NAME

schiff — estimate radiative properties of soft particles

SYNOPSIS

DESCRIPTION

schiff computes the radiative properties of soft particles with an “Approximation Method for Short Wavelength or High Energy Scattering” (Schiff, 1956). The implemented model is detailed in “Monte Carlo Implementation of Schiff's Approximation for Estimating Radiative Properties of Homogeneous, Simple-Shaped and Optically Soft Particles: Application to Photosynthetic Micro-Organisms” (Charon et al., 2015). It relies on the Monte Carlo method to solve Maxwell's equations within Schiff's approximation; it estimates total cross sections (extinction, absorption and scattering cross-sections) in addition of the inverse cumulative phase function.

The shapes of the soft particles are controlled by the schiff-geometry(5) file submitted by the -i option. The per wavelength optical properties of the soft particles are stored in optical_props where each line is formatted as “W N K Ne” with “W” is the wavelength in vacuum expressed in micron, “N” and “K” are the real and imaginary parts, respectively, of the refractive index, and “Ne” the refractive index of the medium. With no optical_props, the optical properties are read from standard input.

The estimated results follows the schiff-output(5) format and are written to the output file or to standard ouptut whether the -o is defined or not, respectively.

The options are as follows:

-a nangles_phase_func

Number of phase function scattering angles to estimate. These angles are uniformaly distributed in [0,PI], i.e. the value of the i^th angle (i in [0,nangles_phase_func]) is i*PI/(nangles_phase_func-1). Default is 1000.

-A nangles_phase_func_invcumul

Number of scattering angles computed from the inverse cumulative phase function. The value of the i^th angle (i in [0,nangles_phase_func_invcumul-1]) is CDF^-1(i/(nangles_phase_func_invcumul-1)). Default is 2000.

-d ninner_samples

Number of conditioned integration variable sampling (incident direction, volume, ray(s)) for each sampled particle-shape. Calculation of optimal value is presented in “Monte Carlo efficiency improvement by multiple sampling of conditioned integration variables” (Weitz et al., 2016). Default is 100.

-D

discard computations of the [[inverse-]cumulative] phase functions for large scattering angles. See the -l option for the definition of large scattering angles.

-g nrealisations

Number of sampled particle-shapes. This the number of realisations of the Monte Carlo algorithm. Default is 10000.

-G nparticles

Sample nparticles soft particles with respect to the defined distribution, dump their geometric data and exit. The data are written to output or the standard output whether the -o option is defined or not, respectively. The outputted data followed the Alias Wavefront obj file format.

-h

Display short help and exit.

-i distribution

Define the schiff-geometry(5) file that controls the geometry distribution of the soft particles.

-l particles_length

Characteristic length in micron of the soft particles. Used for the definition of the angle that sets the limit between small and large scattering angles (see equation 7 in “Approximation for Estimating Radiative Properties of Homogeneous, Simple-Shaped and Optically Soft Particles: Application to Photosynthetic Micro-Organisms”, Charon et al. 2015).

-n nthreads

Hint on the number of threads to use during the integration. Advice on the number of threads to use. By default, schiff uses as many threads as processor cores.

-o output

Output file. If not defined, the results are written to standard output.

-q

Do not print the helper message when no optical_props is submitted.

-w wavelelength[:wavelelength ...]

List of wavelengths in vacuum (expressed in micron) to integrate.

-v

Display version information and exit.

EXIT STATUS

The schiff utility exits 0 on success, and >0 if an error occurs.

EXAMPLES

Estimate the radiative properties of soft particles whose shape is described in the geometry.yaml file and its optical properties in the properties file. The characteristic length of the soft particle shapes is 2.3 microns and the estimations is performed for the wavelengths 0.45 and 0.6 microns. The results are written to the standard output:

schiff -i geometry.yaml -l 2.3 -w 0.45:0.6 properties

The soft particles have a characteristic length of 1 and their shape is controlled by the my_geom.yaml file. Their optical properties are read from the standard input. The estimated wavelelength is 0.66 microns and the results are written to the my_result file:

schiff -w 0.66 -l 1.0 -i my_geom.yaml -o my_result

Sample 10 soft particles whose shape is defined by the geometry.yaml file and write their triangulated geometric data to the output file. Use the csplit(1) command to split the output file in 10 files named particleN, with N in [0,9], each storing the geometric data of a sampled soft particle:

schiff -i geometry.yaml -G 10 -o output
N="$(grep -ce "^g " output)"
csplit -f particle -k -n1 output %^g\ % /^g\ / {$((N-2))}

SEE ALSO

csplit(1), schiff-geometry(5), schiff-output(5)

Leonard Isaac Schiff, Approximation Method for Short Wavelength or High-Energy Scattering, Physical Review, 104, pp. 1481–1485, 1956.

Julien Charon et al., Approximation for Estimating Radiative Properties of Homogeneous, Simple-Shaped and Optically Soft Particles: Application to Photosynthetic Micro-Organisms, Journal of Quantitative Spectroscopy and Radiative Transfer, 172, pp. 3–23, 2015.

Sebastian Weitz et al., Monte Carlo efficiency improvement by multiple sampling of conditioned integration variables, Journal of Computational Physics, 326, pp. 30–34, 2016.

HISTORY

schiff has been developed as part of ANR-11-IDEX-0002-02 ALGUE project.