Rewrite intro

Former-commit-id: c682efe8f85f9dd03372d0a5b09b091fde11a327

lepaper/Tmatrix.bib

@@ -90,6 +90,24 @@
   file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/RQMQMC7H/mstm-manual-2013-v3.0.pdf}
 }
 
+@article{yang_real-time_2015,
+  title = {Real-Time Tunable Lasing from Plasmonic Nanocavity Arrays},
+  volume = {6},
+  copyright = {\textcopyright{} 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
+  abstract = {Plasmon lasers can support ultrasmall mode confinement and ultrafast dynamics with device feature sizes below the diffraction limit. However, most plasmon-based nanolasers rely on solid gain materials (inorganic semiconducting nanowire or organic dye in a solid matrix) that preclude the possibility of dynamic tuning. Here we report an approach to achieve real-time, tunable lattice plasmon lasing based on arrays of gold nanoparticles and liquid gain materials. Optically pumped arrays of gold nanoparticles surrounded by liquid dye molecules exhibit lasing emission that can be tuned as a function of the dielectric environment. Wavelength-dependent time-resolved experiments show distinct lifetime characteristics below and above the lasing threshold. By integrating gold nanoparticle arrays within microfluidic channels and flowing in liquid gain materials with different refractive indices, we achieve dynamic tuning of the plasmon lasing wavelength. Tunable lattice plasmon lasers offer prospects to enhance and detect weak physical and chemical processes on the nanoscale in real time.},
+  language = {en},
+  urldate = {2016-03-18},
+  journal = {Nat Commun},
+  doi = {10.1038/ncomms7939},
+  url = {http://www.nature.com/ncomms/2015/150420/ncomms7939/full/ncomms7939.html},
+  author = {Yang, Ankun and Hoang, Thang B. and Dridi, Montacer and Deeb, Claire and Mikkelsen, Maiken H. and Schatz, George C. and Odom, Teri W.},
+  month = apr,
+  year = {2015},
+  keywords = {Applied physics,Optical physics,Physical sciences},
+  pages = {6939},
+  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/NQ8GH65Z/Real-time tunable lasing from plasmonic nanocavity arrays_Yang_2015.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/SNEVIHT7/Yang et al. - 2015 - Real-time tunable lasing from plasmonic nanocavity.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/GXDQ8EI6/ncomms7939.html}
+}
+
 @book{jackson_classical_1998,
   address = {{New York}},
   edition = {3 edition},
@@ -218,6 +236,19 @@
   file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/9E7R7IRX/Mackowski - 2001 - An effective medium method for calculation of the .pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/D75CJ78C/S002240730100022X.html}
 }
 
+@article{hakala_bose-einstein_2017,
+  title = {Bose-{{Einstein Condensation}} in a {{Plasmonic Lattice}}},
+  abstract = {Bose-Einstein condensation is a remarkable manifestation of quantum statistics and macroscopic quantum coherence. Superconductivity and superfluidity have their origin in Bose-Einstein condensation. Ultracold quantum gases have provided condensates close to the original ideas of Bose and Einstein, while condensation of polaritons and magnons have introduced novel concepts of non-equilibrium condensation. Here, we demonstrate a Bose-Einstein condensate (BEC) of surface plasmon polaritons in lattice modes of a metal nanoparticle array. Interaction of the nanoscale-confined surface plasmons with a room-temperature bath of dye molecules enables thermalization and condensation in picoseconds. The ultrafast thermalization and condensation dynamics are revealed by an experiment that exploits itinerant thermalization and the open cavity character of the system. A crossover from BEC to usual lasing is realized by tailoring the band structure. This new condensate is a manifestation of macroscopic quantum coherence in unprecedented time-scales, with promise for future technologies due to its room-temperature and on-chip nature.},
+  urldate = {2017-08-31},
+  journal = {arXiv:1706.01528, in review in Nature Physics},
+  url = {http://arxiv.org/abs/1706.01528},
+  author = {Hakala, T. K. and Moilanen, A. J. and V{\"a}kev{\"a}inen, A. I. and Guo, R. and Martikainen, J.-P. and Daskalakis, K. S. and Rekola, H. T. and Julku, A. and T{\"o}rm{\"a}, P.},
+  month = jun,
+  year = {2017},
+  keywords = {Condensed Matter - Quantum Gases,Physics - Optics,Quantum Physics},
+  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/V2ZCKC7E/Hakala et al. - 2017 - Bose-Einstein Condensation in a Plasmonic Lattice.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/VJSF4X3I/1706.html}
+}
+
 @book{dresselhaus_group_2008,
   title = {Group {{Theory}}: {{Application}} to the {{Physics}} of {{Condensed Matter}}},
   isbn = {978-3-540-32899-5},
@@ -406,7 +437,8 @@
   publisher = {{Artech House Publishers}},
   url = {http://gen.lib.rus.ec/book/index.php?md5=2A7D2CE03DB8CFC14E7189E9A441F759},
   author = {Chew, Weng Cho and Jin, Jian-Ming and Michielssen, Eric and Song, Jiming},
-  year = {2000}
+  year = {2000},
+  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/TRQY3K55/[Artech House Antennas and Propagation Library] Weng Cho Chew, Jian-Ming Jin, Eric Michielssen, Jiming Song - Fast and Efficient Algorithms in Computational Electromag.djvu}
 }
 
