main part of response to reviewer 1

main.tex

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 \usepackage[colorinlistoftodos]{todonotes}
 \usepackage[colorlinks=true, allcolors=blue]{hyperref}
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-\author{You}
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-\subsection{How to include Figures}
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-First you have to upload the image file from your computer using the upload link the project menu. Then use the includegraphics command to include it in your document. Use the figure environment and the caption command to add a number and a caption to your figure. See the code for Figure \ref{fig:frog} in this section for an example.
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-\includegraphics[width=0.3\textwidth]{frog.jpg}
-\caption{\label{fig:frog}This frog was uploaded via the project menu.}
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-\subsection{How to add Comments}
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-Comments can be added to your project by clicking on the comment icon in the toolbar above. % * <john.hammersley@gmail.com> 2016-07-03T09:54:16.211Z:
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-\subsection{How to add Tables}
-
-Use the table and tabular commands for basic tables --- see Table~\ref{tab:widgets}, for example. 
-
-\begin{table}
-\centering
-\begin{tabular}{l|r}
-Item & Quantity \\\hline
-Widgets & 42 \\
-Gadgets & 13
+\begin{center}
+  Response Letter
+\end{center}
+Dear Editor,
+\vspace{10pt}
+
+Many thanks for sending us referees’ reports on our manuscript
+entitled ``Mie calculation of electromagnetic near-field for a multilayered sphere'' by K. Ladutenko, U. Pal, A. Rivera and O. Pe\~na (CPC manuscript CPC-D-15-00354). We are pleased with
+overall very positive tone of these reports, as well as with referees’
+constructive comments.
+
+We have addressed all the comments of the referees, and we present our
+response and the summary of the changes made to the manuscript below.
+\vspace{10pt}
+\\
+Sincerely Yours,\\
+On behalf of the authors,\\
+%TODO add name
+
+\vspace{10pt}
+
+\newpage
+\textbf{Reviewer \#1 comments}
+
+\vspace{0.5em}
+\begin{tabular}[!H]{l|p{0.9\textwidth}}
+\quad & There are several alternatives currently available, Mathematica GLMT Scripts, for example. It provides both near- and far-field results for multilayered sphere. Moreover, Mathematica can handle Bessel functions up to arbitrary precision without any difficulties, and the code is very transparent and compact. 
 \end{tabular}
-\caption{\label{tab:widgets}An example table.}
-\end{table}
-
-\subsection{How to write Mathematics}
-
-\LaTeX{} is great at typesetting mathematics. Let $X_1, X_2, \ldots, X_n$ be a sequence of independent and identically distributed random variables with $\text{E}[X_i] = \mu$ and $\text{Var}[X_i] = \sigma^2 < \infty$, and let
-\[S_n = \frac{X_1 + X_2 + \cdots + X_n}{n}
-      = \frac{1}{n}\sum_{i}^{n} X_i\]
-denote their mean. Then as $n$ approaches infinity, the random variables $\sqrt{n}(S_n - \mu)$ converge in distribution to a normal $\mathcal{N}(0, \sigma^2)$.
+\vspace{0.5em}
 
+We are actually not very familiar with Mathematica GLMT Scripts, however, fast review of this code revealed a number of significant differences:
+\begin{itemize}
+\item As it is published at \verb+http://photonicsdesign.jimdo.com/software/+ it does not provide any appropriate license condition, particularly it is not clear, is it valid to distribute this code, to modify it (e.g. to put your own model parameters), etc.
+\item You need to buy Mathematica license first to use this license.
+\item This script do not provide near-field evaluation inside the particle, at least all provided examples do not have it.
+\item It does not use Mathematica ability to do arbitrary precision for calculation of Mie coefficients for multilayer sphere. Actually it reference our previous paper in CPC, and uses the same evaluation of spherical functions via series with the same error due to $N_{\mathrm{stop}}$ selection. 
+\end{itemize}
 
-\subsection{How to create Sections and Subsections}
+To the best of our knowledge the only code available which provide similar posibilities is MSTM by Mackowski and Mishchenko. However, it uses T-matrix approach to do the evaluation and has no usage license defined. We actually had verified our code against MSTM results too, however, do not include them to the manuscript due to abovementioned license restrictions.
 
-Use section and subsections to organize your document. Simply use the section and subsection buttons in the toolbar to create them, and we'll handle all the formatting and numbering automatically.
+\vspace{0.5em}
+\begin{tabular}[!H]{l|p{0.9\textwidth}}
+\quad & The only advantage I see of the algorithm presented here is the speed, since it is implemented in the newest C++ language. But, to prove it benchmarking should be performed.
+\end{tabular}
+\vspace{0.5em}
 
-\subsection{How to add Lists}
+We do concern the speed of our implementation, however, this is not the main point of the manuscript. To stress the novelty we provide the following changes to the manuscript:
 
-You can make lists with automatic numbering \dots
+TODO - stress novelty in the abstract, manuscript, and in the conclusion: 
+1) We provide explicit expressions for Mie coefficients inside the sphere.
+2) We suggest to use Ricatti-Bessel functions for vector spherical harmonics evaluations and prove the correctness of this approach.
 
