Update Documentation (#135)

* Update Authors and References

* Fix documentation

* Remove unecessary copyright statements

.github/workflows/python-package-tests.yml

@@ -1,6 +1,6 @@
 name: tests
 
-on: [push, workflow_dispatch]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   tests:

.readthedocs.yaml

@@ -1,11 +1,35 @@
-# File: .readthedocs.yaml
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
+# Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
 
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.10
   install:
-    - requirements: requirements_ci.txt
+    - requirements: docs/requirements.txt

AUTHORS.md

@@ -1,29 +1,34 @@
 Authors & Acknowledgements
 ==========================
 
-Lead developer since 2020 (start of the project): [Gerald E. Fux](https://github.com/gefux)
+- Lead developer since 2020: [**Gerald E. Fux**](https://github.com/gefux) (<[email protected]>)
+- Co-lead developer since 2022: [**Piper Fowler-Wright**](https://github.com/piperfw)  (<[email protected]>)
 
 Major code contributions
 ------------------------
 
+**Version 0.5.0**
+- [Aidan Strathearn](https://github.com/aidanstrathearn): Gibbs state TEMPO [Chiu2022].
+- [Eoin P. Butler](https://github.com/ebutler414), [Eoin O'Neill](https://github.com/eoin-dp-oneill), and [Paul R. Eastham](https://github.com/paulreastham): Process tensor gradients and optimization [Fux2021, Butler2024]
+- [Ewen D.C. Lawrence](https://github.com/ewenlawrence) and [Peter Kirton](https://github.com/peterkirton/): Degeneracy trick in TEMPO and PT-TEMPO.
+- [Roosmarijn de Wit](https://github.com/rmadw): Multi-time system correlations.
+- [Piper Fowler-Wright](https://github.com/piperfw): TEMPO parameter tutorial and automatic estimation.
+
 **Version 0.4.0**
-- [Joel Beckles](https://github.com/JoelANB) and [Piper Fowler-Wright](https://github.com/piperfw): Extension of mean-field evolution to multiple types of system
+- [Joel Beckles](https://github.com/JoelANB) and [Piper Fowler-Wright](https://github.com/piperfw): Extension of mean-field evolution to multiple types of system.
 
 **Version 0.3.0**
-- [Piper Fowler-Wright](https://github.com/piperfw): Open quantum systems with mean-field evolution [FowlerWright2022]
+- [Piper Fowler-Wright](https://github.com/piperfw): Open quantum systems with mean-field evolution [FowlerWright2022].
 
 **Version 0.2.0**
-- [Gerald E. Fux](https://github.com/gefux): Chains of open quantum systems [Fux2022].
-- Dainius Kilda: Precursor code for chains of open quantum systems [Fux2022].
-- [Dominic Gribben](https://github.com/djgribben): Bath dynamics extension [Gribben2021].
-- [Dominic Gribben](https://github.com/djgribben): Multiple environments extension [Gribben2022].
+- [Gerald E. Fux](https://github.com/gefux): Chains of open quantum systems [Fux2023].
+- Dainius Kilda: Precursor code for chains of open quantum systems [Fux2023].
+- [Dominic Gribben](https://github.com/djgribben): Bath dynamics extension [Gribben2022b].
+- [Dominic Gribben](https://github.com/djgribben): Multiple environments extension [Gribben2022a].
 
 **Version 0.1.2 (TimeEvolvingMPO)**
 - [Gerald E. Fux](https://github.com/gefux): Improved memory cut-off [Strathearn2017].
 
-**Version 0.1.1 (TimeEvolvingMPO)**
-- No major code contributions in this version.
-
 **Version 0.1.0 (TimeEvolvingMPO)**
 - [Gerald E. Fux](https://github.com/gefux): Implement process tensor TEMPO (API and backend) [Fux2021].
 - [Gerald E. Fux](https://github.com/gefux): Implement core TEMPO functionality (API and backend) [Strathearn2018].
@@ -33,24 +38,12 @@ Major code contributions
 Acknowledgements
 ----------------
 