 @article{pourjamal_lasing_2019,
@@ -420,7 +452,26 @@
   author = {Pourjamal, Sara and Hakala, Tommi K. and Ne{\v c}ada, Marek and {Freire-Fern{\'a}ndez}, Francisco and Kataja, Mikko and Rekola, Heikki and Martikainen, Jani-Petri and T{\"o}rm{\"a}, P{\"a}ivi and van Dijken, Sebastiaan},
   month = apr,
   year = {2019},
-  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/C4SN68I6/Pourjamal ym. - 2019 - Lasing in Ni Nanodisk Arrays.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/S6AU6FV9/acsnano.html}
+  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/AHGWE573/10.1021@acsnano.9b01006.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/C4SN68I6/Pourjamal ym. - 2019 - Lasing in Ni Nanodisk Arrays.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/S6AU6FV9/acsnano.html}
+}
+
+@article{beyn_integral_2012,
+  series = {Special {{Issue}} Dedicated to {{Heinrich Voss}}'s 65th Birthday},
+  title = {An Integral Method for Solving Nonlinear Eigenvalue Problems},
+  volume = {436},
+  issn = {0024-3795},
+  abstract = {We propose a numerical method for computing all eigenvalues (and the corresponding eigenvectors) of a nonlinear holomorphic eigenvalue problem that lie within a given contour in the complex plane. The method uses complex integrals of the resolvent operator, applied to at least k column vectors, where k is the number of eigenvalues inside the contour. The theorem of Keldysh is employed to show that the original nonlinear eigenvalue problem reduces to a linear eigenvalue problem of dimension k. No initial approximations of eigenvalues and eigenvectors are needed. The method is particularly suitable for moderately large eigenvalue problems where k is much smaller than the matrix dimension. We also give an extension of the method to the case where k is larger than the matrix dimension. The quadrature errors caused by the trapezoid sum are discussed for the case of analytic closed contours. Using well known techniques it is shown that the error decays exponentially with an exponent given by the product of the number of quadrature points and the minimal distance of the eigenvalues to the contour.},
+  number = {10},
+  urldate = {2019-08-03},
+  journal = {Linear Algebra and its Applications},
+  doi = {10.1016/j.laa.2011.03.030},
+  url = {http://www.sciencedirect.com/science/article/pii/S0024379511002540},
+  author = {Beyn, Wolf-J{\"u}rgen},
+  month = may,
+  year = {2012},
+  keywords = {Contour integrals,Nonlinear eigenvalue problems,Numerical methods},
+  pages = {3839-3863},
+  file = {/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/WTJU82S7/beyn2012.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/XSR5YIQM/Beyn - 2012 - An integral method for solving nonlinear eigenvalu.pdf;/u/46/necadam1/unix/.mozilla/firefox/6m8fw48s.default/zotero/storage/D24EDI64/S0024379511002540.html}
 }
 
 

lepaper/arrayscat.lyx

@@ -720,7 +720,14 @@ Consistent notation of balls.
 \end_layout
 
 \begin_layout Itemize
-Abstract.
+It could be nice to include some illustration (example array) to the introductio
+n.
+ Put a specific example of how large system are we able to simulate?
+\end_layout
+
+\begin_layout Itemize
+Maybe mention that in infinite systems, it can be also much faster than
+ other methods.
 \end_layout
 
 \begin_layout Itemize
@@ -770,7 +777,7 @@ The text about symmetries is pretty dense.
 \end_layout
 
 \begin_layout Itemize
-Check whether everything written is correct also for non-symmetric space
+Check whether everything written is correct also for non-symmorphic space
  groups.
 \end_layout
 
@@ -870,7 +877,7 @@ literal "true"
 \begin_inset CommandInset bibtex
 LatexCommand bibtex
 btprint "btPrintCited"
-bibfiles "tmpaper"
+bibfiles "Tmatrix"
 options "plain"
 encoding "default"
 

lepaper/intro.lyx

@@ -137,8 +137,15 @@ s used in nanophotonics: there are modes in which the particles' electric
  the particles are, and the excitations have quadrupolar or higher-degree
  multipolar character.
  These modes typically appear at the band edges where interesting phenomena
- such as lasing or Bose-Einstein condensation have been observed – and CDA
+ such as lasing or Bose-Einstein condensation have been observed 
- by definition fails to capture such modes.
+\begin_inset CommandInset citation
+LatexCommand cite
+key "guo_lasing_2019,pourjamal_lasing_2019,hakala_lasing_2017,yang_real-time_2015,hakala_bose-einstein_2017"
+literal "false"
+
+\end_inset
+
+ – and CDA by definition fails to capture such modes.
 \end_layout
 
 \begin_layout Standard
@@ -183,49 +190,75 @@ TODO přestože blablaba, moc se to nepoužívalo, protože je težké udělat t
 
 \end_inset
 
- Due to the limitations of the existing available codes, we have been developing
- our own implementation of MSTMM, which we have used in several previous
- works studying various physical phenomena in plasmonic nanoarrays (TODO
- examples with refs).
  
 \end_layout
 
 \begin_layout Standard
-Hereby we release our MSTMM implementation, the 
+Due to the limitations of the existing available codes, we have been developing
+ our own implementation of MSTMM, which has been used in several previous
+ works studying various physical phenomena in plasmonic nanoarrays 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "pourjamal_lasing_2019,guo_lasing_2019,hakala_lasing_2017"
+literal "false"
+
+\end_inset
+
+.
+ During the process, it became apparent that although the size of the arrays
+ we were able to simulate with MSTMM was far larger than with other methods,
+ sometimes we were unable to match the full size of our physical arrays
+ (typically consisting of tens of thousands of metallic nanoparticles) due
+ to memory constraints.
+ Moreover, to distinguish the effects attributable to the finite size of
+ the arrays, it became desirable to simulate also 
+\emph on
+infinite periodic systems
+\emph default
+ with the same method, as choosing a completely different method could introduce
+ differences stemming from the method choice itself.
+ Unlike in differential methods where this can be achieved straightforwardly
+ using periodic boundary conditions, this is not trivial in MSTMM where
+ one has to deal with badly behaving infinite lattice sums.
+\end_layout
+
+\begin_layout Standard
+Here we address both challenges: we extend the method on infinite periodic
+ systems using Ewald-type summation techniques, and we exploit symmetries
+ of the system to decompose the problem into several substantially smaller
+ ones, which 1) reduces the demands on computational resources, hence speeds
+ up the computations and allows for simulations of larger systems, and 2)
+ provides better understanding of modes in periodic systems.
+\end_layout
+
+\begin_layout Standard
+We hereby release our MSTMM implementation, the 
 \emph on
 QPMS Photonic Multiple Scattering
 \emph default
- suite, as an open source software under the GNU General Public License
+ suite, as free software under the GNU General Public License version 3.
- version 3.
  (TODO refs to the code repositories.) QPMS allows for linear optics simulations
  of arbitrary sets of compact scatterers in isotropic media.
  The features include computations of electromagnetic response to external
  driving, the related cross sections, and finding resonances of finite structure
 s.
- Moreover, in QPMS we extensively employ group theory to exploit the physical
+ Moreover, it includes the improvements covered in this paper, enabling
- symmetries of the system to further reduce the demands on computational
+ to simulate even larger systems and also infinite structures with periodicity
- resources, enabling to simulate even larger systems.
+ in one, two or three dimensions, which can be e.g.
+ used for quickly evaluating dispersions of such structures, and also their
+ topological invariants (TODO).
+ The QPMS suite contains a core C library, Python bindings and several utilities
+ for routine computations.
  
 \begin_inset Note Note
 status open
 
 \begin_layout Plain Layout
-(TODO put a specific example here of how large system we are able to simulate?)
+, such as TODO.
 \end_layout
 
 \end_inset
 
- Although systems of large 
-\emph on
-finite
-\emph default
- number of scatterers are the area where MSTMM excels the most—simply because
- other methods fail due to their computational complexity—we also extended
- the method onto infinite periodic systems (photonic crystals); this can
- be used for quickly evaluating dispersions of such structures and also
- their topological invariants (TODO).
- The QPMS suite contains a core C library, Python bindings and several utilities
- for routine computations, such as TODO.
  It includes extensive Doxygen documentation, together with description
  of the API, making extending and customising the code easy.
 \end_layout
@@ -238,7 +271,8 @@ reference "sec:Finite"
 
 \end_inset
 
- is devoted to MSTMM theory for finite systems, in Section 
+ provides a review of MSTMM theory for finite systems.
+ In Section 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "sec:Infinite"
@@ -246,15 +280,32 @@ reference "sec:Infinite"
 \end_inset
 
  we develop the theory for infinite periodic structures.
- Section 
+ In section 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:Symmetries"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+ we apply group theory on MSTMM to utilise the symmetries of the simulated
+ system.
+ Finally, section 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "sec:Applications"
 
 \end_inset
 
- demonstrates some basic practical results that can be obtained using QPMS.
+ shows some practical results that can be obtained using QPMS and benchmarks
- Finally, in Section 
+ with BEM.
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+Finally, in Section 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "sec:Comparison"
@@ -265,5 +316,10 @@ reference "sec:Comparison"
  methods.
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \end_body
 \end_document