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DDA calculations should *always* be tested for convergence. In the limit of large N, the error is expected to scale as 1/N^{1/3}, where N is the number of dipoles. If the results are converging, you can then extrapolate to the limit N -> infinity. See, for example, Eq. 15-17 and Figure 6 of

http://adsabs.harvard.edu/abs/2016ApJ...831..109D

The correction will depend on dielectric function and size/lambda, so you may find that resonances will shift in wavelength when this is done.

The extrapolation procedure described in Eq. 15-17 of above reference will give you a fractional correction phi_N, where N is the largest N that you could afford to do. I would guess that the extrapolation itself is uncertain by
some fraction (perhaps 0.1) of phi_N (again, see Fig. 6 of above reference).

Remember also that the DDA realization with finite N is only approximating the geometry of the ideal cylinder with end caps. Again, repeating with larger N will in effect be doing a slightly different geometry. The correction phi_N will include these "geometric" effects.

by drainedraine, 07 Dec 2017 11:48
joseph pearson (guest) 07 Dec 2017 09:17
in discussion DDSCAT / General discussion » Gold Nanorod Extinction Spectra Simulation

Dear Prof. Draine,
Thank you for your reply. I am happy to know that the basic calculation setup was ok and I am understanding the parameterization of the program correctly. Thank you for your assistance with the calculation optimization settings. You saved me a lot of effort in trying to figure out what the appropriate rotational setups are.
Now I am trying to reconcile the difference between my experimental and simulated spectra. The simulated LSPR peak is shifted to the red by ~50 nm. If the medium dielectric constant was increased (as it could likely be due to the surfactant), I would expect the LSPR peak to shift further to the red. Not sure about what else might be likely causing the discrepancy. Is polydispersity the probable culprit?
Thanks and best regards,
Joe

by joseph pearson (guest), 07 Dec 2017 09:17

1. the "aspect ratio" reported for CYLNDRCAP in qtable actually refers
to the cylinder only (not including endcaps) so the value 3.55 does
correspond to your desired 25/7 to within the allowed discretization.
(I will correct this typo in the qtable output for CYLNDRCAP in the
next release.)

2. For this axially-symmetric target you do not need to rotate the
target around the axis a1, so you can reduce the compute time
by a factor 20 by changing

0. 360.0 20 = BETAMI, BETAMX, NBETA (beta=rotation around a1)

to

0. 0. 1 = BETAMI, BETAMX, NBETA (beta=rotation around a1)

3. With the reflection symmetry of this target, there is no
reason to sample THETA outside the range 0 to 90.
You can reduce your computing time by changing

0. 180.0 10 = THETMI, THETMX, NTHETA (theta=angle between a1 and k)

to

0. 90. 6 = THETMI, THETMX, NTHETA (theta=angle between a1 and k)

see section 19.3 for sampling in THETA: with an even value of
NTHETA, this will sample THETA uniformly in cos(THETA) at
cos(THETA)=11/12, 9/12, 7/12, 5/12, 3/12, 1/12

4. There is also really no need to do more than one angle PHI.
The PHI rotations are not very costly in cputime, but in this
case don't seem to be necessary at all if you are using unpolarized
light and are going to average over both polarization states.

by drainedraine, 06 Dec 2017 22:20

I'm not certain what you mean by "longitudinal polarizaiton", but I suppose that you want the electric field to be parallel to the nanorod axis.

With the ddscat.par file that you provided, the cylinder axis will be along the x axis in the Target Frame (TF). If you want the incident electric field to be along this direction, then you have to rotate the target in the Lab Frame (LF) by 90deg. Simply set Theta to 90 by changing the appropriate lines in ddscat.par to read

' Prescribe Target Rotations '
0.00 0.00 1 = BETAMI, BETAMX, NBETA (beta=rotation around a1)
90.00 90.00 1 = THETMI, THETMX, NTHETA (theta=angle between a1 and k)
0.00 0.00 1 = PHIMIN, PHIMAX, NPHI (phi=rotation angle of a1 around k)

With this setting, incident polarization state JP=1 will correspond to incident E along the cylinder axis.

