly strongly
-coupled to structured environments. It allows to conveniently apply several
-numerical methods related to the time evolving matrix product operator
-(TEMPO) [1-2] and the process tensor (PT) approach to open quantum
-systems [3-5]. This includes methods to compute ...
-
-- the dynamics of a quantum system strongly coupled to a bosonic environment [1-2].
-- the process tensor of a quantum system strongly coupled to a bosonic environment [3-4].
-- optimal control procedures for non-Markovian open quantum systems [5].
-- the dynamics of a strongly coupled bosonic environment [6].
-- the dynamics of a quantum system coupled to multiple non-Markovian environments [7].
-- the dynamics of a chain of non-Markovian open quantum systems [8].
-- the dynamics of an open many-body system with one-to-all light-matter
- coupling [9].
-- higher order multi-time correlations (e.g. for 2D electronic spectroscopy).
-
-Up to versions 0.1.x this package was called *TimeEvolvingMPO*.
-
-.. figure:: graphics/overview.png
- :align: center
- :alt: OQuPy - overview
-
-- **[1]** Strathearn et al.,
- `New J. Phys. 19(9), p.093009 <http://dx.doi.org/10.1088/1367-2630/aa8744>`_
- (2017).
-- **[2]** Strathearn et al.,
- `Nat. Commun. 9, 3322 <https://doi.org/10.1038/s41467-018-05617-3>`_
- (2018).
-- **[3]** Pollock et al.,
- `Phys. Rev. A 97, 012127 <http://dx.doi.org/10.1103/PhysRevA.97.012127>`_
- (2018).
-- **[4]** Jørgensen and Pollock,
- `Phys. Rev. Lett. 123, 240602 <http://dx.doi.org/10.1103/PhysRevLett.123.240602>`_
- (2019).
-- **[5]** Fux et al.,
- `Phys. Rev. Lett. 126, 200401 <https://link.aps.org/doi/10.1103/PhysRevLett.126.200401>`_
- (2021).
-- **[6]** Gribben et al.,
- `arXiv:2106.04212 <http://arxiv.org/abs/2106.04212>`_
- (2021).
-- **[7]** Gribben et al.,
- `PRX Quantum 3, 10321 <https://link.aps.org/doi/10.1103/PRXQuantum.3.010321>`_
- (2022).
-- **[8]** Fux et al.,
- `arXiv:2201.05529 <http://arxiv.org/abs/2201.05529>`_ (2022).
-- **[9]** Fowler-Wright at al.,
- `Phys. Rev. Lett. 129, 173001 <https://doi.org/10.1103/PhysRevLett.129.173001>`_
- (2022).
+efficiently compute the dynamics of quantum systems that are possibly
+strongly coupled to structured environments. It facilitates the
+convenient application of several numerical methods that combine the
+conceptional advantages of the process tensor framework [1], with the
+numerical efficiency of tensor networks.
+
+OQuPy includes numerically exact methods (i.e. employing only
+numerically well controlled approximations) for the non-Markovian
+dynamics and multi-time correlations of ...
+
+- quantum systems coupled to a single environment [2-4],
+- quantum systems coupled to multiple environments [5],
+- interacting chains of non-Markovian open quantum systems [6], and
+- ensembles of open many-body systems with many-to-one coupling [7].
+
+Furthermore, OQuPy implements methods to ...
+
+- optimize control protocols for non-Markovian open quantum systems [8,9],
+- compute the dynamics of an non-Markovian environment [10], and
+- obtain the thermal state of a strongly couled quantum system [11].
+
+.. figure:: ./graphics/overview.png
+ :alt: OQuPy - overview
+
+- **[1]** Pollock et al., `Phys. Rev. A 97,
+ 012127 <https://doi.org/10.1103/PhysRevA.97.012127>`__ (2018).
+- **[2]** Strathearn et al., `New J. Phys. 19(9),
+  p.093009 <https://doi.org/10.1088/1367-2630/aa8744>`__ (2017).
+-  **[3]** Strathearn et al., `Nat. Commun. 9,
+  3322 <https://doi.org/10.1038/s41467-018-05617-3>`__ (2018).
+- **[4]** Jørgensen and Pollock, `Phys. Rev. Lett. 123,
+ 240602 <https://doi.org/10.1103/PhysRevLett.123.240602>`__ (2019).
+- **[5]** Gribben et al., `PRX Quantum 3,
+  10321 <https://doi.org/10.1103/PRXQuantum.3.010321>`__ (2022).
+-  **[6]** Fux et al., `Phys. Rev. Research 5,
+  033078 <https://doi.org/10.1103/PhysRevResearch.5.033078%7D>`__
+  (2023).
+-  **[7]** Fowler-Wright et al., `Phys. Rev. Lett. 129,
+  173001 <https://doi.org/10.1103/PhysRevLett.129.173001>`__ (2022).
+- **[8]** Fux et al., `Phys. Rev. Lett. 126,
+ 200401 <https://doi.org/10.1103/PhysRevLett.126.200401>`__ (2021).
+- **[9]** Butler et al., `Phys. Rev. Lett. 132,
+  060401 <https://doi.org/10.1103/PhysRevLett.132.060401%7D>`__ (2024).
+-  **[10]** Gribben et al., `Quantum, 6,
+  847 <https://doi.org/10.22331/q-2022-10-25-847>`__ (2022).
+-  **[11]** Chiu et al., `Phys. Rev. A 106,
+  012204 <https://doi.org/10.1103/PhysRevA.106.012204%7D>`__ (2022).
+
 
