Minor updates to 16/07/23.

doc-source/_config.yml

@@ -211,6 +211,9 @@ parse:
     BLM: "$\\beta_{L,M}$"   # This works, note esc for \ IN MATHS seems required.
     ADMsymbol: "$A_{Q,S}^{K}(t)$"
 
+    # Additional links/cross-refs
+    PARTII: "{ref}`Part II <chpt:extracting-matrix-elements-overview>`"
+
 
 # Global substitutions, see https://jupyterbook.org/en/stable/content/content-blocks.html?highlight=substitutions#define-substitutions-for-your-whole-book
 # parse:

doc-source/_toc.yml

@@ -28,7 +28,7 @@ parts:
     - file: part1/platform_intro_070723
     - file: part1/theory_100723
       sections:
-      - file: part1/theory_photoionization_dynamics_191122
+      - file: part1/theory_photoionization_dynamics_140723
       - file: part1/theory_tensor_formalism_201122
       - file: part1/theory_density_matrices_310123
       - file: part1/theory_symmetry_140723

doc-source/backmatter/glossary.ipynb

@@ -34,7 +34,7 @@
     "\n",
     "\n",
     "anisotropy paramters\n",
-    "  Expansion parameters {{ BLM }} for an expansion in spherical harmonics (or similar basis sets of angular momentum functions in polar coordinates), e.g. Eq. {eq}`eq:AF-PAD-general`. Often referred to simply as \"beta parameters\", and may be dependent on various properties, e.g. $\\beta_{L,M}(\\epsilon,t...)$. Herein upper-case $L,M$ usually refer to observables or the general case, whilst lower-case $(l,m)$ usually refer specifically to the photoelectron wavefunction partial waves, and $(l,\\lambda)$ usually denote these terms referenced specifically to the molecular frame.\n",
+    "  Expansion parameters {{ BLM }} for an expansion in spherical harmonics (or similar basis sets of angular momentum functions in polar coordinates), e.g. Eq. {eq}`eq:AF-PAD-general`. Often referred to simply as \"beta parameters\", and may be dependent on various properties, e.g. $\\beta_{L,M}(\\epsilon,t...)$. Herein upper-case $L,M$ usually refer to observables or the general case, whilst lower-case $(l,m)$ usually refer specifically to the photoelectron wavefunction partial waves (see {term}`partial wave expansion`), and $(l,\\lambda)$ usually denote these terms referenced specifically to the molecular frame.\n",
     "\n",
     "\n",
     "ADMs\n",
@@ -56,8 +56,18 @@
     "HOMO\n",
     "  Highest occupied molecular orbital. Short-hand for the outermost (highest energy) valence orbital, also often used in the form HOMO-n to number lower-lying orbitals in reverse energetic order, e.g. HOMO-1 for the penultimate valence orbital.\n",
     "  \n",
+    "\n",
+    "VMI\n",
+    "  Velocity-map imaging. Experimental technique for measuring energy and angle-resolved photoelectron \"images\".\n",
     "  \n",
     "\n",
+    "RWP\n",
+    "  Rotational wavepacket. A purely rotational wavepacket (superposition of rotational eigenstates) in a molecular system, typically created via cascaded Raman interaction with a (relatively) strong IR pulse ($>10^{12}$~Wcm$^{-2}$). The resulting time-dependent molecular axis distribution can be described by a set of {{ ADMs }}.\n",
+    "\n",
+    "\n",
+    "partial wave expansion\n",
+    "  General term for an expansion of a wavefunction in a spherical-wave basis in scattering theory, typically spherical harmonics $Y_{l,m}$, where the spherical harmonics are the partial wave basis set, and specific $\\psi_{l,m}$ terms can be referred to as partial waves - see for example Refs. {cite}`landau, messiah, Sakurai`. Note conventional use of lower-case $l,m$ for these components, whilst upper-case $L,M$ are usually used for labelling harmonics pertaining to observable quantities (see {{ betas }}). \n",
+    "\n",
     "```"
    ]
   },

doc-source/backmatter/glossary.md

@@ -35,7 +35,7 @@ PADs
 
 
 anisotropy paramters
-  Expansion parameters {{ BLM }} for an expansion in spherical harmonics (or similar basis sets of angular momentum functions in polar coordinates), e.g. Eq. {eq}`eq:AF-PAD-general`. Often referred to simply as "beta parameters", and may be dependent on various properties, e.g. $\beta_{L,M}(\epsilon,t...)$. Herein upper-case $L,M$ usually refer to observables or the general case, whilst lower-case $(l,m)$ usually refer specifically to the photoelectron wavefunction partial waves, and $(l,\lambda)$ usually denote these terms referenced specifically to the molecular frame.
+  Expansion parameters {{ BLM }} for an expansion in spherical harmonics (or similar basis sets of angular momentum functions in polar coordinates), e.g. Eq. {eq}`eq:AF-PAD-general`. Often referred to simply as "beta parameters", and may be dependent on various properties, e.g. $\beta_{L,M}(\epsilon,t...)$. Herein upper-case $L,M$ usually refer to observables or the general case, whilst lower-case $(l,m)$ usually refer specifically to the photoelectron wavefunction partial waves (see {term}`partial wave expansion`), and $(l,\lambda)$ usually denote these terms referenced specifically to the molecular frame.
 
 
 ADMs
@@ -66,6 +66,9 @@ RWP
   Rotational wavepacket. A purely rotational wavepacket (superposition of rotational eigenstates) in a molecular system, typically created via cascaded Raman interaction with a (relatively) strong IR pulse ($>10^{12}$~Wcm$^{-2}$). The resulting time-dependent molecular axis distribution can be described by a set of {{ ADMs }}.
 