Re: Parameterization by drainedraine, 06 Dec 2017 21:46
joseph pearson (guest) 06 Dec 2017 09:22
in discussion DDSCAT / General discussion » Gold Nanorod Extinction Spectra Simulation

Dear Prof. Draine,
Thank you for your assistance. Indeed, the MXITER adjustment worked to get the code to run. I am now able to generate extinction spectra.
Follow up question; As I understand it from the manual, the shape parameters should be set, such that they reflect the aspect ratio of the nanorods I am trying to measure (pg 44 of the ddscat manual "SHPAR1 = cylinder length/d (not including end-caps!) and SHPAR2 = cylinder diameter/d "). For example, I am now trying to model a rod L=32 nm X d=7 nm (where L=total length), aspect ratio=4.57. I set up the .par file to reflect this geometry by setting the shape parameters to be a ratio of 25/7. I double the shape parameters to get a higher number of dipoles (Please correct me if I am not understanding this operation correctly). The aeff=6.48nm is calculated from the total L and d. However, the resulting qtable output has written in the header asp.ratio= 3.5477. Can you please confirm that this is the correct way to try and model this sample with ddscat? My other specific questions are if the incident polarizations and target rotations parameters are setup correctly? My goal is to simulate the extinction spectra of these nanorods in solution, then compare the results with spectrophotometer measurements.
The complete .par file is included below. Note, that this took about a week running MPI on a 12core machine. So I would probably make some changes to try and speed things up.
Thanks in advance for your assistance,
Joe
' ========== Parameter file for v7.3 ==================='
' Preliminaries '
'NOTORQ' = CMDTRQ*6 (DOTORQ, NOTORQ) — either do or skip torque calculations
'PBCGS2' = CMDSOL*6 (PBCGS2, PBCGST, GPBICG, QMRCCG, PETRKP) — CCG method
'GPFAFT' = CMETHD*6 (GPFAFT, FFTMKL) — FFT method
'GKDLDR' = CALPHA*6 (GKDLDR, LATTDR, FLTRCD) — DDA method
'NOTBIN' = CBINFLAG (NOTBIN, ORIBIN, ALLBIN) — binary output?
' Initial Memory Allocation '
100 100 100 = dimensioning allowance for target generation
' Target Geometry and Composition '
'CYLNDRCAP' = CSHAPE*9 shape directive
50.0 14.0 = shape parameters 1 - 2
1 = NCOMP = number of dielectric materials
'../diel/Au_evap' = file with refractive index 1
' 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 '
1000 = MXITER
' Integration limiter for PBC calculations '
1.00e-2 = 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) '
0.48 1.0 130 'LIN' = wavelengths (1st,last,howmany,how=LIN,INV,LOG,TAB)
' Refractive index of ambient medium '
1.333 = NAMBIENT
' Effective Radii (micron) '
0.00648 0.00648 1 'LIN' = eff. radii (1st,last,howmany,how=LIN,INV,LOG,TAB)
' 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. 360.0 20 = BETAMI, BETAMX, NBETA (beta=rotation around a1)
0. 180.0 10 = THETMI, THETMX, NTHETA (theta=angle between a1 and k)
0. 360.0 20 = 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 '
9 = NSMELTS = number of elements of S_ij to print (not more than 9)
11 12 21 22 31 33 44 34 43 = indices ij of elements to print
' Specify Scattered Directions '
'LFRAME' = CMDFRM (LFRAME, TFRAME for Lab Frame or Target Frame)
1 = NPLANES = number of scattering planes
0. 0. 180. 1 = phi, theta_min, theta_max (deg) for plane A

by joseph pearson (guest), 06 Dec 2017 09:22

Respected Prof. Draine,
I have found out that longitudinal polarization along a gold nanorod axis ( set at x-axis) in LF can be achieved by setting the theta value ~ 18 0 , and it is independent on phi and beta value. The results obtained from .sca file are mentioned after the text.
I got puzzled . Why 18 0 ?
Sorry to ask you such a silly question but I have tried and spent couple of nights realizing the 3D space.
Please illuminate me.
Yours sincerely,
Hirak