-\begin{enumerate}
-\item Like this,
-\item and like this.
-\end{enumerate}
-\dots or bullet points \dots
-\begin{itemize}
-\item Like this,
-\item and like this.
-\end{itemize}
+\vspace{0.5em}
+\begin{tabular}[!H]{l|p{0.9\textwidth}}
+\quad & For currently presented test runs only core-shell structures are selected. The last example is, actually, from the same authors, which looks really confusing, since, I guess, they've  used exactly this code. So, they are test themselves with the same code - kind of weird. 
+\end{tabular}
+\vspace{0.5em}
 
-\subsection{How to add Citations and a References List}
+We would like to thank the reviewer for finding, that just referencing our previous paper can lead to misunderstanding. We add to the manuscript after the corresponding reference ``reported recently [10]'' the following sentence `` using full-wave commercial 3D electromagnetic simulation software CST MWS[TODO add link to cst.com in references ]''
 
-You can upload a \verb|.bib| file containing your BibTeX entries, created with JabRef; or import your \href{https://www.overleaf.com/blog/184}{Mendeley}, CiteULike or Zotero library as a \verb|.bib| file. You can then cite entries from it, like this: \cite{greenwade93}. Just remember to specify a bibliography style, as well as the filename of the \verb|.bib|.
+\vspace{0.5em}
+\begin{tabular}[!H]{l|p{0.9\textwidth}}
+\quad & Also, in Fig. 2 they compare published and their results. But in all other figures they show only their results and refer to the literature for comparison. They should present all test and original results in the current manuscript.
+\end{tabular}
+\vspace{0.5em}
 
-You can find a \href{https://www.overleaf.com/help/97-how-to-include-a-bibliography-using-bibtex}{video tutorial here} to learn more about BibTeX.
+TODO we do not compare with published result in Fig.2 - provide changed to the text.
 
-We hope you find Overleaf useful, and please let us know if you have any feedback using the help menu above --- or use the contact form at \url{https://www.overleaf.com/contact}!
+As for other figures, we do not have a permission to reprint figures from other journals, this way we can only provide referenced to them.
 
