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3526585835
lcc (guest) 20 Nov 2018 18:27
in discussion DDSCAT / General discussion » 3526585835

Dear Professor:
I am trying to calculate the Qabs of a target immersed in water with wavelength ranged from 300 nm to 700 nm. Since the refractive index will change with the wavelength frequency, how should I set the refractive index in DDSCAT.par? It seems I could only set a special number instead of variables changing with wavelength. Thanks very much!

3526585835 by lcc (guest), 20 Nov 2018 18:27

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The ONIONSHEL option in DDSCAT is intended for use with a uniaxial anisotropic material like graphite in a spherical shell, but has only been set up to do a single shell with vacuum interior.
If you want multiple shells of anisotropic materials, you will need to write your own code to create a "target file" specifying dipole locations and principal axes of the local dielectric tensor, and read it in using option ANIFRMFIL (see UserGuide sectin 21.2).
For isotropic materials, the option CONELLIPS can be used for two zones (e.g., ellipsoidal shell with vacuum interior), but for three layers you will need to write your own target generator and read the file in with option FROM_FILE (see UserGuide section 21.1).

Dear Sir,
I want to investigate the properties using shape parameter ONIONSHEL for three layers with the spherical shape.
So, as given in DDSCAT manual on page no. 21, if SHPAR1 =1, then we have to define NCOMP = 3.
Now, problem is that how to set the thickness or radius of first, second and third layers with shape parameter SHPAR1, SHPAR2, and SHPAR3?
Please give the example with setting the values SHPAR1, SHPAR2, and SHPAR3 to run the ddscat.par file.
I wish you will reply soon and explain it with depth.
Thanking You
Your Sincerely
Bhatia P.

ONIONSHEL=Onion like spherical shell study by Pradeep Bhatia (guest), 24 Oct 2018 12:31

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If your shape.dat file was generated by TARELL (as appears to be the case), it seems to be for a single sphere, not two contacting spheres.
For two contacting spheres, it is easy to use the built-in target option SPHROID_2 (see the UserGuide for details). Or you could use SPHERES_N.

Re: contacting 2 spheres model by drainedraine, 15 Sep 2018 15:20

Dear DDSCAT community,

Hello, I am new and learning to use DDSCAT 7.3. I am at first trying to reproduce results from Dr. Flatau’s 2-spheres model that are in contact with each other (APPLIED OPTICS / Vol. 32, No. 18 / 20 June 1993 ). I have tried to reproduce the data, but with no luck. First of all, my S11 and S22 values are the same. Also, when I plot and compare the points to the literature values, the forward scattering looks like it reproduces S11, whereas the backscattering looks more like S22 character. Please let me know if you have suggestions for me.

Here is my input file, and header of my shape.dat file.

Thank you,
Yohanna White

*
shape.dat:

>TARELL ellipsoidal grain; AX,AY,AZ= 32.0000 32.0000 32.0000
34512 = NAT
1.000000 0.000000 0.000000 = A_1 vector
0.000000 1.000000 0.000000 = A_2 vector
1.000000 1.000000 1.000000 = lattice spacings (d_x,d_y,d_z)/d
-15.50000 0.50000 0.50000 = lattice offset x0(1-3) = (x_TF,y_TF,z_TF)/d for dipole 0 0 0
JA IX IY IZ ICOMP(x,y,z)
1 -2 -4 -16 1 1 1
2 -1 -4 -16 1 1 1
3 0 -4 -16 1 1 1
4 1 -4 -16 1 1 1
5 -3 -3 -16 1 1 1

ddscat.par:

' ========== Parameter file for v7.3 ==================='
' Preliminaries '
'NOTORQ' = CMTORQ*6 (DOTORQ, NOTORQ) — either do or skip torque calculations
'PBCGS2' = CMDSOL*6 (PBCGS2, PBCGST, GPBICG, QMRCCG, PETRKP) — CCG method
'FFTMKL' = CMETHD*6 (GPFAFT, FFTMKL) — FFT method
'GKDLDR' = CALPHA*6 (GKDLDR, LATTDR, FLTRCD) — DDA method
'NOTBIN' = CBINFLAG (ALLBIN, ORIBIN, NOTBIN)
' Initial Memory Allocation '
100 100 100 = dimensioning allowance for target generation
' Target Geometry and Composition '
'FROM_FILE' = CSHAPE*9 shape directive
no SHPAR parameters needed
2 = NCOMP = number of dielectric materials
'm1.33_0.001' = name of file containing RI info
'm1.33_0.001' = name of file containing RI info
' Additional Nearfield calculation? '
0 = NRFLD (=0 to skip nearfield calc., =1 to calculate nearfield E)
0.0 0.0 0.0 0.0 0.0 0.0 (fract. extens. of calc. vol. in -x,+x,-y,+y,-z,+z)
' Error tolerance '
1.00e-5 = TOL = MAX ALLOWED (NORM OF |G>=AC|E>-ACA|X>)/(NORM OF AC|E>)
' maximum number of iterations allowed '
300 = MXITER
' Interaction cutoff parameter for PBC calculations '
1.00e-5 = GAMMA (1e-2 is normal, 3e-3 for greater accuracy)