DDSCAT - DDSCAT 7.3.0 [13.05.03]
TARGET -
Cyl.prism, NAT= 6385 NFAC= 225 NLAY= 17 asp.ratio= 1.0044
GKDLDR - DDA method
PBCGS2 -
CCG method
CYLNDRCAP - shape
6385 = NAT0 = number of dipoles
0.08689122 = d/aeff for this target [d=dipole spacing]
0.002377 = d (physical units)
- physical extent of target volume in Target Frame -—-
-0.039214 0.039214 = xmin,xmax (physical units)
-0.020201 0.020201 = ymin,ymax (physical units)
-0.020201 0.020201 = zmin,zmax (physical units)
AEFF= 0.020156 = effective radius (physical units)
WAVE= 0.624000 = wavelength (in vacuo, physical units)
K*AEFF= 0.275406 = 2*pi*aeff/lambda
NAMBIENT= 1.357000 = refractive index of ambient medium
n= ( 0.1435 , 2.4668), eps.= ( -6.0645 , 0.7078) |m|kd= 0.0591 for subs. 1
TOL= 1.000E-05 = error tolerance for CCG method
( 1.00000 0.00000 0.00000 ) = target axis A1 in Target Frame
( 0.00000 1.00000 0.00000 ) = target axis A2 in Target Frame
NAVG= 248 = (theta,phi) values used in comp. of Qsca,g
( 0.02273 -0.00747 0.00000 ) = k vector (latt. units) in TF
( 0.30362, 0.00000 )( 0.92375, 0.00000 )(-0.23345, 0.00000 )=inc.pol.vec. 1 in TF
( 0.07289, 0.00000 )( 0.22177, 0.00000 )( 0.97237, 0.00000 )=inc.pol.vec. 2 in TF
( 0.95000 0.30362 0.07289 ) = target axis A1 in Lab Frame
(-0.31225 0.92375 0.22177 ) = target axis A2 in Lab Frame
( 0.02393 0.00000 0.00000 ) = k vector (latt. units) in Lab Frame
( 0.00000, 0.00000 )( 1.00000, 0.00000 )( 0.00000, 0.00000 )=inc.pol.vec. 1 in LF
( 0.00000, 0.00000 )(-0.00000, 0.00000 )( 1.00000,-0.00000 )=inc.pol.vec. 2 in LF
BETA = 0.000 = rotation of target around A1
THETA= 18.195 = angle between A1 and k
PHI = 13.500 = rotation of A1 around k
0.5000 = ETASCA = param. controlling # of scatt. dirs used to calculate <cos> etc.
Qext Qabs Qsca g(1)=<cos> <cos^2> Qbk Qpha
JO=1: 1.6468E+00 1.3128E+00 3.3396E-01 1.7513E-03 2.3078E-01 5.9597E-03 5.7771E-01
JO=2: 2.7998E-01 2.3300E-01 4.6979E-02 1.1112E-02 3.3016E-01 3.4188E-03 7.5858E-01
mean: 9.6337E-01 7.7289E-01 1.9047E-01 2.9057E-03 2.4304E-01 4.6893E-03 6.6814E-01
Qpol= 1.3668E+00 dQpha= -1.8087E-01
Qsca*g(1) Qsca*g(2) Qsca*g(3) iter mxiter Nsca
JO=1: 5.8488E-04 -2.3407E-04 4.2185E-05 99 10000 248
JO=2: 5.2201E-04 2.1309E-04 -4.7081E-05 106 10000 248
mean: 5.5344E-04 -1.0490E-05 -2.4484E-06
Mueller matrix elements for selected scattering directions in Target Frame
theta phi Pol. S_11 S_12 S_21 S_22 S_31 S_41 S_34 S_43
0.00 0.00 0.05336 8.2200E-04 -3.9079E-05 -4.386E-05 7.324E-04 2.765E-10 -5.275E-11 2.206E-07 -1.965E-07
10.00 0.00 0.10003 9.6275E-04 8.5808E-05 9.631E-05 8.578E-04 -7.130E-10 -4.075E-10 -4.875E-04 4.343E-04
20.00 0.00 0.35199 1.3385E-03 4.1977E-04 4.711E-04 1.193E-03 5.239E-10 -1.164E-10 -9.614E-04 8.567E-04
30.00 0.00 0.54439 1.9058E-03 9.2442E-04 1.037E-03 1.698E-03 -6.694E-10 4.075E-10 -1.408E-03 1.254E-03
40.00 0.00 0.66563 2.5985E-03 1.5411E-03 1.730E-03 2.315E-03 4.511E-10 1.426E-09 -1.813E-03 1.615E-03
50.00 0.00 0.73951 3.3343E-03 2.1970E-03 2.466E-03 2.971E-03 -4.366E-10 -1.222E-09 -2.163E-03 1.927E-03
60.00 0.00 0.78458 4.0244E-03 2.8133E-03 3.157E-03 3.586E-03 -6.476E-10 0.000E+00 -2.447E-03 2.180E-03