-**Members of the TEMPO collaboration:**
-- Kristín Arnardóttir (*University of St Andrews*) <[email protected]>
-- [Piper Fowler-Wright](https://github.com/piperfw) (*University of St Andrews*) <[email protected]>
-- [Gerald E. Fux](https://github.com/gefux) (*University of St Andrews*) <[email protected]>
-- [Erik Gauger](https://github.com/erikgauger) (*Heriot-Watt University*) <[email protected]>
-- [Dominic Gribben](https://github.com/djgribben) (*University of St Andrews*)
-- Jonathan Keeling (*University of St Andrews*) <[email protected]>
-- Dainius Kilda (*Max Planck Institute of Quantum Optics*)
-- [Peter Kirton](https://github.com/peterkirton) (*University of Strathclyde*) <[email protected]>
-- [Thibaut Lacroix](https://github.com/tfmlaX) (*University of St Andrews*) <[email protected]>
-- Brendon W. Lovett (*University of St Andrews*) <[email protected]>
-
-**Project administrators:**
-- [Gerald E. Fux](https://github.com/gefux) (<[email protected]>)
-- Jonathan Keeling (<[email protected]>)
-- Brendon W. Lovett (<[email protected]>)
-
-
-**Project maintainers:**
-- [Piper Fowler-Wright](https://github.com/piperfw) (<[email protected]>)
-- [Gerald E. Fux](https://github.com/gefux) (<[email protected]>)
+**Scientific advisors:**
+- Jonathan Keeling (*University of St Andrews*)
+- Brendon W. Lovett (*University of St Andrews*)
+
+**Other Collaborators:**
+- Kristín Arnardóttir (*University of Southern Denmark*)
+- [Erik Gauger](https://github.com/erikgauger) (*Heriot-Watt University*)
+- [Thibaut Lacroix](https://github.com/tfmlaX) (*University of St Andrews*)
+

BIBLIOGRAPHY.md

@@ -3,24 +3,55 @@ Bibliography
 
 The code in this project is based on ideas from the following publications:
 
-- **[Strathearn2017]** Strathearn et al., *Efficient real-time path integrals for non-Markovian spin-boson models*. [New J. Phys. 19(9), p.093009](http://dx.doi.org/10.1088/1367-2630/aa8744) (2017).
+- **[Strathearn2017]** Strathearn et al., *Efficient real-time path integrals for non-Markovian spin-boson models*. [New J. Phys. 19(9), p.093009](https://doi.org/10.1088/1367-2630/aa8744) (2017).
 - **[Strathearn2018]** Strathearn et al., *Efficient non-Markovian quantum dynamics using time-evolving matrix product operators*, [Nat. Commun. 9, 3322](https://doi.org/10.1038/s41467-018-05617-3)
   (2018).
-- **[Pollock2018]** Pollock et al., *Non-Markovian quantum processes: Complete framework and efficient characterization*, [Phys. Rev. A 97, 012127](http://dx.doi.org/10.1103/PhysRevA.97.012127) (2018).
-- **[Jorgensen2019]** Jørgensen and Pollock, *Exploiting the causal tensor network structure of quantum processes to efficiently simulate non-Markovian path integrals*, [Phys. Rev. Lett. 123, 240602](http://dx.doi.org/10.1103/PhysRevLett.123.240602) (2019).
-- **[Strathearn2019]** Strathearn, *Modelling Non-Markovian Quantum Systems Using Tensor Networks*, [Springer Theses](http://link.springer.com/10.1007/978-3-030-54975-6) (2020).
-- **[Fux2020]** Fux et al., *Efficient exploration of Hamiltonian parameter space for optimal control of non-Markovian open quantum systems*, [Phys. Rev. Lett. 126, 200401](https://link.aps.org/doi/10.1103/PhysRevLett.126.200401) (2021).
-- **[Gribben2021]** Gribben et al., *Using the Environment to Understand non-Markovian Open Quantum Systems*,  [arXiv:20106.0412](http://arxiv.org/abs/2106.04212) (2021).
-- **[Gribben2022]** Gribben et al., *Exact dynamics of non-additive environments in non-Markovian open quantum systems*, [PRX Quantum 3, 10321](https://link.aps.org/doi/10.1103/PRXQuantum.3.010321) (2021).
+- **[Pollock2018]** Pollock et al., *Non-Markovian quantum processes: Complete framework and efficient characterization*, [Phys. Rev. A 97, 012127](https://doi.org/10.1103/PhysRevA.97.012127) (2018).
+- **[Jorgensen2019]** Jørgensen and Pollock, *Exploiting the causal tensor network structure of quantum processes to efficiently simulate non-Markovian path integrals*, [Phys. Rev. Lett. 123, 240602](https://doi.org/10.1103/PhysRevLett.123.240602) (2019).
+- **[Strathearn2019]** Strathearn, *Modelling Non-Markovian Quantum Systems Using Tensor Networks*, [Springer Theses](https://doi.org/10.1007/978-3-030-54975-6) (2020).
+- **[Fux2021]** Fux et al., *Efficient exploration of Hamiltonian parameter space for optimal control of non-Markovian open quantum systems*, [Phys. Rev. Lett. 126, 200401](https://doi.org/10.1103/PhysRevLett.126.200401) (2021).
+- **[Gribben2022a]** Gribben et al., *Exact dynamics of non-additive environments in non-Markovian open quantum systems*, [PRX Quantum 3, 10321](https://doi.org/10.1103/PRXQuantum.3.010321) (2022).
+- **[Gribben2022b]** Gribben et al., *Using the Environment to Understand non-Markovian Open Quantum Systems*,  [Quantum, 6, 847](https://doi.org/10.22331/q-2022-10-25-847) (2022).
+- **[Chiu2022]** Chiu et al., *Numerical evaluation and robustness of the quantum mean-force Gibbs state*, [Phys. Rev. A 106, 012204](https://doi.org/10.1103/PhysRevA.106.012204}) (2022).
 - **[FowlerWright2022]** Fowler-Wright et al., *Efficient Many-Body Non-Markovian Dynamics of Organic Polaritons*, [Phys. Rev. Lett. 129, 173001](https://doi.org/10.1103/PhysRevLett.129.173001) (2022).
-- **[Fux2022]** Fux et al., *Thermalization of a spin chain strongly coupled to its environment*, [arXiv:2201.05529](http://arxiv.org/abs/2201.05529) (2022).
+- **[Fux2023]** Fux et al., *Tensor network simulation of chains of non-Markovian open quantum systems*, [Phys. Rev. Research 5, 033078 ](https://doi.org/10.1103/PhysRevResearch.5.033078}) (2023).
+- **[Butler2024]** Butler et al., *Optimizing Performance of Quantum Operations with Non-Markovian Decoherence: The Tortoise or the Hare?*, [Phys. Rev. Lett. 132, 060401 ](https://doi.org/10.1103/PhysRevLett.132.060401}) (2024).
 
