Merge pull request qutip#2534 from gsuarezr/bath_pr_refactor2

Adding the environment module with classes to describe bosonic / fermionic environments

.github/workflows/tests.yml

@@ -141,7 +141,7 @@ jobs:
           # Install the extra requirement
           python -m pip install pytest>=5.2 pytest-rerunfailures  # tests
           python -m pip install ipython  # ipython
-          python -m pip install loky tqdm  # extras
+          python -m pip install loky tqdm mpmath  # extras
           python -m pip install "coverage${{ matrix.coverage-requirement }}" chardet
           python -m pip install pytest-cov coveralls pytest-fail-slow
 

doc/apidoc/apidoc.rst

@@ -13,6 +13,7 @@ complete list of QuTiP's public classes and functions.
    quantumobject.rst
    time_dep.rst
    solver.rst
+   environments.rst
    heom.rst
    piqs.rst
    visualization.rst

doc/apidoc/environments.rst

@@ -0,0 +1,52 @@
+************
+Environments
+************
+
+Bosonic Environments
+--------------------
+
+.. autoclass:: qutip.core.BosonicEnvironment
+    :members:
+
+.. autoclass:: qutip.core.DrudeLorentzEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.UnderDampedEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.OhmicEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.CFExponent
+    :members:
+
+.. autoclass:: qutip.core.ExponentialBosonicEnvironment
+    :members:
+    :show-inheritance:
+
+.. autofunction:: qutip.core.environment.system_terminator
+
+
+Fermionic Environments
+----------------------
+
+.. autoclass:: qutip.core.FermionicEnvironment
+    :members:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.LorentzianEnvironment
+    :members:
+    :show-inheritance:
+
+.. autoclass:: qutip.core.ExponentialFermionicEnvironment
+    :members:
+    :show-inheritance:

doc/apidoc/utilities.rst

@@ -7,7 +7,7 @@ Utility Functions
 -----------------
 
 .. automodule:: qutip.utilities
-    :members: n_thermal, clebsch, convert_unit
+    :members: n_thermal, clebsch, convert_unit, iterated_fit
 
 
 .. _fileio:

doc/biblio.rst

@@ -3,78 +3,86 @@
 Bibliography
 ============
 
+.. Note: first letter of entries must be escaped to avoid rst parsing as enumerated list
+   https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#enumerated-lists
+
 .. [BCSZ08]
-    W. Bruzda, V. Cappellini, H.-J. Sommers, K. Życzkowski, *Random Quantum Operations*, Phys. Lett. A **373**, 320-324 (2009). :doi:`10.1016/j.physleta.2008.11.043`.
+    \W. Bruzda, V. Cappellini, H.-J. Sommers, K. Życzkowski, *Random Quantum Operations*, Phys. Lett. A **373**, 320-324 (2009). :doi:`10.1016/j.physleta.2008.11.043`.
 
 .. [Hav03]
-    Havel, T. *Robust procedures for converting among Lindblad, Kraus and matrix representations of quantum dynamical semigroups*. Journal of Mathematical Physics **44** 2, 534 (2003). :doi:`10.1063/1.1518555`.
+    \T. Havel, *Robust procedures for converting among Lindblad, Kraus and matrix representations of quantum dynamical semigroups*, J. Math. Phys. **44** 2, 534 (2003). :doi:`10.1063/1.1518555`.
 
 .. [Wat13]
-    Watrous, J. |theory-qi|_, lecture notes.
-
-..  The trick with |text|_ is to get an italic link, and is described in the
-    Docutils FAQ at https://docutils.sourceforge.net/FAQ.html#is-nested-inline-markup-possible.
-
-.. |theory-qi| replace:: *Theory of Quantum Information*
-.. _theory-qi: https://cs.uwaterloo.ca/~watrous/TQI-notes/
+    \J. Watrous, |theory-qi|_, lecture notes.
 
 .. [Mez07]
-    F. Mezzadri, *How to generate random matrices from the classical compact groups*, Notices of the AMS **54** 592-604 (2007). :arxiv:`math-ph/0609050`.
+    \F. Mezzadri, *How to generate random matrices from the classical compact groups*, Notices of the AMS **54**, 592-604 (2007). :arxiv:`math-ph/0609050`.
 
 .. [Moh08]
-    M. Mohseni, A. T. Rezakhani, D. A. Lidar, *Quantum-process tomography: Resource analysis of different strategies*, Phys. Rev. A **77**, 032322 (2008). :doi:`10.1103/PhysRevA.77.032322`.
+    \M. Mohseni, A. T. Rezakhani, D. A. Lidar, *Quantum-process tomography: Resource analysis of different strategies*, Phys. Rev. A **77**, 032322 (2008). :doi:`10.1103/PhysRevA.77.032322`.
 
