Merge remote-tracking branch 'upstream/main' into feature/ntbk_smesolve

Author: nwlambert

tutorials-v4/lectures/Lecture-11-Charge-Qubits.md

@@ -39,7 +39,7 @@ where $E_C$ is the charge energy, $E_J$ is the Josephson energy, and $\left| n\r
 
 #### References
 
- * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](http://link.aps.org/doi/10.1103/PhysRevA.76.042319)
+ * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.76.042319)
  * [Y.A. Pashkin et al, Quantum Inf Process 8, 55 (2009)](http://dx.doi.org/10.1007/s11128-009-0101-5)
 
 

tutorials-v4/lectures/Lecture-2B-Single-Atom-Lasing.md

@@ -63,9 +63,9 @@ in units where $\hbar = 1$.
 
 References:
 
- * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](http://dx.doi.org/10.1103/PhysRevA.46.5944)
+ * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.46.5944)
 
- * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](http://dx.doi.org/10.1103/PhysRevLett.98.067204)
+ * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.067204)
 
  * [S. Ashhab, J.R. Johansson, A.M. Zagoskin, F. Nori, New J. Phys. 11, 023030 (2009)](http://dx.doi.org/10.1088/1367-2630/11/2/023030)
 

tutorials-v4/lectures/Lecture-3A-Dicke-model.md

@@ -49,7 +49,7 @@ $\displaystyle J_\pm = \sum_{i=1}^N \sigma_\pm^{(i)}$
 
 ### References
 
- * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](http://dx.doi.org/10.1103/PhysRev.93.99)
+ * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](https://journals.aps.org/pr/abstract/10.1103/PhysRev.93.99)
 
 
 ## Setup problem in QuTiP
@@ -198,7 +198,7 @@ fig.tight_layout()
 
 ### References
 
-* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](http://dx.doi.org/10.1103/PhysRevLett.92.073602).
+* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.92.073602).
 
 ```python
 def calulcate_entropy(M, N, g_vec):

tutorials-v4/lectures/Lecture-3B-Jaynes-Cumming-model-with-ultrastrong-coupling.md

@@ -51,11 +51,11 @@ The regime $g$ is large compared with all other energy scales in the Hamiltonian
 
 References:
 
- * [P. Nataf et al., Phys. Rev. Lett. 104, 023601 (2010)](http://dx.doi.org/10.1103/PhysRevLett.104.023601)
+ * [P. Nataf et al., Phys. Rev. Lett. 104, 023601 (2010)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.104.023601)
 
- * [J. Casanova et al., Phys. Rev. Lett. 105, 26360 (2010)](http://dx.doi.org/10.1103/PhysRevLett.105.263603).
+ * [J. Casanova et al., Phys. Rev. Lett. 105, 26360 (2010)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.263603).
 
- * [S. Ashhab et al., Phys. Rev. A 81, 042311 (2010)](http://dx.doi.org/10.1103/PhysRevA.81.042311)
+ * [S. Ashhab et al., Phys. Rev. A 81, 042311 (2010)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.81.042311)
 <!-- #endregion -->
 
 <!-- #region -->

tutorials-v4/lectures/Lecture-4-Correlation-Functions.md

@@ -152,7 +152,7 @@ $L(\tau) = 2\langle Q(\tau)Q(0)\rangle - \langle Q(2\tau)Q(0)\rangle \leq 1$
 
 ### References
 
-* [A. J. Leggett and A. Garg, Phys. Rev. Lett. 54, 857 (1985)](http://dx.doi.org/10.1103/PhysRevLett.54.857)
+* [A. J. Leggett and A. Garg, Phys. Rev. Lett. 54, 857 (1985)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.54.857)
 * [A. J. Leggett, J. Phys. Condens. Matter 14, R415 (2002)](http://dx.doi.org/10.1088/0953-8984/14/15/201)
 <!-- #endregion -->
 
@@ -186,7 +186,7 @@ def leggett_garg(c_mat):
 
 References:
 
- * [N. Lambert, J.R. Johansson, F. Nori, Phys. Rev. B 82, 245421 (2011)](http://dx.doi.org/10.1103/PhysRevB.84.245421).
+ * [N. Lambert, J.R. Johansson, F. Nori, Phys. Rev. B 82, 245421 (2011)](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245421).
 <!-- #endregion -->
 
