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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 0.73
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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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email: [email protected]
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$Date:: $
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Copyright (C) 2006-2008 University of Amsterdam
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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], [email protected]
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last revised: 28 February 2006
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Copyright (C) 2006 M.A. Yurkin and A.G. Hoekstra
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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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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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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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at the University of Amsterdam. From the very beginning the code was intended to
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run on a multiprocessor system (parallelizing a single DDA simulation). Recently
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the code was significantly rewritten and improved by Yurkin. ADDA is intended to
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be a versatile tool, suitable for a wide variety of applications ranging from
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development was conducted by Hoekstra and coworkers for more than 10 years in
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University of Amsterdam. From the very beginning the code was intended to run on
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a multiprocessor system (parallelizing a single DDA simulation). Recently the
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code was significantly rewritten and improved by Yurkin. ADDA is intended to be
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a versatile tool, suitable for a wide variety of applications ranging from
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interstellar dust and atmospheric aerosols to biological particles; its
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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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Detailed instructions for using ADDA and all relevant issuse 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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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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The authors make this code openly available to others, in the hope that
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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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* If you publish results obtained using ADDA, please consider acknowledging the
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source of the code.
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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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3. OBTAINING THE SOURCE CODE
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****************************
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The recent version can be downloaded from:
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http://www.science.uva.nl/research/scs/Software/adda/
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The package contains the following:
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We are currently working to make a www page for ADDA, where it will be
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possible to download it. Currently, the latest version of ADDA can be obtained
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by sending a request to one of the authors: [email protected] or
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[email protected]. The package contains the following:
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doc/ - documentation
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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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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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manual.pdf - User Manual for ADDA in PDF format.
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readme - this file
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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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avg_params.dat - parameters for orientation averaging
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scat_params.dat - parameters for grid of scattering angles
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misc/ - additional files, not supported by the authors.
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sample/ - sample output and other files
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run000_sphere_g16m1_5/ - sample output directory, contains "log", "mueller",
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and "CrossSec-Y".
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test.pbs - sample PBS script for MPI system
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test.sge - sample SGE script for MPI system
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batch - sample PBS script for MPI system
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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, GenerateB.c, io.c/h, iterative.c, make_particle.c,
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matvec.c, memory.c/h, prec_time.c/h, Romberg.c/h, timing.c, 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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cfft99D.f - source file for Temperton FFT
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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).

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