Doc: Restructure Examples

Restructure examples by science case.

.github/workflows/source/wrongFileNameInExamples

@@ -18,6 +18,7 @@ do
        [[ ${file:0:12} != PICMI_inputs ]] &&
        [[ ${file:0:8 } != analysis     ]] &&
        [[ ${file:  -4} != yaml         ]] &&
+       [[ ${file:0:4 } != plot         ]] &&
        [[ ${file:0:6 } != README       ]]
     then
         files+=($file)

Docs/source/refs.bib

@@ -20,6 +20,32 @@ @article{Geddes2008
 journal = {Journal of Physics: Conference Series}
 }
 
+@article{TajimaDawson1982,
+    author = {Tajima, T. and Dawson, J. M.},
+    title = "{Laser accelerator by plasma waves}",
+    journal = {AIP Conference Proceedings},
+    volume = {91},
+    number = {1},
+    pages = {69-93},
+    year = {1982},
+    month = {09},
+    abstract = "{Parallel intense laser beam ω0, k0 and ω1, k1 shone on a plasma with frequency separation equal to the plasma frequency ωp is capable of creating a coherent large electrostatic field and accelerating particles to high energies in large flux. The photon beam excites through the forward Raman scattering large amplitude plasmons whose phase velocity is equal to (ω−ω1)/(k0−k1), close to c in an underdense plasma. The plasmon traps electrons with electrostatic field EL=γ1/2⊥ mcωp/c, of the order of a few GeV/cm for plasma density to 1018 cm−3. Because of the phase velocity of the field close to c this field carries trapped electrons to high energies: W=2mc2(ω0/ωp)2. Preaccelerated particles (ions, for examples) coherent with the plasmon fields can also be accelerated. The (multiple) forward Raman instability saturates only when a sizable electron population is trapped and most of the electromagnetic energy is cascaded down to the frequency close to the cut‐off (ωp).}",
+    issn = {0094-243X},
+    doi = {10.1063/1.33805},
+    url = {https://doi.org/10.1063/1.33805}
+}
+
+@article{Esarey1996,
+  author={Esarey, E. and Sprangle, P. and Krall, J. and Ting, A.},
+  journal={IEEE Transactions on Plasma Science},
+  title={Overview of plasma-based accelerator concepts},
+  year={1996},
+  volume={24},
+  number={2},
+  pages={252-288},
+  doi={10.1109/27.509991}
+}
+
 @techreport{Geddes2009,
 title={Laser plasma particle accelerators: Large fields for smaller facility sources},
 author={Geddes, Cameron GR and Cormier-Michel, Estelle and Esarey, Eric H and Schroeder, Carl B and Vay, Jean-Luc and Leemans, Wim P and Bruhwiler, David L and Cary, John R and Cowan, Ben and Durant, Marc and others},
@@ -496,3 +522,80 @@ @book{Stix1992
     year = {1992},
     bdsk-url-1 = {https://books.google.com/books?id=OsOWJ8iHpmMC}
 }
+
+@article{Macchi2013,
+  title = {Ion acceleration by superintense laser-plasma interaction},
+  author = {Macchi, Andrea and Borghesi, Marco and Passoni, Matteo},
+  journal = {Rev. Mod. Phys.},
+  volume = {85},
+  issue = {2},
+  pages = {751--793},
+  numpages = {0},
+  year = {2013},
+  month = {May},
+  publisher = {American Physical Society},
+  doi = {10.1103/RevModPhys.85.751},
+  url = {https://link.aps.org/doi/10.1103/RevModPhys.85.751}
+}
+
+@article{Wilks2001,
+    author = {Wilks, S. C. and Langdon, A. B. and Cowan, T. E. and Roth, M. and Singh, M. and Hatchett, S. and Key, M. H. and Pennington, D. and MacKinnon, A. and Snavely, R. A.},
+    title = "{Energetic proton generation in ultra-intense laser–solid interactions}",
+    journal = {Physics of Plasmas},
+    volume = {8},
+    number = {2},
+    pages = {542-549},
+    year = {2001},
+    month = {02},