70.00 0.00 0.81160 4.5838E-03 3.3147E-03 3.720E-03 4.084E-03 -1.615E-09 2.910E-10 -2.653E-03 2.363E-03
80.00 0.00 0.82635 4.9422E-03 3.6388E-03 4.084E-03 4.404E-03 -5.311E-10 -2.095E-09 -2.773E-03 2.471E-03
90.00 0.00 0.83165 5.0536E-03 3.7448E-03 4.203E-03 4.503E-03 -6.476E-10 2.212E-09 -2.805E-03 2.499E-03
100.00 0.00 0.82837 4.9027E-03 3.6186E-03 4.061E-03 4.368E-03 -1.062E-09 -8.731E-10 -2.746E-03 2.447E-03
110.00 0.00 0.81571 4.5073E-03 3.2759E-03 3.677E-03 4.016E-03 -8.549E-10 -6.403E-10 -2.602E-03 2.318E-03
120.00 0.00 0.79086 3.9158E-03 2.7594E-03 3.097E-03 3.489E-03 -8.440E-10 -1.164E-09 -2.378E-03 2.119E-03
130.00 0.00 0.74787 3.2013E-03 2.1332E-03 2.394E-03 2.852E-03 -4.075E-10 4.948E-10 -2.086E-03 1.858E-03
140.00 0.00 0.67522 2.4509E-03 1.4745E-03 1.655E-03 2.184E-03 -8.949E-10 1.310E-09 -1.735E-03 1.546E-03
150.00 0.00 0.55206 1.7554E-03 8.6345E-04 9.691E-04 1.564E-03 -8.731E-11 -1.892E-09 -1.340E-03 1.194E-03
160.00 0.00 0.34991 1.1979E-03 3.7346E-04 4.191E-04 1.067E-03 -5.384E-10 2.183E-10 -9.111E-04 8.118E-04
170.00 0.00 0.08337 8.4419E-04 6.2705E-05 7.038E-05 7.522E-04 -3.056E-10 -1.455E-10 -4.608E-04 4.105E-04
180.00 0.00 0.04916 7.3574E-04 -3.2226E-05 -3.617E-05 6.555E-04 -2.910E-11 6.912E-11 1.673E-07 -1.491E-07
190.00 0.00 0.12656 8.8517E-04 9.9820E-05 1.120E-04 7.887E-04 -1.164E-10 -4.366E-11 4.610E-04 -4.108E-04
200.00 0.00 0.39033 1.2751E-03 4.4345E-04 4.977E-04 1.136E-03 -4.075E-10 -3.638E-10 9.111E-04 -8.118E-04
210.00 0.00 0.57830 1.8599E-03 9.5834E-04 1.076E-03 1.657E-03 8.877E-10 8.731E-11 1.339E-03 -1.193E-03
220.00 0.00 0.69135 2.5707E-03 1.5835E-03 1.777E-03 2.290E-03 7.567E-10 -2.328E-10 1.735E-03 -1.545E-03
230.00 0.00 0.75801 3.3226E-03 2.2441E-03 2.519E-03 2.960E-03 5.239E-10 3.783E-10 2.084E-03 -1.857E-03
240.00 0.00 0.79742 4.0251E-03 2.8599E-03 3.210E-03 3.586E-03 1.062E-09 -8.149E-10 2.376E-03 -2.117E-03
250.00 0.00 0.81999 4.5926E-03 3.3554E-03 3.766E-03 4.092E-03 4.584E-10 -2.328E-10 2.599E-03 -2.316E-03
260.00 0.00 0.83104 4.9555E-03 3.6694E-03 4.118E-03 4.415E-03 8.949E-10 2.037E-09 2.743E-03 -2.444E-03
270.00 0.00 0.83303 5.0696E-03 3.7629E-03 4.223E-03 4.517E-03 5.020E-10 1.339E-09 2.802E-03 -2.496E-03
280.00 0.00 0.82650 4.9219E-03 3.6246E-03 4.068E-03 4.385E-03 1.019E-09 5.821E-11 2.771E-03 -2.469E-03
290.00 0.00 0.81035 4.5320E-03 3.2722E-03 3.672E-03 4.038E-03 6.512E-10 9.895E-10 2.650E-03 -2.361E-03
300.00 0.00 0.78145 3.9496E-03 2.7500E-03 3.086E-03 3.519E-03 8.004E-10 8.731E-10 2.445E-03 -2.178E-03
310.00 0.00 0.73355 3.2472E-03 2.1223E-03 2.382E-03 2.893E-03 7.421E-10 -6.403E-10 2.162E-03 -1.926E-03
320.00 0.00 0.65506 2.5107E-03 1.4654E-03 1.645E-03 2.237E-03 5.966E-10 4.948E-10 1.812E-03 -1.615E-03
330.00 0.00 0.52635 1.8286E-03 8.5757E-04 9.625E-04 1.629E-03 3.783E-10 -4.657E-10 1.408E-03 -1.254E-03
340.00 0.00 0.32422 1.2812E-03 3.7012E-04 4.154E-04 1.142E-03 -4.366E-11 -1.164E-10 9.615E-04 -8.567E-04
350.00 0.00 0.07151 9.3236E-04 5.9410E-05 6.668E-05 8.307E-04 1.601E-10 -4.366E-11 4.878E-04 -4.346E-04
360.00 0.00 0.05336 8.2200E-04 -3.9079E-05 -4.386E-05 7.324E-04 3.201E-10 -7.822E-11 2.201E-07 -1.961E-07