-\bibliographystyle{alpha}
-\bibliography{sample}
+\vspace{0.5em}
+\begin{tabular}[!H]{l|p{0.9\textwidth}}
+\quad & On another note, since there are plenty of Mie based simulators which can be found at scattport.org I would encourage the authors to add GUI to their code to provide more flexibility and user-friendly environment. Otherwise, it's easier to code generalised Mie solution in Mathematica, which is perfectly suitable for it, and I don't see any advantage of the current program compare to others. Near field can now also be accessed in other programs I've mentioned and found at scattport.org
+\end{tabular}
+\vspace{0.5em}
+
+We have checked each and every program listed at ``Mie type codes'' section off Scattport here http://www.scattport.org/index.php/light-scattering-software/mie-type-codes before starting the development of our code. Most of listed code re-implement Mie solution as it was published in classical book of Bohren and Huffman ``Absorption and Scattering of Light by Small Particles'' (usually referenced ad BHMIE) or MIEV0 code by Wiscombe.  The original approaches that we were able to find were referenced in the manuscript as [11-18,22,23]. Note, that most of this solutions to not provide the ability to evaluate field distribution inside the particle.
+
+
+
+
+\newpage
+\section{Reviewer \#2}
+\begin{verbatim}
+1
+Introduction
+This reviewer approaches the manuscript and contributed code by Ladutenko
+et al (herinafter “the paper”, “the code” and “the authors” respectively)
+with background experience in electromagnetic theory and radar cross-sect-
+ion computation.
+2
+General Comments
+The paper does not make any claim to originality as far as the algorithm is
+concerned. The authors claim is that the code is the first publicly-available
+implementation of a scattering code for a multi-layered sphere that includes
+near-field calculation. This reviewer has no knowledge that would contradict
+that claim. They also claim that use of Yang’s [1] algorithm yields a robust
+code that can handle “extreme” cases.
+The authors’ contribution is relevant to two long-established application
+areas in different wavelength ranges, radar cross-section prediction at mi-
+crowave frequencies and aerosol and grain scattering at optical and infra-red
+frequencies, as well as the new area of nanoparticles. The authors’ citation
+list does acknowledge some of this earlier work.
+The first recursive algorithm for the multi-layered sphere known to this
+reviewer was published by Wait [2] in 1963, although this work does not
+address the numerical issues tackled by the approach of Yang. The algorithm
+is described in a 1970 textbook [3].
+It is the personal experience of this reviewer that the long history of
+published work on sphere scattering has led to many layers of derivative
+1publications that have introduced and propagated mathematical and typo-
+graphical errors in sloppy work that has not been properly checked by its
+authors or reviewers.
+To the credit of the authors, they have corrected two typographical er-
+rors in their re-statement of equations from Yang [1], but have created ty-
+pographical errors of their own and propagated a misunderstanding from
+Yang.
+\end{verbatim}
+
+\begin{verbatim}
+3 The Write-up
+The introductory section of the write-up includes an incidental citation of the
+authors’ reference [18], which is a paper on the T-matrix method. This re-
+viewer understands the T-matrix method as being applicable to a collection
+of spheres side-by-side, not to a multi-layered sphere defined by concentric
+spherical shells. If the authors agree, reference [18] should be omitted.
+This reviewer approves of the level of detail provided by the authors in
+their derivation of the background theory and their algorithm. However, he
+makes the following suggestion to improve the logical progression of the de-
+velopment and to avoid the near-repetition of the definition of the spherical
+waves occurring in equations (2.1)–(2.4) and (9.1)–(9.4).
+First, the reader could be given more guidance to the source of the
+definitions by including the section in the citation of Bohren and Huffman
+and the continue as follows: “Vector spherical harmonics can be calculated
+using the expressions [12, Section 4.3], re-stated in terms of Ricatti-Bessel
+functions for numerical reasons [17] as. . . ” followed by equations (9.1)–(9.4).
+(1)
+(3)
+\end{verbatim}
+% The definitions of r n , ψ n , ζ n , D n and D n should be given at this early
+%point in the presentation so that they are ready to be used in equations
+%(5.1)–(5.4), (6.1)–(6.4) and (7.1)–(7.4), rather than being left until later.
+%If the authors choose to leave equations (2.1)–(2.4) as they occur in the
+%submitted version of the paper, they should correct the inconsistency in
+%notation: superscript (j) is used in (2.1) but (i) is used in (2.2)–(2.4).
+%This reviewer failed to reproduce the derivation of equations (6.1)–(6.4)
+%until he realised that there is a typographical error in equation (7.4), which
+%should read
+%T 4 (m l+1 x l ) = c (l+1)
+%D n (1) (m l+1 x l )ψ n (m l+1 x l ) − b (l+1)
+%D n (3) (m l+1 x l )ζ n (m l+1 x l )
+%n
+%n
+%The authors must correct this error and confirm that the correct T 4 has been
+%used in the code.
+%The authors have repeated the misunderstanding of Yang [1] regarding
+%the justification of the boundary conditions at the centre of the sphere:
+%(1)
+%(1)
+%a n = 0 and b n = 0. The correct reason is given by Bohren and Huffman [4]
+%in their Sections 4.3 and 8.1. The point is that only the j n (kr) dependence
+%gives a finite, non-singular behaviour at the origin, and so can be the only
+%2radial dependence occurring in the spherical wave expansion of the fields
+%in the core, region 1. A radial dependence of j n (kr) represents a standing
+%wave, that is, a superposition of both incoming and outgoing waves.
+%
+\begin{verbatim}
+The authors mention that the code can accommodate a perfectly-conduct-
+ing shell. Perfect conductor (PEC) is an idealisation that must be distin-
+guished from real conductors. The only place a PEC layer should appear in
+the model is at the core. It is futile to enclose other materials inside a PEC
+shell since such a shell would exclude all fields from its interior.
+There are several omissions from the reference list. No DOIs are given for
+[8], [9] and [22] and no ISBN is given for [12]. Several authors have second
+initials which have been omitted: J.R. Wait for [13] and M.V. Bashevoy,
+V.A. Fedotov and N.I. Zheludev for [20]. The final page number for [19]
+should be given; this reviewer cannot ascertain whether it is 4735 or 4736
+since he does not have ready access to the full paper. The full citation
+for [21] is Nat. Commun. 5:3402(2014). [26] appears to be an unpublished
+report, so readers should be told how to access it; a URL should be given.
+4
+The Code Package
+This reviewer has successfully compiled the standalone programs and run
+the supplied tests. However, he has failed to compile the python and cython
+extensions.
+The authors should put much more effort into providing a greatly ex-
+panded README file, the first place any new user would look. Step-by-step
+instructions should be provided in detail for the compilation of the various
+programs in the package including any unusual dependencies on external li-
+braries and commands. Step-by-step instructions for running the programs
+should also be given, with an explanation of the command-line arguments
+and expected outputs.
+5
+Recommendations
+This paper and code should not be published in their present form.
+They may be suitable for publication if the authors accept the sugges-
+tions and undertake the extensions and revisions described above.
+The editors should refer any revisions to this reviewer to confirm that
+the authors have acted on his suggestions and taken his recommendations
+seriously.
+The authors have chosen to use make their code publicly available on
+the Web as well as submitting it to the CPC Library. The editors must
+confirm that this action does not prevent the addition of the code to the
+CPC Library.
+\end{verbatim}
+
+
+%\bibliographystyle{alpha}
+%\bibliography{sample}
 
 \end{document}