 .. [Gri98]
-    M. Grifoni, P. Hänggi, *Driven quantum tunneling*, Physics Reports **304**, 299 (1998). :doi:`10.1016/S0370-1573(98)00022-2`.
+    \M. Grifoni, P. Hänggi, *Driven quantum tunneling*, Phys. Rep. **304**, 299 (1998). :doi:`10.1016/S0370-1573(98)00022-2`.
 
 .. [Gar03]
-    Gardineer and Zoller, *Quantum Noise* (Springer, 2004).
+    Gardiner and Zoller, *Quantum Noise* (Springer, 2004).
 
 .. [Bre02]
     H.-P. Breuer and F. Petruccione, *The Theory of Open Quantum Systems* (Oxford, 2002).
 
 .. [Coh92]
-    C. Cohen-Tannoudji, J. Dupont-Roc, G. Grynberg, *Atom-Photon Interactions: Basic Processes and Applications*, (Wiley, 1992).
+    \C. Cohen-Tannoudji, J. Dupont-Roc, G. Grynberg, *Atom-Photon Interactions: Basic Processes and Applications*, (Wiley, 1992).
 
 .. [WBC11]
-    C. Wood, J. Biamonte, D. G. Cory, *Tensor networks and graphical calculus for
-    open quantum systems*. :arxiv:`1111.6950`
+    \C. Wood, J. Biamonte, D. G. Cory, *Tensor networks and graphical calculus for open quantum systems*. :arxiv:`1111.6950`
 
 .. [AKN98]
-    D. Aharonov, A. Kitaev, and N. Nisan, *Quantum circuits with mixed states*, in Proceedings of the 
-    thirtieth annual ACM symposium on Theory of computing, 20-30 (1998). :arxiv:`quant-ph/9806029`
+    \D. Aharonov, A. Kitaev, N. Nisan, *Quantum circuits with mixed states*, in Proceedings of the Thirtieth Annual ACM STOC, 20-30 (1998). :arxiv:`quant-ph/9806029`
 
 .. [dAless08]
-    D. d’Alessandro, *Introduction to Quantum Control and Dynamics*, (Chapman & Hall/CRC, 2008).
+    \D. d’Alessandro, *Introduction to Quantum Control and Dynamics*, (Chapman & Hall/CRC, 2008).
 
 .. [Byrd95]
-    R. H. Byrd, P. Lu, J. Nocedal, and C. Zhu, *A Limited Memory Algorithm for Bound Constrained Optimization*, SIAM J. Sci. Comput. **16**, 1190 (1995). :doi:`10.1137/0916069`
+    \R. H. Byrd, P. Lu, J. Nocedal, C. Zhu, *A Limited Memory Algorithm for Bound Constrained Optimization*, SIAM J. Sci. Comput. **16**, 1190 (1995). :doi:`10.1137/0916069`
 
 .. [Flo12]
-    F. F. Floether, P. de Fouquieres, and S. G. Schirmer, *Robust quantum gates for open systems via optimal control: Markovian versus non-Markovian dynamics*, New J. Phys. **14**, 073023 (2012). :doi:`10.1088/1367-2630/14/7/073023`
+    \F. F. Floether, P. de Fouquieres, S. G. Schirmer, *Robust quantum gates for open systems via optimal control: Markovian versus non-Markovian dynamics*, New J. Phys. **14**, 073023 (2012). :doi:`10.1088/1367-2630/14/7/073023`
 
 .. [Lloyd14]
-    S. Lloyd and S. Montangero, *Information theoretical analysis of quantum optimal control*, Phys. Rev. Lett. **113**, 010502 (2014). :doi:`10.1103/PhysRevLett.113.010502`
+    \S. Lloyd, S. Montangero, *Information theoretical analysis of quantum optimal control*, Phys. Rev. Lett. **113**, 010502 (2014). :doi:`10.1103/PhysRevLett.113.010502`
 
 .. [Doria11]
-    P. Doria, T. Calarco & S. Montangero, *Optimal Control Technique for Many-Body Quantum Dynamics*, Phys. Rev. Lett. **106**, 190501 (2011). :doi:`10.1103/PhysRevLett.106.190501`
+    \P. Doria, T. Calarco, S. Montangero, *Optimal Control Technique for Many-Body Quantum Dynamics*, Phys. Rev. Lett. **106**, 190501 (2011). :doi:`10.1103/PhysRevLett.106.190501`
 
