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‎doc/README‎

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Maxim A. Yurkin
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Institute of Chemical Kinetics and Combustion,
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Siberian Branch of the Russian Academy of Sciences,
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Institutskaya 3, Novosibirsk, 630090, Russia,
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tel: +7-383-333-3240, fax: +7-383-334-2350
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Alfons G. Hoekstra
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Faculty of Science, Section Computational Science,
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of the University of Amsterdam,
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ADDA 0.76
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***********
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"Amsterdam DDA"
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Maxim A. Yurkin(1,2) and Alfons G. Hoekstra(1)
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(1) Faculty of Science, Section Computational Science,
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of the University of Amsterdam,
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Kruislaan 403, 1098 SJ, Amsterdam, The Netherlands,
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tel: +31-20-525-7530, fax: +31-20-525-7490
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(2) Institute of Chemical Kinetics and Combustion,
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Siberian Branch of the Russian Academy of Sciences,
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Institutskaya 3, Novosibirsk 630090 Russia,
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tel: +7-3832-333240, fax: +7-3832-342350
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email: [email protected]
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last revised: 9 October 2006
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$Date:: $
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Copyright (C) 2006-2008 University of Amsterdam
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Copyright (C) 2006 University of Amsterdam
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This software package is covered by the GNU General Public License.
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1. INTRODUCTION
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***************
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ADDA is a C software package to calculate scattering and absorption of
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electromagnetic waves by particles of arbitrary geometry using the Discrete
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Dipole Approximation (DDA). In this approximation the volume of the scatterer
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1. INTRODUCTION
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***************
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ADDA is a C software package to calculate scattering and absorption of
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electromagnetic waves by particles of arbitrary geometry using the Discrete
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Dipole Approximation (DDA). In this approximation the volume of the scatterer
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is divided into small cubical subvolumes ("dipoles"), interaction of which is
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considered approximately based on the integral equation for the electric field.
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Initially DDA (sometimes referred to as the "coupled dipole approximation") was
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proposed replacing the scatterer by a set of point dipoles (hence the name of
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the technique).
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the technique).
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ADDA is a C implementation of the DDA developed by the authors. The
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development has been conducted by Hoekstra and coworkers for more than 10 years
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applicability is limited only by available computer resources. As provided, ADDA
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should be usable for many applications without modification, but the program is
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written in a modular form, so that modifications, if required, should be fairly
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straightforward.
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straightforward.
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Detailed instructions for using ADDA and all relevant issues are contained in
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the User Manual for ADDA. The User Manual is in the file "manual.pdf" in PDF
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the User Manual for ADDA. The User Manual is in the file "manual.pdf" in PDF
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format. It contains instructions for:
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* compiling and linking the code;
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* running a sample simulation;
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* specifying what scattering quantities should be calculated;
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* understanding the computational aspects and timing of the code;
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* understanding the command line options and formats of input and output files.
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* modifying the source code for added functionality
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2. AVAILABILITY
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it will prove to be a useful tool. We ask only that:
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* If you publish results obtained using ADDA, you should acknowledge the source
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of the code. We recommend the following general reference:
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M. A. Yurkin, V. P. Maltsev, and A.G. Hoekstra, "The discrete dipole
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approximation for simulation of light scattering by particles much larger than
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the wavelength", J. Quant. Spectros. Radiat. Transf. 106, 546-557 (2007).
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of the code. Please contact the authors ([email protected]) for the most
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recent reference.
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* If you discover any errors in the code, please promptly communicate them to
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the authors.
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Public License) of the Free Software Foundation: you may copy, distribute,
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and/or modify the software identified as coming under this agreement. If
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you distribute copies of this software, you must give the recipients all the
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rights which you have. See the file "copyleft" distributed with the ADDA
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rights which you have. See the file "copyleft" distributed with the ADDA
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software.
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We also strongly encourage you to send email to the authors identifying
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copyleft - GNU General Public License
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history - complete history of ADDA development
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faq - frequently asked questions
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manual.doc - source of User Manual in MS Word format
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manual.pdf - user Manual for ADDA in PDF format
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manual.pdf - User Manual for ADDA in PDF format
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README - this file
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todo.xls - source of the todo list in MS Excel format
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todo.pdf - todo list in PDF format
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input/ - default input files
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tables/ - 10 auxiliary files with tables of integrals
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alldir_params.dat - parameters for integral scattering quantities
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stdout - stdout of a sample simulation
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src/
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Makefile, make_seq, make_mpi - makefiles
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ADDAmain.c, CalculateE.c, calculator.c, cmplx.h, const.h, crosssec.c/h,
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comm.c/h, debug.c/h, fft.c, function.h, GenerateB.c, io.c/h, iterative.c,
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make_particle.c, matvec.c, memory.c/h, os.h, param.c/h, parbas.h,
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prec_time.c/h, Romberg.c/h, sinint.c, timing.c/h, types.h, vars.c/h
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ADDAmain.c, CalculateE.c, calculator.c, cmplx.h, const.h, crosssec.c/h,
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comm.c/h, debug.c/h, fft.c, function.h, GenerateB.c, io.c/h, iterative.c,
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make_particle.c, matvec.c, memory.c/h, os.h, param.c/h, prec_time.c/h,
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Romberg.c/h, timing.c/h, types.h, vars.c/h
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- source and header files of ADDA
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cfft99D.f - source file for Temperton FFT
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mt19937ar.c/h - source and header files for Mersenne Twister random generator.
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mt19937ar.c/h - source and header files for Mersenne Twister random generator.
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4. COMPILING AND LINKING
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************************
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4. COMPILING AND LINKING
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************************
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On Unix systems, while positioned in src/, type
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On Unix systems, while positioned in src/, type
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> make seq
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or
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or
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> make mpi
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for sequential and MPI versions respectively. By default you need FFTW to be
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for sequential and MPI versions respectively. By default you need FFTW to be
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installed (www.fftw.org) on your system.
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Please read the User Manual (manual.pdf).