+    abstract = "{An explanation for the energetic ions observed in the PetaWatt experiments is presented. In solid target experiments with focused intensities exceeding 1020 W/cm2, high-energy electron generation, hard bremsstrahlung, and energetic protons have been observed on the backside of the target. In this report, an attempt is made to explain the physical process present that will explain the presence of these energetic protons, as well as explain the number, energy, and angular spread of the protons observed in experiment. In particular, we hypothesize that hot electrons produced on the front of the target are sent through to the back off the target, where they ionize the hydrogen layer there. These ions are then accelerated by the hot electron cloud, to tens of MeV energies in distances of order tens of μm, whereupon they end up being detected in the radiographic and spectrographic detectors.}",
+    issn = {1070-664X},
+    doi = {10.1063/1.1333697},
+    url = {https://doi.org/10.1063/1.1333697},
+    eprint = {https://pubs.aip.org/aip/pop/article-pdf/8/2/542/12669088/542\_1\_online.pdf},
+}
+
+@article{Bulanov2008,
+  title = {Accelerating monoenergetic protons from ultrathin foils by flat-top laser pulses in the directed-Coulomb-explosion regime},
+  author = {Bulanov, S. S. and Brantov, A. and Bychenkov, V. Yu. and Chvykov, V. and Kalinchenko, G. and Matsuoka, T. and Rousseau, P. and Reed, S. and Yanovsky, V. and Litzenberg, D. W. and Krushelnick, K. and Maksimchuk, A.},
+  journal = {Phys. Rev. E},
+  volume = {78},
+  issue = {2},
+  pages = {026412},
+  numpages = {6},
+  year = {2008},
+  month = {Aug},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevE.78.026412},
+  url = {https://link.aps.org/doi/10.1103/PhysRevE.78.026412}
+}
+
+@article{Dromey2004,
+    author = {Dromey, B. and Kar, S. and Zepf, M. and Foster, P.},
+    title = "{The plasma mirror—A subpicosecond optical switch for ultrahigh power lasers}",
+    journal = {Review of Scientific Instruments},
+    volume = {75},
+    number = {3},
+    pages = {645-649},
+    year = {2004},
+    month = {02},
+    abstract = "{Plasma mirrors are devices capable of switching very high laser powers on subpicosecond time scales with a dynamic range of 20–30 dB. A detailed study of their performance in the near-field of the laser beam is presented, a setup relevant to improving the pulse contrast of modern ultrahigh power lasers (TW–PW). The conditions under which high reflectivity can be achieved and focusability of the reflected beam retained are identified. At higher intensities a region of high specular reflectivity with rapidly decreasing focusability was observed, suggesting that specular reflectivity alone is not an adequate guide to the ideal range of plasma mirror operation. It was found that to achieve high reflectivity with negligible phasefront distortion of the reflected beam the inequality csΔt\\<λLaser must be met (cs: sound speed, Δt: time from plasma formation to the peak of the pulse). The achievable contrast enhancement is given by the ratio of plasma mirror reflectivity to cold reflectivity.}",
+    issn = {0034-6748},
+    doi = {10.1063/1.1646737},
+    url = {https://doi.org/10.1063/1.1646737},
+    eprint = {https://pubs.aip.org/aip/rsi/article-pdf/75/3/645/8814694/645\_1\_online.pdf},
+}
+
+@article{Roedel2010,
+  title = {High repetition rate plasma mirror for temporal contrast enhancement of terawatt femtosecond laser pulses by three orders of magnitude},
+  volume = {103},
+  ISSN = {1432-0649},
+  url = {http://dx.doi.org/10.1007/s00340-010-4329-7},
+  DOI = {10.1007/s00340-010-4329-7},
+  number = {2},
+  journal = {Applied Physics B},
+  publisher = {Springer Science and Business Media LLC},
+  author = {R\"{o}del,  C. and Heyer,  M. and Behmke,  M. and K\"{u}bel,  M. and J\"{a}ckel,  O. and Ziegler,  W. and Ehrt,  D. and Kaluza,  M. C. and Paulus,  G. G.},
+  year = {2010},
+  month = nov,
+  pages = {295–302}
+}