Calculation for a spectrum of wavelengths

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Implement convenient simulation of spectrum, either inside of ADDA, or with
a separate script. Possibly optimize calculation by simultaneous solving
for many wavelength values in one iterative sequence  (should be especially
relevant in case of Rayleigh particles).

Original issue reported on code.google.com by yurkin on 24 Dec 2008 at 7:05

[GoogleCodeExporter]

Currently Baptiste Auguie is developing R package including ADDA wrapper, which
presumably can be used to calculate spectrum in a convenient way
http://r-forge.r-project.org/projects/photonics/

But I haven't tried it myself.

@baptiste

Original comment by yurkin on 11 Jun 2009 at 5:49

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Baptiste has provided a sample script, which can be easily adjusted to a number 
of scripting languages.
http://groups.google.com/group/adda-discuss/msg/3f3d87fcce18808c

Original comment by yurkin on 5 Jan 2011 at 4:56

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Baptiste's wrapper is available at 
https://github.com/baptiste/adda/wiki/wrapper_primer together with usage 
example specifically for spectrum calculation.

Since this wrapper is simple and can be easily adapted to any needs, 
implementing the same functionality in ADDA doesn't seem useful. The only 
motivation for this is optimization of simultaneous runs, which is, however, of 
low priority. 

Original comment by yurkin on 18 May 2013 at 7:38

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This is related to issue 54. Overall, there are a number of papers, where 
repeated DDA simulations are optimized:

1. Y. Okada, I. Mann, I. Sano, and S. Mukai, “Acceleration of the iterative 
solver in the discrete dipole approximation: Application to the orientation 
variation of irregularly shaped particles,” J. Quant. Spectrosc. Radiat. 
Transfer 109, 1461–1473 (2008). http://dx.doi.org/10.1016/j.jqsrt.2008.01.004 
2. K. Muinonen and E. Zubko, “Optimizing the discrete-dipole approximation 
for sequences of scatterers with identical shapes but differing sizes or 
refractive indices,” J. Quant. Spectrosc. Radiat. Transfer 100, 288–294 
(2006). http://dx.doi.org/10.1016/j.jqsrt.2005.11.045
3. P. C. Chaumet, K. Belkebir, and A. Rahmani, “Coupled-dipole method in time 
domain,” Opt. Express 16, 20157–20165 (2008). 
http://dx.doi.org/10.1364/OE.16.020157

Some more involved options are discussed in Section 2.4.2.3 of
M. A. Yurkin, “Computational approaches for plasmonics,” in _Handbook of 
Molecular Plasmonics_, F. Della Sala and S. D’Agostino, Eds., pp. 83–135, 
Pan Stanford Publishing, Singapore (2013).
PDF available at 
http://sites.google.com/site/yurkin/publications/chapters/Yurkin%20-%20Computati
onal%20Approaches%20for%20Plasmonics.pdf

Original comment by yurkin on 16 Jan 2014 at 5:59

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Based on a few user requests (some prefer DDSCAT just it performs spectrum 
calculation automatically), it seems that there is need to provide some basic 
scripts to do basic spectrum calculation. For now, I am leaning towards Bash 
scripts, since I do have a number of them already.

Such scripts can also include a complicated parser (parsing any number of 
specified values, including Mueller matrix or some values from log file) and 
possibilities to submit multiple jobs with qsub and/or run several 
(corresponding to available number of cores) sequential jobs in parallel.

The main problem is to make it robust and user-friendly. This will most 
probably go to misc/ folder.

Original comment by yurkin on 6 May 2014 at 10:38

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[myurkin]

/cc @to266

[myurkin]

/cc @alkichigin