 
 BibTeX:
 -------
 
-
 ```
+@article{Butler2024,
+  title = {Optimizing Performance of Quantum Operations with Non-Markovian Decoherence: The Tortoise or the Hare?},
+  author = {Butler, Eoin P. and Fux, Gerald E. and Ortega-Taberner, Carlos and Lovett, Brendon W. and Keeling, Jonathan and Eastham, Paul R.},
+  journal = {Phys. Rev. Lett.},
+  volume = {132},
+  issue = {6},
+  pages = {060401},
+  numpages = {7},
+  year = {2024},
+  month = {Feb},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevLett.132.060401},
+  url = {https://doi.org/10.1103/PhysRevLett.132.060401}
+}
+
+@article{Chiu2022,
+  title = {Numerical evaluation and robustness of the quantum mean-force Gibbs state},
+  author = {Chiu, Yiu-Fung and Strathearn, Aidan and Keeling, Jonathan},
+  journal = {Phys. Rev. A},
+  volume = {106},
+  issue = {1},
+  pages = {012204},
+  numpages = {8},
+  year = {2022},
+  month = {Jul},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevA.106.012204},
+  url = {https://doi.org/10.1103/PhysRevA.106.012204}
+}
+
 @article{FowlerWright2022,
   title = {Efficient Many-Body Non-Markovian Dynamics of Organic Polaritons},
   author = {Fowler-Wright, Piper and Lovett, Brendon W. and Keeling, Jonathan},
@@ -48,30 +79,25 @@ BibTeX:
   month = {May},
   publisher = {American Physical Society},
   doi = {10.1103/PhysRevLett.126.200401},
-  url = {https://link.aps.org/doi/10.1103/PhysRevLett.126.200401}
+  url = {https://doi.org/10.1103/PhysRevLett.126.200401}
 }
 
-@article{Fux2022,
-  title = {{Thermalization of a spin chain strongly coupled to its environment}},
+@article{Fux2023,
+  title = {Tensor network simulation of chains of non-Markovian open quantum systems},
   author = {Fux, Gerald E. and Kilda, Dainius and Lovett, Brendon W. and Keeling, Jonathan},
-  archivePrefix = {arXiv},
-  arxivId = {2201.05529},
-  eprint = {2201.05529},
-  url = {http://arxiv.org/abs/2201.05529},
-  year = {2022}
-}
-
-@article{Gribben2021,
-  title = {{Using the Environment to Understand non-Markovian Open Quantum Systems}},
-  author = {Gribben, Dominic and Strathearn, Aidan and Fux, Gerald E. and Kirton, Peter and Lovett, Brendon W.},
-  archivePrefix = {arXiv},
-  arxivId = {2106.04212},
-  eprint = {2106.04212},
-  url = {http://arxiv.org/abs/2106.04212},
-  year = {2021}
+  journal = {Phys. Rev. Res.},
+  volume = {5},
+  issue = {3},
+  pages = {033078},
+  numpages = {14},
+  year = {2023},
+  month = {Aug},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevResearch.5.033078},
+  url = {https://doi.org/10.1103/PhysRevResearch.5.033078}
 }
 
-@article{Gribben2022,
+@article{Gribben2022a,
   title = {Exact Dynamics of Nonadditive Environments in Non-Markovian Open Quantum Systems},
   author = {Gribben, Dominic and Rouse, Dominic M. and Iles-Smith, Jake and Strathearn, Aidan and Maguire, Henry and Kirton, Peter and Nazir, Ahsan and Gauger, Erik M. and Lovett, Brendon W.},