 .. |binder-tutorial| image:: https://mybinder.org/badge_logo.svg
  :target: https://mybinder.org/v2/gh/tempoCollaboration/OQuPy/main?filepath=tutorials%2Fquickstart.ipynb
@@ -85,12 +85,13 @@ Up to versions 0.1.x this package was called *TimeEvolvingMPO*.
 
  pages/tutorials/quickstart
  pages/tutorials/pt_tempo
+ pages/tutorials/parameters
+ pages/tutorials/n_time_correlations
+ pages/tutorials/pt_gradient/pt_gradient
  pages/tutorials/bath_dynamics
  pages/tutorials/pt_tebd
  pages/tutorials/mf_tempo
- pages/tutorials/n_time_correlations
- pages/tutorials/parameters
-
+
 .. toctree::
  :maxdepth: 1
  :caption: API Reference

diff --git a/docs/pages/api.rst b/docs/pages/api.rst
@@ -38,7 +38,7 @@ class :class:`oqupy.system.TimeDependentSystemWithField`
  Markovian decay) that depends on both time and the expectation value of
  a field (a complex scalar) to which the system couples.
 
-class :class:`oqupy.system.ParametrizedSystem`
+class :class:`oqupy.system.ParameterizedSystem`
  Encodes a system Hamiltonian that depends on a set of parameters.
 
 class :class:`oqupy.system.MeanFieldSystem`
@@ -62,21 +62,21 @@ class :class:`oqupy.control.ChainControl`
 Environment
 ***********
 
-class :class:`oqupy.correlations.BaseCorrelations`
+class :class:`oqupy.bath_correlations.BaseCorrelations`
  Abstract class representing the environments auto-correlations.
 
- class :class:`oqupy.correlations.CustomCorrelations`
+ class :class:`oqupy.bath_correlations.CustomCorrelations`
  Encode an explicitly given environment auto-correlation function.
 
- class :class:`oqupy.correlations.CustomSD`
+ class :class:`oqupy.bath_correlations.CustomSD`
  Encodes the auto-correlations for a given spectral density.
 
- class :class:`oqupy.correlations.PowerLawSD`
+ class :class:`oqupy.bath_correlations.PowerLawSD`
  Encodes the auto-correlations for a given spectral density of a power law
  form.
 
 class :class:`oqupy.bath.Bath`
- Bundles a :class:`oqupy.correlations.BaseCorrelations` object
+ Bundles a :class:`oqupy.bath_correlations.BaseCorrelations` object
  together with a coupling operator.
 
 
@@ -114,7 +114,7 @@ PT-TEMPO
 ********
 (Process Tensor - Time Evolving Matrix Product Operator)
 
-class :class:`oqupy.pt_tempo.PtTempo`function oqupy.gradient.state_gradient()
+class :class:`oqupy.pt_tempo.PtTempo`
  Class to facilitate a PT-TEMPO computation.
 
  method :meth:`oqupy.pt_tempo.PtTempo.compute`
@@ -125,25 +125,25 @@ class :class:`oqupy.pt_tempo.PtTempo`function oqupy.gradient.state_gradient()
 Process Tensor Applications
 ***************************
 
-function :func:`oqupy.contractions.compute_dynamics`
+function :func:`oqupy.system_dynamics.compute_dynamics`
  Compute a :class:`oqupy.dynamics.Dynamics` object for given
  :class:`oqupy.system.System` or
  :class:`oqupy.system.TimeDependentSystem` and
  :class:`oqupy.control.Control` and
  :class:`oqupy.process_tensor.BaseProcessTensor` objects.
 
-function :func:`oqupy.contractions.compute_dynamics_with_field`
+function :func:`oqupy.system_dynamics.compute_dynamics_with_field`
  Compute a :class:`oqupy.dynamics.MeanFieldDynamics` object for given
  :class:`oqupy.system.MeanFieldSystem` and list of
  :class:`oqupy.control.Control` objects and list of
  :class:`oqupy.process_tensor.BaseProcessTensor` objects.
- 
-function :func:`oqupy.contractions.compute_correlations_nt`
+
+function :func:`oqupy.system_dynamics.compute_correlations_nt`
  Compute ordered multi-time correlations for given
  :class:`oqupy.system.BaseSystem` and
  :class:`oqupy.process_tensor.BaseProcessTensor` objects.
 