 ```python

tutorials-v4/quantum-circuits/qip-toffoli-cnot.md

@@ -5,9 +5,9 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
-    display_name: Python 3 (ipykernel)
+    display_name: qutip-dev
     language: python
     name: python3
 ---
@@ -39,7 +39,7 @@ q.add_gate("TOFFOLI", controls=[0, 2], targets=[1])
 ```
 
 ```python
-q.png
+q.draw()
 ```
 
 ```python
@@ -53,7 +53,7 @@ q2 = q.resolve_gates()
 ```
 
 ```python
-q2.png
+q2.draw()
 ```
 
 ```python

tutorials-v4/quantum-circuits/quantum-gates.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -63,7 +63,7 @@ cphase(pi / 2)
 ```python
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("CSIGN", controls=[0], targets=[1])
-q.png
+q.draw()
 ```
 
 ### Rotation about X-axis
@@ -74,8 +74,8 @@ rx(pi / 2)
 
 ```python
 q = QubitCircuit(1, reverse_states=False)
-q.add_gate("RX", targets=[0], arg_value=pi / 2, arg_label=r"\frac{\pi}{2}")
-q.png
+q.add_gate("RX", targets=[0], arg_value=pi / 2, style={"showarg": True})
+q.draw()
 ```
 
 ### Rotation about Y-axis
@@ -86,8 +86,8 @@ ry(pi / 2)
 
 ```python
 q = QubitCircuit(1, reverse_states=False)
-q.add_gate("RY", targets=[0], arg_value=pi / 2, arg_label=r"\frac{\pi}{2}")
-q.png
+q.add_gate("RY", targets=[0], arg_value=pi / 2, style={"showarg": True})
+q.draw()
 ```
 
 ### Rotation about Z-axis
@@ -98,8 +98,8 @@ rz(pi / 2)
 
 ```python
 q = QubitCircuit(1, reverse_states=False)
-q.add_gate("RZ", targets=[0], arg_value=pi / 2, arg_label=r"\frac{\pi}{2}")
-q.png
+q.add_gate("RZ", targets=[0], arg_value=pi / 2, style={"showarg": True})
+q.draw()
 ```
 
 ### CNOT
@@ -111,7 +111,7 @@ cnot()
 ```python
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("CNOT", controls=[0], targets=[1])
-q.png
+q.draw()
 ```
 
 ### CSIGN
@@ -123,7 +123,7 @@ csign()
 ```python
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("CSIGN", controls=[0], targets=[1])
-q.png
+q.draw()
 ```
 
 ### Berkeley
@@ -135,7 +135,7 @@ berkeley()
 ```python
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("BERKELEY", targets=[0, 1])
-q.png
+q.draw()
 ```
 
 ### SWAPalpha
@@ -162,7 +162,7 @@ toffoli()
 swap()
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("SWAP", targets=[0, 1])
-q.png
+q.draw()
 ```
 
 ### ISWAP
@@ -171,7 +171,7 @@ q.png
 iswap()
 q = QubitCircuit(2, reverse_states=False)
 q.add_gate("ISWAP", targets=[0, 1])
-q.png
+q.draw()
 ```
 
 ### SQRTiSWAP
@@ -234,7 +234,7 @@ cnot(N=3)
 ```python
 q = QubitCircuit(3, reverse_states=False)
 q.add_gate("CNOT", controls=[1], targets=[2])
-q.png
+q.draw()
 ```
 
 Furthermore, the control and target qubits (when applicable) can also be similarly specified using keyword arguments `control` and `target` (or in some cases `controls` or `targets`):
@@ -246,7 +246,7 @@ cnot(N=3, control=2, target=0)
 ```python
 q = QubitCircuit(3, reverse_states=False)
 q.add_gate("CNOT", controls=[0], targets=[2])
-q.png
+q.draw()
 ```
 
 ## Setup of a Qubit Circuit
@@ -261,7 +261,7 @@ In the following example, we take a SWAP gate. It is known that a swap gate is e
 N = 2
 qc0 = QubitCircuit(N)
 qc0.add_gate("ISWAP", [0, 1], None)
-qc0.png
+qc0.draw()
 ```
 
 ```python
@@ -275,7 +275,7 @@ qc1 = QubitCircuit(N)
 qc1.add_gate("CNOT", 0, 1)
 qc1.add_gate("CNOT", 1, 0)
 qc1.add_gate("CNOT", 0, 1)
-qc1.png
+qc1.draw()
 ```
 
 ```python
@@ -288,7 +288,7 @@ In place of manually converting the SWAP gate to CNOTs, it can be automatically
 
 ```python
 qc2 = qc0.resolve_gates("CNOT")
-qc2.png
+qc2.draw()
 ```
 
 ```python
@@ -301,7 +301,7 @@ From QuTiP 4.4, we can also add gate at arbitrary position in a circuit.
 