Re: Parameterization by hirakhirak, 28 Nov 2017 07:22
Bruce Draine (guest) 27 Nov 2017 13:26
in discussion DDSCAT / General discussion » Multilayered Ellipsoid

If the target material is isotropic, then you will want to use target option FROM_FILE.
FROM_FILE allows the target to be composed of more than one material — you simply need to specify the composition at each occupied lattice site.
The UserGuide has instructions for the format of target option FROM_FILE. The shape.dat file is a simple ascii file. In examples_exp/FROM_FILE you will find an example.

If the target material is anisotropic, then you can use target option ANIFRMFIL. The shape.dat file is again a plain ascii file, but now becomes more complicated, because at each lattice site you must specify the "composition" corresponding to each of the three principal
axes of the dielectric tensor, and you must specify the orientation of these three principal axes in the Target Frame (because the optical axes of the local material may not coincide with the x,y,z axes of the Target Frame). The UserGuide describes the formatting of this (plain ascii) file.

by Bruce Draine (guest), 27 Nov 2017 13:26

Respected Prof.Draine,
I have designed the .stl file for the multilayered shape.
Now, I need to convert it to shape format.
If you kindly introduce me to the format, it will be very much helpful for me to write a code to convert them directly.
Thanks and regards,
Hirak

Re: Multilayered Ellipsoid by hirakhirak, 27 Nov 2017 09:09

Your choice of software depends on what soot aggregate structure you want.