' Angular resolution for calculation of <cos>, etc. '
0.5 = ETASCA (number of angles is proportional to [(3+x)/ETASCA]^2 )
' Wavelengths (micron) '
6.283 6.2833 1 'LIN' = wavelengths (first, last, how many, how=LIN,INV,LOG,TAB)
' Refractive index of ambient medium'
1.000 = NAMBIENT
' Effective Radii (micron) '
10.000 10.000 1 'LIN' = eff. radii (first, last, how many, how=LIN,INV,LOG)
' Define Incident Polarizations '
(0,0) (1.,0.) (0.,0.) = Polarization state e01 (k along x axis)
2 = IORTH (=1 to do only pol. state e01; =2 to also do orth. pol. state)
' Specify which output files to write '
0 = IWRKSC (=0 to suppress, =1 to write ".sca" file for each target orient.
' Specify Target Rotations '
0. 0. 1 = BETAMI, BETAMX, NBETA (beta=rotation around a1)
0. 0. 1 = THETMI, THET MX, NTHETA (theta=angle between a1 and k)
0. 0. 1 = PHIMIN, PHIMAX, NPHI (phi=rotation angle of a1 around k)
' Specify first IWAV, IRAD, IORI (normally 0 0 0) '
0 0 0 = first IWAV, first IRAD, first IORI (0 0 0 to begin fresh)
' Select Elements of S_ij Matrix to Print '
2 = NSMELTS = number of elements of S_ij to print (not more than 9)
11 22 = indices ij of elements to print
' Specify Scattered Directions '
'LFRAME' = CMDFRM (LFRAME, TFRAME for Lab Frame or Target Frame)
2 = NPLANES = number of scattering planes
0. 0. 180. 5 = phi, thetan_min, thetan_max, dtheta (in degrees) for plane 1
90. 0. 180. 5 = phi, thetan_min, thetan_max, dtheta (in degrees) for plane 2

contacting 2 spheres model by yohanna1yohanna1, 14 Sep 2018 20:56

Hello again,

Is there a way for ddpostprocess.exe to take the nearfield calculations from wxxxryyykzzz.E1 and wxxxryyykzzz.E2 at the same time?
I'm looking to plot a contour map of the nearfield for an asymmetric geometry where the polarization direction is important, and I can only seem to plot it for one polarization direction at a time from either .E1 or .E2

Any suggestions?

Thank you for your reply!
I figured out the problem after looking through a bit of the code for ddpostprocess.f90 and thought I'd share for any future people encountering a similar error - I had accidentally assigned multiple compositions to the same lattice positions, which caused the ICOMP(k,x,y,z) function to return 0 for a few lattice positions and the J1 iterator to miscount the number of dipoles in the target geometry.

Re: Inconsistent j1 Issue by DrPseudoDrPseudo, 31 Aug 2018 18:39

1. Have you tried running ddpostprocess on any of the examples? For example, ELLIPSOID_NEARFIELD ? (This works for me).
2. Because of a possible error involving sym links, the previous distribution of ddscat7.3.2 source code might have included an obsolete file. I just uploaded an up-to-date distribution, ddscat7.3.2_180829.tgz to this site.
If you continue to have trouble with ddpostprocess, I suggest going to Donwloads, download ddscat7.3.2_180829.tgz, and then recompile ddscat and ddpostprocess.

Re: Inconsistent j1 Issue by drainedraine, 29 Aug 2018 21:04

Hello,

I've downloaded the latest DDSCAT 7.3.2 version, compiled it using gfortran/MINGW for windows (windows 10), and run ddscat.exe
This works, however ddpostprocess.exe, which was compiled at the same time as ddscat.exe (so same architecture), always throws the error "readnf sanity failure: inconsistent j1 = 86343 and nat0 = 87601"

readnf is clearly having an issue reading the wxxxryyykzzz.E1 file, and seems to be finding an incorrect number of dipoles in some iterative loop its running to do calculations, as j1 is a variable counting the iterations of a set of loops in readnf.

How would you recommend remedying this problem?
Could my wxxxryyykzzz.E1 file contain NAN values, which get skipped by readnf?

Thanks!