 ```python
 qc1.add_gate("CSIGN", index=[1], targets=[0], controls=[1])
-qc1.png
+qc1.draw()
 ```
 
 ## Example of basis transformation
@@ -313,7 +313,7 @@ qc3.add_gate("RX", 0, None, pi / 2, r"\pi/2")
 qc3.add_gate("RY", 1, None, pi / 2, r"\pi/2")
 qc3.add_gate("RZ", 2, None, pi / 2, r"\pi/2")
 qc3.add_gate("ISWAP", [1, 2])
-qc3.png
+qc3.draw()
 ```
 
 ```python
@@ -325,7 +325,7 @@ U3
 
 ```python
 qc4 = qc3.resolve_gates("CNOT")
-qc4.png
+qc4.draw()
 ```
 
 ```python
@@ -335,7 +335,7 @@ U4
 
 ```python
 qc5 = qc3.resolve_gates("ISWAP")
-qc5.png
+qc5.draw()
 ```
 
 ```python
@@ -347,7 +347,7 @@ U5
 
 ```python
 qc6 = qc3.resolve_gates(["ISWAP", "RX", "RY"])
-qc6.png
+qc6.draw()
 ```
 
 ```python
@@ -357,7 +357,7 @@ U6
 
 ```python
 qc7 = qc3.resolve_gates(["CNOT", "RZ", "RX"])
-qc7.png
+qc7.draw()
 ```
 
 ```python
@@ -373,7 +373,7 @@ Interactions between non-adjacent qubits can be resolved by QubitCircuit to a se
 ```python
 qc8 = QubitCircuit(3)
 qc8.add_gate("CNOT", 2, 0)
-qc8.png
+qc8.draw()
 ```
 
 ```python
@@ -393,7 +393,7 @@ U9
 
 ```python
 qc10 = qc9.resolve_gates("CNOT")
-qc10.png
+qc10.draw()
 ```
 
 ```python
@@ -418,7 +418,7 @@ From QuTiP 4.4 on, user defined gates can be defined by a python function that t
 ```python
 def user_gate1(arg_value):
     # controlled rotation X
-    mat = np.zeros((4, 4), dtype=np.complex)
+    mat = np.zeros((4, 4), dtype=complex)
     mat[0, 0] = mat[1, 1] = 1.0
     mat[2:4, 2:4] = rx(arg_value)
     return Qobj(mat, dims=[[2, 2], [2, 2]])

tutorials-v4/time-evolution/002_larmor-precession.md

@@ -21,7 +21,7 @@ Author: C. Staufenbiel, 2022
 This notebook guides you through the process of setting up a Schrödinger
 equation in QuTiP and using the corresponding solver to obtain the time
 evolution. We will investigate the example of the Larmor precession to
-explore the functionality of [`qutip.sesolve()`](https://qutip.readthedocs.io/en/latest/apidoc/functions.html?highlight=sesolve#module-qutip.sesolve).
+explore the functionality of [`qutip.sesolve()`](https://qutip.readthedocs.io/en/latest/apidoc/solver.html#module-qutip.solver.sesolve).
 
 You can also find more on time evolutions with QuTiP [here](https://qutip.readthedocs.io/en/latest/guide/guide-dynamics.html).
 