‎doc/faq‎

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Frequently Asked Questions
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about ADDA
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about Amsterdam DDA
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$Date:: $
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last revised: 5 October 2006
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Q: I have found a bug in ADDA. What should I do?
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A: 1) Make sure you are using the latest version of ADDA (check the ADDA
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homepage). If you have modified the code yourself, try the original release.
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A: 1) Make sure you are using the latest version of ADDA (check the ADDA
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homepage). If you have modified the code yourself, try the original release.
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2) Look at the list of known bugs at the ADDA homepage, maybe your bug is
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already known.
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already known.
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3) Try to understand how exactly the bug occurs, write down the sequence of
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actions that lead to it.
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actions that lead to it.
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4) Please try to localize the bug, i.e. try to remove as much command line
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parameters as possible without removing the bug. Also try to use defautl
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parameters as possible without removing the bug. Also try to use defautl
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versions of input files, that you have modified.
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5) Send the results of (3) and (4) to the authors, together with all input
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files and Makefiles that you have used for compilation. Do not forget to
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include all the relevant output files, at least 'log'. Please also include
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files and Makefiles that you have used for compilation. Please also include
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a brief description of your operation system and hardware. We will try to
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fix the bug as soon as possible.
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Q: I do not understand how to ...? I run ADDA and get strange output or
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something different from what I have expected. What should I do?
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A: 1) Make sure you are using the latest version of ADDA (check the ADDA
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homepage). Read carefully the relevant parts of the manual.
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2) Check the FAQ section of ADDA homepage.
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3) If that does not help, you're encouraged to send your question to the
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authors. Please try to make your question as specific as possible. If your
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question is based on a particular run, provide all relevant input and output
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files, at least 'log'.
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Q: Can I use ADDA to calculate scattering by a particle near the infinite
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dielectric plane surface?
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A: Basically, no. ADDA can not rigorously solve such light scattering problem.
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Such a rigorous solution requires a significant modification of the code,
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therefore it will not be implemented in the near future. However, you may
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approach this problem using the current version of ADDA.
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1) You may completely ignore the surface, this may be accurate enough if
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particle is far from the surface and the refractive index change when
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crossing the surface is small.
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2) A little more accurate approach is to consider the "incident field" in
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ADDA as a sum of incident and reflected plane waves. However, currently
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such incident field is not implemented, therefore it need first to be coded
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into ADDA.
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3) Another approach is to take a large computational box around the
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particle, and discretize the surface that falls into it. This is rigorous
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in the limit of infinite size of computational box, but requires enormous
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computational time. It also requires you to specify the shape files for all
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different sizes of the computational box.
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Q: Can I calculate near-field using ADDA?
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A: We are currently working to implement this feature in a convenient manner.
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1) You may save dipole polarizations to file by ADDA and then compute the
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near-field yourself, using a simple formula.
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2) Or you may extend the computational box with "dummy" dipoles located at
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points where you wish to calculate near-field. Saving the internal fields
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by ADDA will then produce the desired result, but at expense of extra
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computational time.
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Please see the manual for details.
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Q: How can I simulate light scattering by a particle which shape can not be
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described by any of the ADDA predefined shapes?
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A: The simplest is to specify your particle by a shape file. However, if your
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shape can easily be described in some parametric form and you are going to
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simulate a lot of particles with shapes from this class or if you think
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other users will probably simulate the same shapes, you are encouraged to
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implement new shape inside ADDA. There is an extensive instruction in the
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appendix of the manual on how to do it. Afterwards, please send modified
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source files to the authors so they would be incorporated in the next
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release for the benefit of the community.
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Q: How is the Mueller matrix, produced by ADDA, defined and/or normalized?
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A: It is defined as in Bohren & Huffman "Absorption and scattering of Light by
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Small Particles" (1983), and it is not normalized. Some other codes may
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compute Stokes scattering matrix, which is normalized so that 1,1-element
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is equal to 1 after averaging over the whole solid angle. This matrix
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should be multiplied by (pi*Csca/(lambda^2)) to get Mueller matrix. Csca is
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the scattering cross section for unpolarized light, equal to average of
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scattering cross sections for any two perpendicular incident polarizations.
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This list is far from being complete. Please send your questions to
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This list is far from being complete. Please send your questions to
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[email protected]

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