-function :func:`oqupy.contractions.compute_correlations`
+function :func:`oqupy.system_dynamics.compute_correlations`
  Compute two time correlations for given
  :class:`oqupy.system.BaseSystem` and
  :class:`oqupy.process_tensor.BaseProcessTensor` objects.
@@ -161,7 +161,7 @@ class :class:`oqupy.bath_dynamics.TwoTimeBathCorrelations`
 
 function :func:`oqupy.gradient.state_gradient`
  Compute the dynamics and gradient with respect to some objective function for
- a given :class:`oqupy.system.ParametrizedSystem`. 
+ a given :class:`oqupy.system.ParameterizedSystem`.
 
 PT-TEBD
 *******

diff --git a/docs/pages/install.rst b/docs/pages/install.rst
@@ -7,20 +7,20 @@ Installation
 How To Install
 --------------
 
-* Make sure you have `python3.6` or higher installed
+* Make sure you have `python3.10` or higher installed
 
  .. code-block:: none
 
  $ python3 --version
- Python 3.6.9
+ Python 3.10.14
 
 
-* Make sure you have `pip3` version 20.0 or higher installed
+* Make sure you have `pip3` version 23.0 or higher installed
 
  .. code-block:: none
 
  $ python3 -m pip --version
- pip 20.0.2 from /home/gefux/.local/lib/python3.6/site-packages/pip (python 3.6)
+ pip 23.3.1 from /home/gefux/anaconda3/envs/oqupy-ci/lib/python3.10/site-packages/pip (python 3.10)
 
 
 * Install OQuPy via pip

diff --git a/docs/pages/modules.rst b/docs/pages/modules.rst
@@ -9,10 +9,10 @@ oqupy.base_api
  :members:
 
 
-oqupy.bath
-----------
+oqupy.bath_correlations
+-----------------------
 
-.. automodule:: oqupy.bath
+.. automodule:: oqupy.bath_correlations
  :show-inheritance:
  :members:
 
@@ -25,10 +25,10 @@ oqupy.bath_dynamics
  :members:
 
 
-oqupy.contractions
-------------------
+oqupy.bath
+----------
 
-.. automodule:: oqupy.contractions
+.. automodule:: oqupy.bath
  :show-inheritance:
  :members:
 
@@ -41,14 +41,6 @@ oqupy.control
  :members:
 
 
-oqupy.correlations
-------------------
-
-.. automodule:: oqupy.correlations
- :show-inheritance:
- :members:
-
-
 oqupy.dynamics
 --------------
 
@@ -57,18 +49,11 @@ oqupy.dynamics
  :members:
 
 
-oqupy.exceptions
-----------------
-
-.. automodule:: oqupy.exceptions
- :show-inheritance:
- :members:
-
-
 oqupy.gradient
 --------------
 
 .. automodule:: oqupy.gradient
+ :show-inheritance:
  :members:
 
 
@@ -98,42 +83,38 @@ oqupy.process_tensor
 --------------------
 
 .. automodule:: oqupy.process_tensor
+ :show-inheritance:
+ :members:
 
- .. autoclass:: oqupy.process_tensor.BaseProcessTensor
- :show-inheritance:
- :members:
-
- .. autoclass:: oqupy.process_tensor.FileProcessTensor
- :show-inheritance:
-
- .. autoclass:: oqupy.process_tensor.SimpleProcessTensor
- :show-inheritance:
 
- .. autoclass:: oqupy.process_tensor.TrivialProcessTensor
- :show-inheritance:
+oqupy.pt_tebd
+-------------
 
- .. autofunction:: oqupy.process_tensor.import_process_tensor
+.. automodule:: oqupy.pt_tebd
+ :show-inheritance:
+ :members:
 
 
-oqupy.pt_tebd
---------------------
+oqupy.pt_tmpo
+-------------
 
-.. automodule:: oqupy.pt_tebd
+.. automodule:: oqupy.pt_tempo
+ :show-inheritance:
  :members:
 
 
-oqupy.system
-------------
+oqupy.system_dynamics
+---------------------
 
-.. automodule:: oqupy.system
+.. automodule:: oqupy.system_dynamics
  :show-inheritance:
  :members:
 
 
-oqupy.pt_tempo
---------------
+oqupy.system
+------------
 
-.. automodule:: oqupy.pt_tempo
+.. automodule:: oqupy.system
  :show-inheritance:
  :members: