Implement Päivi's suggestions except the Applications part.

Former-commit-id: 1a2846bf8762bfa4c22ce7ff2eb83c37cc17da37

lepaper/Tmatrix.bib

@@ -1040,8 +1040,7 @@ matrix method for multilayer calculations.},
   number = {1}
 }
 
-@article{vakevainen_plasmonic_2014-1,
+@article{vakevainen_plasmonic_2014,
-  ids = {vakevainen\_plasmonic\_2014},
   title = {Plasmonic {{Surface Lattice Resonances}} at the {{Strong Coupling Regime}}},
   author = {V{\"a}kev{\"a}inen, A. I. and Moerland, R. J. and Rekola, H. T. and Eskelinen, A.-P. and Martikainen, J.-P. and Kim, D.-H. and T{\"o}rm{\"a}, P.},
   year = {2014},

lepaper/arrayscat.lyx

@@ -491,6 +491,67 @@ These are compatibility macros for the (...)-old files:
 \end_layout
 
 \begin_layout Title
+Multiple-scattering 
+\begin_inset Formula $T$
+\end_inset
+
+-matrix simulations for nanophotonics: symmetries and periodic lattices
+\end_layout
+
+\begin_layout Author
+Marek Nečada
+\begin_inset Foot
+status open
+
+\begin_layout Plain Layout
+\begin_inset CommandInset href
+LatexCommand href
+target "marek@necada.org"
+type "mailto:"
+literal "false"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+, Päivi Törmä
+\begin_inset Foot
+status open
+
+\begin_layout Plain Layout
+\begin_inset CommandInset href
+LatexCommand href
+target "paivi.torma@aalto.fi"
+type "mailto:"
+literal "false"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Address
+Department of Applied Physics, Aalto University School of Science, P.O.
+ Box 15100, FI-00076 Aalto, Finland
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+Alternative titles:
+\end_layout
+
+\begin_layout Itemize
 Many-particle 
 \begin_inset Formula $T$
 \end_inset
@@ -499,18 +560,6 @@ Many-particle
  modes
 \end_layout
 
-\begin_layout Standard
-Alternative titles:
-\end_layout
-
-\begin_layout Itemize
-Multiple-scattering 
-\begin_inset Formula $T$
-\end_inset
-
--matrix simulations for nanophotonics: symmetries and periodic lattices.
-\end_layout
-
 \begin_layout Itemize
 Many-particle 
 \begin_inset Formula $T$
@@ -527,6 +576,11 @@ Many-particle
 -matrix simulations in finite and infinite systems of electromagnetic scatterers
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \begin_inset Note Note
 status open
@@ -610,10 +664,7 @@ The T-matrix multiple scattering method (TMMSM) can be used to solve the
  retaining a good level of accuracy while using relatively few degrees of
  freedom, largely surpassing other methods in the number of scatterers it
  can deal with.
-\end_layout
+ Here we extend the method to infinite periodic structures using Ewald-type
-
-\begin_layout Abstract
-Here we extend the method to infinite periodic structures using Ewald-type
  lattice summation, and we exploit the possible symmetries of the structure
  to further improve its efficiency, so that systems containing tens of thousands
  of particles can be studied with relative ease.
@@ -636,10 +687,6 @@ Should I mention also the cross sections formulae in abstract / intro?
 
 \end_inset
 
-
-\end_layout
-
-\begin_layout Abstract
 We release a modern implementation of the method, including the theoretical
  improvements presented here, under GNU General Public Licence.
 \end_layout

lepaper/examples.lyx

@@ -289,6 +289,11 @@ wide false
 sideways false
 status open
 
+\begin_layout Plain Layout
+\align center
+\begin_inset Note Note
+status open
+
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
@@ -305,6 +310,11 @@ status open
 \end_inset
 
  
+\end_layout
+
+\end_inset
+
+
 \begin_inset Caption Standard
 
 \begin_layout Plain Layout
@@ -361,6 +371,11 @@ status open
 
 \end_layout
 
+\begin_layout Plain Layout
+\align center
+\begin_inset Note Note
+status open
+
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
@@ -370,6 +385,11 @@ status open
 \end_inset
 
 
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -570,6 +590,11 @@ wide false
 sideways false
 status open
 
+\begin_layout Plain Layout
+\align center
+\begin_inset Note Note
+status open
+
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
@@ -579,6 +604,11 @@ status open
 \end_inset
 
 
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -690,6 +720,11 @@ wide false
 sideways false
 status open
 
+\begin_layout Plain Layout
+\align center
+\begin_inset Note Note
+status open
+
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
@@ -699,6 +734,11 @@ status open
 \end_inset
 