@@ -85,7 +85,7 @@ b.show()
 
 ## Simulation with varying magnetic field
 
-Above we passed a constant Hamiltonian to `sesolve`. In QuTiP these constant operators are represented by `Qobj`. However, `sesolve` can also take time-dependent operators as an argument, which are represented by [`QobjEvo`](https://qutip.readthedocs.io/en/latest/apidoc/classes.html?highlight=qobjevo#qutip.QobjEvo) in QuTiP. In this section we define the magnetic field with a linear and a periodic field strength, and observe the changes in the expecation value of $\sigma_y$.
+Above we passed a constant Hamiltonian to `sesolve`. In QuTiP these constant operators are represented by `Qobj`. However, `sesolve` can also take time-dependent operators as an argument, which are represented by [`QobjEvo`](https://qutip.readthedocs.io/en/latest/apidoc/time_dep.html#qutip.core.cy.qobjevo.QobjEvo) in QuTiP. In this section we define the magnetic field with a linear and a periodic field strength, and observe the changes in the expecation value of $\sigma_y$.
 You can find more information on `QobjEvo` in [this notebook](https://nbviewer.jupyter.org/github/qutip/qutip-notebooks/blob/master/examples/qobjevo.ipynb).
 
 We start by defining two functions for the field strength of the magnetic field. To be passed on to `QobjEvo` the functions need two arguments: the times and optional arguments.

tutorials-v4/time-evolution/003_qubit-dynamics.md

@@ -21,7 +21,7 @@ Modified by: C. Staufebiel (2022)
 ### Introduction
 In this notebook we will explore the dynamics of a single-qubit interacting with an environment. The evolution of the qubit state is governed by the Master equation. We will make use of the master equation solver `qutip.mesolve` implemented in qutip, to obtain the time-evolution of the qubit for different settings.
 
-You can read more about the master equation solver (and the theory behind it) in the [QuTiP docs](https://qutip.readthedocs.io/en/latest/apidoc/functions.html?highlight=sesolve#module-qutip.sesolve).
+You can read more about the master equation solver (and the theory behind it) in the [QuTiP docs](https://qutip.readthedocs.io/en/latest/apidoc/time_dep.html#qutip.core.cy.qobjevo.QobjEvo).
 
 ### Import
 Here we import the required modules for this example.

tutorials-v5/heom/heom-5b-fermions-discrete-boson-model.md

@@ -20,7 +20,7 @@ kernelspec:
 
 Here we model a single fermion coupled to two electronic leads or reservoirs (e.g.,  this can describe a single quantum dot, a molecular transistor, etc), also coupled to a discrete bosonic (vibronic) mode.
 
-Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his Dissertation https://opus4.kobv.de/opus4-fau/files/10984/DissertationChristianSchinabeck.pdf and related publications. In particular this example reproduces some results from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.94.201407
+Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his Dissertation https://open.fau.de/items/36fdd708-a467-4b59-bf4e-4a2110fbc431 and related publications. In particular this example reproduces some results from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.94.201407
 
 Notation:
 

tutorials-v5/lectures/Lecture-11-Charge-Qubits.md

@@ -39,7 +39,7 @@ where $E_C$ is the charge energy, $E_J$ is the Josephson energy, and $\left| n\r
 
 #### References
 
- * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](http://link.aps.org/doi/10.1103/PhysRevA.76.042319)
+ * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.76.042319)
  * [Y.A. Pashkin et al, Quantum Inf Process 8, 55 (2009)](http://dx.doi.org/10.1007/s11128-009-0101-5)
 
 

tutorials-v5/lectures/Lecture-2B-Single-Atom-Lasing.md

@@ -63,9 +63,9 @@ in units where $\hbar = 1$.
 
 References:
 
- * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](http://dx.doi.org/10.1103/PhysRevA.46.5944)
+ * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.46.5944)
 
- * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](http://dx.doi.org/10.1103/PhysRevLett.98.067204)
+ * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.067204)
 
  * [S. Ashhab, J.R. Johansson, A.M. Zagoskin, F. Nori, New J. Phys. 11, 023030 (2009)](http://dx.doi.org/10.1088/1367-2630/11/2/023030)
 

tutorials-v5/lectures/Lecture-3A-Dicke-model.md

@@ -49,7 +49,7 @@ $\displaystyle J_\pm = \sum_{i=1}^N \sigma_\pm^{(i)}$
 
 ### References
 
- * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](http://dx.doi.org/10.1103/PhysRev.93.99)
+ * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](https://journals.aps.org/pr/abstract/10.1103/PhysRev.93.99)
 
 
 ## Setup problem in QuTiP
@@ -198,7 +198,7 @@ fig.tight_layout()
 
 ### References
 
-* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](http://dx.doi.org/10.1103/PhysRevLett.92.073602).
+* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.92.073602).
 
 ```python
 def calulcate_entropy(M, N, g_vec):