Inconsistent j1 Issue by DrPseudoDrPseudo, 29 Aug 2018 16:50

Hello,

I have been trying to run DDSCAT for some custom shapes (FROM_FILE), with the shape.dat files generated from a MATLAB code or from the nanoHUB DDA Convert tool using Blender shapes. These are always created with the shape center at (0, 0, 0). The extinction spectra appear correct, and the E-field intensities generally make sense, but I run into issues somewhere between running ddpostprocess and using MayaVi or Paraview to visualize.

Despite the shape being centered, the E-field intensity map is always off-center and the shape outlines are thus cut off at the edges since they lay outside the computational volume (as ddpostprocess tells me when I try to select tracks from one edge of my shape to the other). I tried to visualize the target.out VTR files on the same set of axes in Paraview, and it looks like the entire shape is somehow thrown off-center since it matches up with the E-field plot. In MayaVi, however, I can only seem to visualize each separately, and while the E-field is still off-center, the target shape appears complete and centered in the outline box. This doesn't seem to change regardless of what I use to create the shape.dat file or what I use to visualize the ddpostprocess output.

While I know I can get a more complete image by changing the fractional extension of calculation volume in ddscat.par, my main concern is that the tracks I specify in ddpostprocess.par will not be directly through the center of the target as desired, since the entire shape is offset by some amount. Does anyone have any insight on how to resolve this issue? Would the output point towards some error in shape generation, in writing ddscat.par, or in writing ddpostprocess.par?

Thanks,
Rahil U.

E-Field Visualization Centering by Rahil U. (guest), 28 Aug 2018 18:00

Assuming that you are using DDSCAT 7.3.2:
Probably you need to increase the initial memory allocation in ddscat.par
In ddscat.par, change the line following

' Initial Memory Allocation '

to larger numbers. The three numbers refer to the max target extent in the x,y,z directions.
For example,

' Initial Memory Allocation '
30 40 50 = dimensioning allowance for target generation

allows use of targets that do not extend more than 30 lattice spacings in x, 40 in y, 50 in z.
Increase the values as needed. Note that once the target has been generated, DDSCAT will reallocate only as much memory as is required for the actual problem, so it is OK to use numbers in ddscat.par that are significantly larger than needed, as long as they don't exceed the available memory available on your system.

Dear Ya-fei Wang,

(1) Yes, what you wrote appears to be correct for specifying elliptically polarized e01. If you use IORTH=2, DDSCAT should generate an orthogonal e02 for the second incident state.

(2) Good question. The answer is "No". Think about a chiral target: Even if randomly-oriented, the cross section for absorption or scattering can be different for circularly-polarized than for linearly-polarized light. If you want to calculate the absorption or extinction cross sections, the calculation should use the actual polarization state of interest.

However, for scattering, if you calculate the Mueller scattering matrix S_ij for the desired scattering direction, then you *can* calculate the differential scattering cross section for elliptically-polarized light even if you used linearly-polarized e01 for the DDSCAT calculation. Therefore, you could in principle obtain the integrated scattering cross section Qsca and the anisotropy parameter <cos(theta)> by integrating over many scattering directions. However, this approach requires calculating S_ij for many scattering directions, which is tedious and may be numerically expensive.
If you are interested in total cross sections for polarized light, it is most efficient to calculate Q_abs, Q_sca, and Q_ext by specifying the incident polarization state of interest in ddscat.par

(3) Yes. The numbers written out in wxxxryyy.avg for JO=1 and JO=2 give <Qabs>, <Qsca>, <cos(theta)>, and <cos^2(theta)> for incident polarization states e01 and e02, averaged over the specified target orientations.

So far as I know DDSCAT is correct, but I must stress that testing of the treatment of elliptical polarization has been limited, therefore please remain alert for any results that seem suspicious. You may want to do some simple tests, such as calculating the orientationally-averaged Mueller matrix using linearly-polarized e01, and then repeating the calculation using elliptically-polarized e01. The resulting Mueller matrix S_ij should (ideally) be identical for both cases, but of course the numerically-calculated values of S_ij will differ slightly because of (1) round-off errors and (2) termination of iterative improvmenet when the error tolerance is satisfied.

Re: Incident polarization state by drainedraine, 22 Aug 2018 17:13
zack (guest) 22 Aug 2018 17:07
in discussion DDSCAT / General discussion » How to choose number of cores?