If you want a cluster of spheres, all of the same composition, it is easiest to simply use the SPHERES_N target option. You simply need a file specifying the position of the center of each sphere, and its radius (in arbitrary units). The spheres can be overlapping if desired. See the DDSCAT UserGuide for details, and the example provided in examples_exp/SPHERES_N

If you want samples of random aggregates produced by ballistic agglomeration of equal-sized spheres, see the target files available for clusters of 8, 16, 32,64, 128, 256, … spheres at

http://www.astro.princeton.edu/~draine/agglom.html

Examples are given for the standard ballistic agglomeration, and two variants (BAM1 and BAM2) that give higher density aggregates, as described by Shen, Draine & Johnson (2008: Astrophys. J., 689, 260). However, you will need to modify these files for compatibility with DDSCAT:

  • delete the first line in the file
  • delete the numbers in the column labeled "j"
  • change all the numbers in the column labeled "2*a(j)" from 1 to 0.5

If you want a cluster of spheres of various different materials, see target option SPH_ANI_N


The value of the interdipole separation "d" is determined automatically by DDSCAT after you specify the value of AEFF = radius of equal volume sphere (in physical units, e.g., microns) and (if you are using target option SPHERES_N) the parameter SHPAR1 setting the target extent in the x direction, in units of d.
DDSCAT will report the derived value of d in physical units.

draine (guest) 21 Nov 2017 13:19
in discussion DDSCAT / General discussion » Gold Nanorod Extinction Spectra Simulation

ddscat writes diagnostic information to standard output (on unix/linux systems one can store this running output to a file with a command like "ddscat >& ddscat.log"). When I run ddscat 7.3.2 with your ddscat.par file, the last few lines of output look like

> FATAL ERROR IN PROCEDURE: ZBCG2WP
> ITERN>ITERMX
> EXECUTION ABORTED

Your ddscat.par file includes the line
100 = MXITER

ddscat reached IT=100 iterations but hadn't quite reached the specified error tolernace of 1.e-5, so it terminated the calculation. If you increase the value of MXITER (to, e.g., 1000) I think that you will find that ddscat will run successfully (on my laptop, IT=133 iterations were required for convergence to ferr < 1.e-5).

by draine (guest), 21 Nov 2017 13:19

I have been attempting to use DDSCAT for modeling the Vis/NIR extinction spectra of gold nanorods. I am trying to recreate the ddscat 2013 simulations published in:(doi:/10.1021/jp4078344). The install is fine, I can run the example for the RCTGLPRSM, and the output all looks like it should for the example. However, when I setup a new ddscat.par file with the CYLNDRCAP geometry, the program runs and closes out before generating extinction data.
To do this I put the ddscat program, and ddscat.par file in a new directory. When I run the program it generates the mtable, qtable, qtable2 and target.out files, but not any .avg, .fml or .sca files. The qtable extinction data is empty. When executing, the program appears to make it through the 100 iterations, but then closes out after. The problem seems to be related to the aeff and/or the shape parameters. When I make the aeff too small or the shape parameters too large, then I get the problem as I described. I have been trying to keep the shape parameters large enough to have ~10000 dipoles. But if I set the aeff to match my experimental samples, then the program doesn't generate extinction data (it does seem to work for much larger aeff sizes).
Below is an example of a .par file that I have been using for a gold rod with dimensions L=37 nm (including end caps) and d=7 nm. Therefore the aeff for this geometry is 0.0068 microns. I tried to make the shape parameters a multiple of 2 (60 x 14), to get over 10000 dipoles.
I have tried this on the Windows precompiled version, as well as on a Linux system with the latest version. I would be tremendously grateful if you could give me any insight on what I might be doing wrong.

