schiff.1 (5626B)
1 .\" Copying and distribution of this file, with or without modification, 2 .\" are permitted in any medium without royalty provided the copyright 3 .\" notice and this notice are preserved. This file is offered as-is, 4 .\" without any warranty. 5 .TH SCHIFF 1 6 .SH NAME 7 schiff \- estimate radiative properties of soft particles 8 .SH SYNOPSIS 9 .nf 10 \fBschiff \fR[\fIOPTIONS\fR]... [\fIFILE\fR] 11 .fi 12 .SH DESCRIPTION 13 \fBschiff\fR computes the radiative properties of soft particles with an 14 "Approximation Method for Short Wavelength or High Energy Scattering" [1]. The 15 implemented model is detailed in [2]. It relies on the Monte\-Carlo method to 16 solve Maxwell's equations within Schiff's approximation; it estimates total 17 cross sections (extinction, absorption and scattering cross-sections) in 18 addition of the inverse cumulative phase function. 19 .PP 20 The shapes of the soft particles are controlled by the 21 .BR schiff-geometry (5) 22 file submitted by the \fB\-i\fR option. The per wavelength optical properties 23 of the soft particles are stored in \fIFILE\fR where each line is formatted as 24 "W N K Ne" whith "W" is the wavelength in vacuum expressed in micron, "N" and 25 "K" are the real and imaginary parts, respectively, of the refractive index, 26 and "Ne" the refractive index of the medium. With no \fIFILE\fR, the optical 27 properties are read from standard input. 28 .PP 29 The estimated results follows the 30 .BR schiff-output (5) 31 format and are written to the \fIOUTPUT\fR file or to standard ouptut whether 32 the \fB\-o \fIOUTPUT\fR option is defined or not, respectively. 33 .SH OPTIONS 34 .TP 35 .B \-a \fINUM_ANGLES\fR 36 number of phase function scattering angles to estimate. These angles are 37 uniformaly distributed in [0, PI], i.e. the value of the i^th angle, i in 38 [0, \fINUM_ANGLES\fR-1], is i*PI/(\fINUM_ANGLES\fR-1). Default is 1000. 39 .TP 40 .B \-A \fINUM_ANGLES\fR 41 number of scattering angles computed from the inverse cumulative phase 42 function. The value of the i^th angle, i in [0, \fINUM_ANGLES\fR-1], is 43 CDF^-1(i/(\fINUM_ANGLES-1\fR). Default is 2000. 44 .TP 45 .B \-d \fINUM_DIRS\fR 46 number of sampled directions for each sampled geometry. Default is 100. 47 .TP 48 .B \-g \fINUM_PARTICLES\fR 49 number of sampled soft particle instances. This is actually the number of 50 realisations. Default is 10000. 51 .TP 52 .B \-G \fICOUNT\fR 53 sample \fICOUNT\fR soft particles with respect to the defined distribution, 54 dump their geometric data and exit. The data are written to \fIOUTPUT\fR or the 55 standard output whether the \fB-o\fR \fIOUTPUT\fR option is defined or not, 56 respectively. The outputted data followed the Alias Wavefront obj file format. 57 .TP 58 .B \-h 59 display short help and exit. 60 .TP 61 .B \-i \fIDISTRIBUTION\fR 62 define the 63 .BR schiff-geometry (5) 64 file that controls the geometry distribution of the soft particles. 65 .TP 66 .B \-l \fILENGTH\fR 67 characteristic length in micron of the soft particles. Used for the definition 68 of the angle that sets the limit between small and large scattering angles (see 69 equation. 7 in [2]). 70 .TP 71 .B \-n \fINUM_THREADS\fR 72 hint on the number of threads to use during the integration. By default use as 73 many threads as CPU cores. 74 .TP 75 .B \-o \fIOUTPUT\fR 76 write results to \fIOUTPUT\fR with respect to the 77 .BR schiff-output (5) 78 format. If not defined, write results to standard output. 79 .TP 80 .B \-q 81 do not print the helper message when no \fIFILE\fR is submitted. 82 .TP 83 .B \-w \fIW0\fR[\fB:\fIW1\fR]... 84 list of wavelengths in vacuum (expressed in micron) to integrate. 85 .SH EXAMPLES 86 Estimate the radiative properties of soft particles whose shape is described in 87 the \fBgeometry.yaml\fR file and its optical properties in the \fBproperties\fR 88 file. The characteristic length of the soft particle shapes is \fB2.3\fR 89 microns and the estimations is performed for the wavelengths \fB0.45\fR and 90 \fB0.6\fR microns. The results are written to the standard output: 91 .PP 92 .RS 4 93 .nf 94 $ schiff -i geometry.yaml -l 2.3 -w 0.45:0.6 properties 95 .fi 96 .RE 97 .PP 98 The soft particles have a characteristic length of \fB1\fR and their shape is 99 controlled by the \fBmy_geom.yaml\fR file. Their optical properties are read 100 from the standard input. The estimated wavelelength is \fB0.66\fR microns and 101 the results are written to the \fBmy_result\fR file: 102 .PP 103 .RS 4 104 .nf 105 $ schiff -w 0.66 -l 1.0 -i my_geom.yaml -o my_result 106 .fi 107 .RE 108 .PP 109 Sample \fB10\fR soft particles whose shape is defined by the \fBgeometry.yaml\fR 110 file and write their triangulated geometric data to the \fBtemp_output\fR file. 111 Use the 112 .BR csplit (1) 113 Unix command to split the \fBtemp_output\fR file in 10 files named 114 particle<\fINUM\fR>.obj, with NUM in [0, 9], each storing the geometric data of 115 a sampled soft particle: 116 .PP 117 .RS 4 118 .nf 119 $ schiff -i geometry.yaml -G 10 -o temp_output 120 $ csplit temp_output -z /^g\\ / {*} -f particle -b %d.obj 121 .fi 122 .RE 123 .PP 124 .SH NOTES 125 .PP 126 [1] L. I. Schiff, 1956. Approximation Method for Short Wavelength or High\-Energy 127 Scattering. Phys. Rev. 104 \- 1481\-1485. 128 .PP 129 [2] J. Charon, S. Blanco, J. F. Cornet, J. Dauchet, M. El Hafi, R. Fournier, M. 130 Kaissar Abboud, S. Weitz, 2015. Monte Carlo Implementation of Schiff's 131 Approximation for Estimating Radiative Properties of Homogeneous, 132 Simple\-Shaped and Optically Soft Particles: Application to Photosynthetic 133 Micro-Organisms. Journal of Quantitative Spectroscopy and Radiative Transfer 134 172 \- 3\-23. 135 .SH COPYRIGHT 136 \fBschiff\fR is copyright \(co CNRS 2015-2016. License GPLv3+: GNU GPL version 137 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are 138 free to change and redistribute it. There is NO WARRANTY, to the extent 139 permitted by law. 140 .SH SEE ALSO 141 .BR csplit (1), 142 .BR schiff-geometry (5), 143 .BR schiff-output (5)