You have to run ddscat with mpiexec -np <number of processes>

for example,

mpiexec -np 3 ./ddscat
should run ddscat with NUMPROC= 3 (you can check this in the output / log file)

by zack (guest), 22 Aug 2018 17:07

FATAL ERROR IN PROCEDURE: TARCYL

NAT.GT.MXNAT

target problem (how to solve) by Giordano (guest), 22 Aug 2018 15:16
Incident polarization state
Ya-fei Wang (guest) 22 Aug 2018 07:38
in discussion DDSCAT / General discussion » Incident polarization state

Dear Professor Draine,

I am using DDSCAT 7.3 to calculate the orientationally-averaged values of Qabs, Qsca and <cosθ> of randomly-oriented soot aggregates interacting with monochromatic plane waves with specified polarization states. According to User Guide for the Discrete Dipole Approximation Code DDSCAT 7.3, DDSCAT allows the user to specify a general elliptical polarization state for the incident radiation, by specifying the (complex) polarization vector ${\hat e_{01}}$ (see §24). Moreover, if ddscat.par specifies IORTH = 2, the orthonormal polarization state ${\hat e_{02}} = {\hat x_{LF}} \times \hat e_{01}^*$is generated automatically. However, there are some confusing questions on how to specify an arbitrary polarization state for the incident plane wave in ddscat.par as follows:

(1) Assume that the incident plane wave has a specified polarization state represented by the following Jones vector:

(1)
\begin{align} J = \left[ {\begin{array}{*{20}{c}} {{E_{0y}}{e^{{\text{ - }}i{\delta _y}}}} \\ {{E_{0z}}{e^{{\text{ - }}i{\delta _z}}}} \end{array}} \right] \Leftrightarrow \left\{ {\begin{array}{*{20}{c}} {J = \frac{1}{{\sqrt {E_{0y}^2 + E_{0z}^2} }}\left[ {\begin{array}{*{20}{c}} {{E_{0y}}} \\ {{E_{0z}}{e^{{\text{ - }}i\delta }}} \end{array}} \right]} \\ {\delta = {\delta _z} - {\delta _y}} \\ {\cos \beta = \frac{{{E_{0y}}}}{{\sqrt {E_{0y}^2 + E_{0z}^2} }}} \\ {s{\text{in}}\beta = \frac{{{E_{0z}}}}{{\sqrt {E_{0y}^2 + E_{0z}^2} }}} \end{array}} \right\} \Rightarrow J = \left[ {\begin{array}{*{20}{c}} {\cos \beta } \\ {s{\text{in}}\beta \cos \delta - is{\text{in}}\beta s{\text{in}}\delta } \end{array}} \right] \end{align}

where E0y and E0z are the amplitude of the two components of the electric field vector, while δy and δz are the phase of the two components of the electric field vector, should we simply set ${\hat e_{01}}$ by specifying (0, 0) (cosβ, 0) (sinβcosδ, - sinβsinδ) in ddscat.par ?

(2) Assume that we simply set ${\hat e_{01}} = {\hat y_{LF}}$ and ${\hat e_{02}} = {\hat z_{LF}}$, and calculate the orientationally-averaged values of Qabs, Qsca and <cosθ> in the two orthonormal polarization states, can we calculate the orientationally-averaged values of Qabs, Qsca and <cosθ> in an arbitrary incident polarization state, just based on the orientationally-averaged values of Qabs, Qsca and <cosθ> in the two orthonormal polarization states ?

(3) In wxxxryyy.avg, there are two lines like this:
Qext Qabs Qsca g(1)=<cos> <cos^2> Qbk Qpha
JO=1: 9.2037E-01 8.1852E-01 1.0185E-01 7.2936E-02 4.0114E-01 1.0141E-02 5.3381E-01
JO=2: 9.2037E-01 8.1852E-01 1.0185E-01 7.2936E-02 4.0114E-01 1.0141E-02 5.3380E-01

I am wondering if the data in the lines of JO=1 and JO=2 in the red box are the calculation results of Qabs, Qsca and <cosθ> in the incident polarization states ${\hat e_{01}}$ and ${\hat e_{02}}$, respectively ?

It is highly appreciated if you would instruct me on these questions, and I am looking forward to your reply.

Sincerely yours
Ya-fei Wang

Incident polarization state by Ya-fei Wang (guest), 22 Aug 2018 07:38

Respected Sir,
I need to model a nanoshell filled with a liquid having zero k value. I used CONELLIPSE module, but it did not converge.
I have tried to fix the problem in many other ways, I failed.
Please help.
Thanks,
Hirak

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As explained in section 30.1 of the 7.3.2 UserGuide, each "track" is specified by one line in ddpostprocess.par
In principle, ddpostprocess.par can specify many tracks (one line per track).

If this doesn't address your requirements, then you may need to modify the program ddpostprocess.f90 to create a new version to write out what you want — see section 30.2 of the UserGuide for a few words about this. The critical piece of code is subroutine readnf.f90 (called by ddpostprocess.f90) which reads the stored data file (e.g., 'w000r000k000.E1') from disk, and returns information about the polarization, electric field, etc at each lattice site. You will probably need prior experience with f90 programming if you are going to undertake this route.

It would be nice if some DDSCAT user would write some MATLAB code to do this, and make it available, but so far as I am aware this hasn't happened.

by drainedraine, 05 Jun 2018 17:15
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