 .. [Caneva11]
-    T. Caneva, T. Calarco, & S. Montangero, *Chopped random-basis quantum optimization*, Phys. Rev. A **84**, 022326 (2011). :doi:`10.1103/PhysRevA.84.022326`
+    \T. Caneva, T. Calarco, S. Montangero, *Chopped random-basis quantum optimization*, Phys. Rev. A **84**, 022326 (2011). :doi:`10.1103/PhysRevA.84.022326`
 
 .. [Rach15]
-    N. Rach, M. M. Müller, T. Calarco, and S. Montangero, *Dressing the chopped-random-basis optimization: A bandwidth-limited access to the trap-free landscape*, Phys. Rev. A. **92**, 062343 (2015). :doi:`10.1103/PhysRevA.92.062343`
+    \N. Rach, M. M. Müller, T. Calarco, S. Montangero, *Dressing the chopped-random-basis optimization: A bandwidth-limited access to the trap-free landscape*, Phys. Rev. A. **92**, 062343 (2015). :doi:`10.1103/PhysRevA.92.062343`
 
 .. [Wis09]
-
-    Wiseman, H. M. & Milburn, G. J. *Quantum Measurement and Control*, (Cambridge University Press, 2009).
+    \H. M. Wiseman, G. J. Milburn, *Quantum Measurement and Control*, (Cambridge University Press, 2009).
 
 .. [NKanej]
-
-    N Khaneja et. al. *Optimal control of coupled spin dynamics: Design of NMR pulse sequences by gradient ascent algorithms.* J. Magn. Reson. **172**, 296–305 (2005). :doi:`10.1016/j.jmr.2004.11.004`
+    \N. Khaneja *et al.*, *Optimal control of coupled spin dynamics: Design of NMR pulse sequences by gradient ascent algorithms.* J. Magn. Reson. **172**, 296–305 (2005). :doi:`10.1016/j.jmr.2004.11.004`
 
 .. [Donvil22]
-    B. Donvil, P. Muratore-Ginanneschi, *Quantum trajectory framework for general time-local master equations*, Nat Commun **13**, 4140 (2022). :doi:`10.1038/s41467-022-31533-8`.
+    \B. Donvil, P. Muratore-Ginanneschi, *Quantum trajectory framework for general time-local master equations*, Nat Commun **13**, 4140 (2022). :doi:`10.1038/s41467-022-31533-8`.
 
 .. [Abd19]
-    M. Abdelhafez, D. I. Schuster, J. Koch, *Gradient-based optimal control of open quantum systems using quantumtrajectories and automatic differentiation*, Phys. Rev. A **99**, 052327 (2019). :doi:`10.1103/PhysRevA.99.052327`.
+    \M. Abdelhafez, D. I. Schuster, J. Koch, *Gradient-based optimal control of open quantum systems using quantumtrajectories and automatic differentiation*, Phys. Rev. A **99**, 052327 (2019). :doi:`10.1103/PhysRevA.99.052327`.
+
+.. [BoFiN23]
+    \N. Lambert, T. Raheja, S. Cross, P. Menczel, S. Ahmed, A. Pitchford, D. Burgarth, F. Nori, *QuTiP-BoFiN: A bosonic and fermionic numerical hierarchical-equations-of-motion library with applications in light-harvesting, quantum control, and single-molecule electronics*, Phys. Rev. Research **5**, 013181 (2023). :doi:`10.1103/PhysRevResearch.5.013181`.
+
+.. [Lambert19]
+    \N. Lambert, S. Ahmed, M. Cirio, F. Nori, *Modelling the ultra-strongly coupled spin-boson model with unphysical modes*, Nat Commun **10**, 3721 (2019). :doi:`10.1038/s41467-019-11656-1`.
+
+
+
+..  The trick with |text|_ is to get an italic link, and is described in the
+    Docutils FAQ at https://docutils.sourceforge.net/FAQ.html#is-nested-inline-markup-possible.
+    This is at the bottom of the source file to avoid extra whitespace.
+
+.. |theory-qi| replace:: *Theory of Quantum Information*
+.. _theory-qi: https://cs.uwaterloo.ca/~watrous/TQI-notes/

doc/changes/2534.feature

@@ -0,0 +1 @@
+This change introduces the qutip.core.environment module, which contains classes that characterize bosonic and fermionic thermal environments.