   journal = {PRX Quantum},
@@ -83,7 +109,21 @@ BibTeX:
   month = {Feb},
   publisher = {American Physical Society},
   doi = {10.1103/PRXQuantum.3.010321},
-  url = {https://link.aps.org/doi/10.1103/PRXQuantum.3.010321}
+  url = {https://doi.org/10.1103/PRXQuantum.3.010321}
+}
+
+@article{Gribben2022b,
+  doi = {10.22331/q-2022-10-25-847},
+  url = {https://doi.org/10.22331/q-2022-10-25-847},
+  title = {Using the {E}nvironment to {U}nderstand non-{M}arkovian {O}pen {Q}uantum {S}ystems},
+  author = {Gribben, Dominic and Strathearn, Aidan and Fux, Gerald E. and Kirton, Peter and Lovett, Brendon W.},
+  journal = {{Quantum}},
+  issn = {2521-327X},
+  publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}},
+  volume = {6},
+  pages = {847},
+  month = oct,
+  year = {2022}
 }
 
 @article{Jorgensen2019,
@@ -99,7 +139,7 @@ BibTeX:
   month = {Dec},
   publisher = {American Physical Society},
   doi = {10.1103/PhysRevLett.123.240602},
-  url = {https://link.aps.org/doi/10.1103/PhysRevLett.123.240602}
+  url = {https://doi.org/10.1103/PhysRevLett.123.240602}
 }
 
 @misc{OQuPy,
@@ -123,9 +163,7 @@ BibTeX:
   pages = {012127},
   title = {{Non-Markovian quantum processes: Complete framework and
             efficient characterization}},
-  url = {https://link.aps.org/doi/10.1103/PhysRevA.97.012127
-         http://arxiv.org/abs/1512.00589
-         http://dx.doi.org/10.1103/PhysRevA.97.012127},
+  url = {https://doi.org/10.1103/PhysRevA.97.012127},
   volume = {97},
   year = {2018}
 }
@@ -169,7 +207,7 @@ BibTeX:
   publisher = {Springer International Publishing},
   series = {Springer Theses},
   title = {{Modelling Non-Markovian Quantum Systems Using Tensor Networks}},
-  url = {http://link.springer.com/10.1007/978-3-030-54975-6},
+  url = {https://doi.org/10.1007/978-3-030-54975-6},
   year = {2020}
 }
 

HOW_TO_CITE.md

@@ -5,18 +5,21 @@ How to Cite this Project
 Citing the Code
 ---------------
 
-- **[OQuPy]** The TEMPO collaboration, *OQuPy: A Python 3 package to efficiently compute non-Markovianopen quantum systems*, [GitHub](https://doi.org/10.5281/zenodo.4428316) (2020).
+- **[OQuPy]** The TEMPO collaboration, *OQuPy: A Python 3 package to efficiently compute non-Markovian open quantum systems*, [GitHub](https://doi.org/10.5281/zenodo.4428316) (2020).
 
 
 Please consider citing
 ----------------------
 
 - TEMPO algorithm: **[Strathearn2018]**, **[Strathearn2019]**
-- Process tensor approach: **[Pollock2018]**, **[Jorgensen2019]**, **[Fux2021]**
-- Bath dynamics: **[Gribben2021]**
-- Multiple environments: **[Gribben2022]**
-- Chains (PT-TEBD): **[Fux2022]**
+- Process tensor approach: **[Pollock2018]**, **[Jorgensen2019]**
+- Optimization: **[Fux2021]**, **[Bulter2024]**
+- Multiple environments: **[Gribben2022a]**
+- Bath dynamics: **[Gribben2022b]**
+- Chains (PT-TEBD): **[Fux2023]**
 - Mean-Field TEMPO: **[FowlerWright2022]**
+- Gibbs TEMPO: **[Chiu2022]**
+
 
 BibTeX
 ------