 
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout

lepaper/infinite.lyx

@@ -2139,7 +2139,7 @@ If we assume that
 
  is chosen to represent the (rough) maximum tolerated magnitude of the summand
  with regard to target accuracy.
- This adjustment means that, in worst-case scenario, with growing wavenumber
+ This adjustment means that, in the worst-case scenario, with growing wavenumber
  one has to include an increasing number of terms in the long-range sum
  in order to achieve a given accuracy, the number of terms being proportional
  to 
@@ -2271,8 +2271,8 @@ noprefix "false"
  translation operator: 
 \begin_inset Formula 
 \begin{align}
-\vswfrtlm{\tau}lm\left(\kappa\vect r\right) & =\sum_{m'=-1}^{1}\tropr_{\tau lm;21m'}\left(\kappa\vect r\right)\vswfrtlm21{m'}\left(0\right),\nonumber \\
+\vswfrtlm{\tau}lm\left(\kappa\vect r\right) & =\sum_{m'=-1}^{1}\tropr_{\tau lm;21m'}\left(\kappa\vect r\right)\vswfrtlm 21{m'}\left(0\right),\nonumber \\
-\vswfouttlm{\tau}lm\left(\kappa\vect r\right) & =\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\vect r\right)\vswfrtlm21{m'}\left(0\right),\label{eq:VSWFs expressed as translated dipole waves}
+\vswfouttlm{\tau}lm\left(\kappa\vect r\right) & =\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\vect r\right)\vswfrtlm 21{m'}\left(0\right),\label{eq:VSWFs expressed as translated dipole waves}
 \end{align}
 
 \end_inset
@@ -2299,7 +2299,7 @@ noprefix "false"
 \end_inset
 
  and the fact that all the other regular VSWFs except for 
-\begin_inset Formula $\vswfrtlm21{m'}$
+\begin_inset Formula $\vswfrtlm 21{m'}$
 \end_inset
 
  vanish at origin.
@@ -2372,10 +2372,10 @@ status open
 \begin_inset Formula 
 \begin{align*}
 \vect E_{\mathrm{scat}}\left(\vect r\right) & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect n,\alpha}{\tau}lm\vect u_{\tau lm}\left(\kappa\left(\vect r-\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\\
- & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect0,\alpha}{\tau}lme^{i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\left(\vect r-\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm21{m'}\left(0\right)\\
+ & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect 0,\alpha}{\tau}lme^{i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\left(\vect r-\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm 21{m'}\left(0\right)\\
- & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect0,\alpha}{\tau}lme^{-i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\left(\vect r+\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm21{m'}\left(0\right),\text{FIXME signs}\\
+ & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect 0,\alpha}{\tau}lme^{-i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\trops_{\tau lm;21m'}\left(\kappa\left(\vect r+\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm 21{m'}\left(0\right),\text{FIXME signs}\\
- & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect0,\alpha}{\tau}lme^{-i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\psi_{\lambda,m-m'}\left(\kappa\left(\vect r+\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm21{m'}\left(0\right)\\
+ & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect 0,\alpha}{\tau}lme^{-i\vect k\cdot\vect R_{\vect n}}\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\psi_{\lambda,m-m'}\left(\kappa\left(\vect r+\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\vswfrtlm 21{m'}\left(0\right)\\
- & =\sum_{\alpha\in\mathcal{P}_{1}}e^{-i\vect k\cdot\left(\vect r-\vect r_{\alpha}\right)}\sum_{\tau lm}\outcoeffptlm{\vect0,\alpha}{\tau}lm\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\sigma_{\lambda,m-m'}\left(\vect k,\vect r-\vect r_{\alpha}\right)
+ & =\sum_{\alpha\in\mathcal{P}_{1}}e^{-i\vect k\cdot\left(\vect r-\vect r_{\alpha}\right)}\sum_{\tau lm}\outcoeffptlm{\vect 0,\alpha}{\tau}lm\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\sigma_{\lambda,m-m'}\left(\vect k,\vect r-\vect r_{\alpha}\right)
 \end{align*}
 
 \end_inset
@@ -2393,7 +2393,7 @@ TODO fix signs and exponential phase factors
 \begin_inset Formula 
 \begin{align*}
 \vect E_{\mathrm{scat}}\left(\vect r\right) & =\sum_{\left(\vect n,\alpha\right)\in\mathcal{P}}\sum_{\tau lm}\outcoeffptlm{\vect n,\alpha}{\tau}lm\vect u_{\tau lm}\left(\kappa\left(\vect r-\text{\vect R_{\vect n}-\vect r_{\alpha}}\right)\right)\\
- & =\sum_{\alpha\in\mathcal{P}_{1}}e^{-i\vect k\cdot\left(\vect r-\vect r_{\alpha}\right)}\sum_{\tau lm}\outcoeffptlm{\vect0,\alpha}{\tau}lm\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\sigma_{\lambda,m-m'}\left(\vect k,\vect r-\vect r_{\alpha}\right).
+ & =\sum_{\alpha\in\mathcal{P}_{1}}e^{-i\vect k\cdot\left(\vect r-\vect r_{\alpha}\right)}\sum_{\tau lm}\outcoeffptlm{\vect 0,\alpha}{\tau}lm\sum_{m'=-1}^{1}\sum_{\lambda=\left|l-1\right|+\left|\tau-2\right|}^{l+1}\tropcoeff_{\tau lm;21m'}^{\lambda}\sigma_{\lambda,m-m'}\left(\vect k,\vect r-\vect r_{\alpha}\right).
 \end{align*}
 
 \end_inset