 
+partial wave expansion
+  General term for an expansion of a wavefunction in a spherical-wave basis in scattering theory, typically spherical harmonics $Y_{l,m}$, where the spherical harmonics are the partial wave basis set, and specific $\psi_{l,m}$ terms can be referred to as partial waves - see for example Refs. {cite}`landau, messiah, Sakurai`. Note conventional use of lower-case $l,m$ for these components, whilst upper-case $L,M$ are usually used for labelling harmonics pertaining to observable quantities (see {{ betas }}). 
+
 ```
 
 ```{code-cell} ipython3

doc-source/bibs/MF_recon_manuscript_June2020_bbt_bibtex_ongoing.bib

@@ -3333,6 +3333,15 @@ @article{Lambropoulos1998
   keywords = {\#nosource}
 }
 
+@book{landau,
+  title = {Quantum {{Mechanics}} ({{Non-relativistic Theory}})},
+  author = {Landau, L D and Lifshitz, E M},
+  year = {1977},
+  edition = {3},
+  publisher = {{Pergamon Press}},
+  keywords = {\#nosource}
+}
+
 @article{Laurent2013,
   title = {Attosecond Pulse Characterization},
   author = {Laurent, G and Cao, W and {Ben-Itzhak}, I. and Cocke, C L},
@@ -3999,6 +4008,15 @@ @article{Menzel-Jones2013a
   file = {D\:\\literature\\LiteratureStore\\Journal of Physical Chemistry Letters\\2013\\Menzel-Jones_Shapiro_2013_Using_time-resolved_experiments_and_coherent_control_to_determine_the_phase_of.pdf}
 }
 
+@book{messiah,
+  title = {Quantum {{Mechanics Volume I}}},
+  author = {Messiah, Albert},
+  year = {1970},
+  publisher = {{North-Holland Publishing Company}},
+  keywords = {\#nosource},
+  file = {D\:\\literature\\LiteratureStore\\North-Holland Publishing Company\\1970\\Messiah_1970_Quantum_Mechanics_Volume_I.pdf}
+}
+
 @article{Mikosch2013,
   title = {The Quantitative Determination of Laser-Induced Molecular Axis Alignment.},
   author = {Mikosch, Jochen and Bisgaard, Christer Z and Boguslavskiy, Andrey E and Wilkinson, Iain and Stolow, Albert},
@@ -5088,6 +5106,17 @@ @book{RTscattering
   keywords = {\#nosource}
 }
 
+@book{Sakurai,
+  title = {Modern Quantum Mechanics},
+  author = {Sakurai, Jun John},
+  year = {1994},
+  edition = {Revised edition},
+  publisher = {{Addison-Wesley}},
+  address = {{Reading, MA}},
+  url = {https://cds.cern.ch/record/1167961},
+  file = {D\:\\literature\\LiteratureStore\\Addison-Wesley\\1994\\Sakurai_1994_Modern_quantum_mechanics.pdf}
+}
+
 @article{Schalk2011,
   title = {Rotational Dephasing of Symmetric Top Molecules: {{Analytic}} Expressions and Applications},
   author = {Schalk, Oliver and Hockett, Paul},

doc-source/part1/theory_100723.ipynb

@@ -60,9 +60,19 @@
     "\n",
     "In this chapter a number of fundamentals are outlined. Only a brief introduction to the necessary physics (which already has a rich literature) is presented, and the emphasis is instead on code and numerical examples. These are intended both to give readers an insight into the physics, and also illustrate aspects of the {{ PEMtk_repo }} and {{ ePSproc_full }} that can be used for these problems. These methods will form the basis for the numerical reconstruction work presented in Part II.\n",
     "\n",
-    "Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section - sections {numref}`Sect. %s: <sect:theory:observables>` {ref}`<sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` {ref}`<sec:info-content>` should provide sufficient background for pure reconstruction problems.\n",
-    "\n"
+    "Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section; {numref}`Sect. %s: <sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` should provide sufficient background for pure reconstruction problems.\n",
+    "\n",
+    "% Issues with {ref} cases here... not sure why.\n",
+    "% Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section - sections {numref}`Sect. %s: <sect:theory:observables>` {ref}`<sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` {ref}`<sec:info-content>` should provide sufficient background for pure reconstruction problems."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "76c18809-d1f5-4fc2-9945-8f4dcde6ef7d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -84,7 +94,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

doc-source/part1/theory_100723.md

@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.5
+    jupytext_version: 1.14.7
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -61,4 +61,11 @@ TODO (from https://github.com/phockett/Quantum-Metrology-with-Photoelectrons-Vol
 
 In this chapter a number of fundamentals are outlined. Only a brief introduction to the necessary physics (which already has a rich literature) is presented, and the emphasis is instead on code and numerical examples. These are intended both to give readers an insight into the physics, and also illustrate aspects of the {{ PEMtk_repo }} and {{ ePSproc_full }} that can be used for these problems. These methods will form the basis for the numerical reconstruction work presented in Part II.
 
-Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section - sections {numref}`Sect. %s: <sect:theory:observables>` {ref}`<sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` {ref}`<sec:info-content>` should provide sufficient background for pure reconstruction problems.
+Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section; {numref}`Sect. %s: <sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` should provide sufficient background for pure reconstruction problems.
+
+% Issues with {ref} cases here... not sure why.
+% Readers only interested in fitting problems from an experimental perspective may wish to skip most of this section - sections {numref}`Sect. %s: <sect:theory:observables>` {ref}`<sect:theory:observables>` and {numref}`Sect. %s: <sec:info-content>` {ref}`<sec:info-content>` should provide sufficient background for pure reconstruction problems.
+
+```{code-cell} ipython3
+
+```