' ========== Parameter file for v7.3 ==================='
' Preliminaries '
'NOTORQ' = CMDTRQ*6 (DOTORQ, NOTORQ) — either do or skip torque calculations
'PBCGS2' = CMDSOL*6 (PBCGS2, PBCGST, GPBICG, QMRCCG, PETRKP) — CCG method
'GPFAFT' = CMETHD*6 (GPFAFT, FFTMKL) — FFT method
'GKDLDR' = CALPHA*6 (GKDLDR, LATTDR, FLTRCD) — DDA method
'NOTBIN' = CBINFLAG (NOTBIN, ORIBIN, ALLBIN) — binary output?
' Initial Memory Allocation '
100 100 100 = dimensioning allowance for target generation
' Target Geometry and Composition '
'CYLNDRCAP' = CSHAPE*9 shape directive
60 14 = shape parameters 1 - 2
1 = NCOMP = number of dielectric materials
'../diel/Au_evap' = file with refractive index 1
' 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 '
100 = MXITER
' Integration limiter for PBC calculations '
1.00e-2 = 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) '
0.650 0.650 1 'LIN' = wavelengths (1st,last,howmany,how=LIN,INV,LOG,TAB)
' Refractive index of ambient medium '
1.333 = NAMBIENT
' Effective Radii (micron) '
0.0068 0.0068 1 'LIN' = eff. radii (1st,last,howmany,how=LIN,INV,LOG,TAB)
' Define Incident Polarizations '
(0,0) (1.,0.) (0.,0.) = Polarization state e01 (k along x axis)
1 = 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, THETMX, 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 '
9 = NSMELTS = number of elements of S_ij to print (not more than 9)
11 12 21 22 31 33 44 34 43 = indices ij of elements to print
' Specify Scattered Directions '
'LFRAME' = CMDFRM (LFRAME, TFRAME for Lab Frame or Target Frame)
1 = NPLANES = number of scattering planes
0. 0. 180. 1 = phi, theta_min, theta_max (deg) for plane A

Gold Nanorod Extinction Spectra Simulation by joseph pearson (guest), 21 Nov 2017 08:50

Which software is best to generate soot aggregate structure (shape.dat file)? and How to choose the lattice spacing 'd' value?

How to fix lattice spacing 'd' value? by Prasanth (guest), 15 Nov 2017 06:23
Prasanth (guest) 15 Nov 2017 06:21
in discussion DDSCAT / General discussion » target size

Which software is best to generate soot aggregate structure (shape.dat file)? and How to choose the lattice spacing 'd' value?

by Prasanth (guest), 15 Nov 2017 06:21
hirakhirak 09 Nov 2017 10:14
in discussion DDSCAT / General discussion » Running ddscat with MPI

please follow up your e-mail.

by hirakhirak, 09 Nov 2017 10:14

Dear Hirak,

I have sent you a private message in your wikidot mailbox.
Regards,
Stefany

by stefany02stefany02, 08 Nov 2017 21:25
hirakhirak 08 Nov 2017 11:58
in discussion DDSCAT / General discussion » Running ddscat with MPI

please sendme your e mail

by hirakhirak, 08 Nov 2017 11:58

Dear Hirak,

thanks for your reply.
Yes, it will be great to provide me with your sample makefile.
regards,
Stefany

by stefany02stefany02, 08 Nov 2017 02:23
hirak (guest) 07 Nov 2017 07:31
in discussion DDSCAT / General discussion » Running ddscat with MPI

Dear Stephany02,
I have implemented MPI in our workstation and it is working fully. I think your problem is originating from threading the makefile properly. If you want I can send you my makefile for test.
Hirak

by hirak (guest), 07 Nov 2017 07:31

Dear ddscat users,
one month ago, I posted a worry about convergence problems I encountered with ddscat/MPI
Does somebody have an idea with what went wrong?
I copy the message below.
Regards,
Stefany

previous message:
I did a serial calculation with a sphere easily. but when I try a parallel calculation with MPI, I find very high values.

It is the same for all the algorithms
ZBCG2 IT= 1 f.err= NaN

cgcommon ckpt 20
iter= 8 frac.err= NaN

GPBICG IT= 10 f.err= 6.167E+00


sqrt(rnorm/bnorm)= 3 174106950333229.
sqrt(rnorm/bnorm)= 4 NaN

Other codes using MPI have been successfully implemented in our system, and the job submission procedures are correctly implemented.
The administrator followed all the instructions in the USer Guide. Did we miss an important information?

Running ddscat with MPI by stefany02stefany02, 06 Nov 2017 02:45

Respected Prof. Draine,
Thank you very much for such a helpful and insightful reply.
I have set the volume of a nanorod as a function of their aspect ratio ( here, L/D) so that the dipole distance remains constant for a group of calculations. I have used the "au_evap" file for dielectric function and wavelength range was fixed from 0.3 um to 1 um.
I will repeat the calculation suggested by you, Sir.
Were the configurations for the target orientation right? Please let me know.
Thanks and regards,
Hirak

Parameterization by hirakhirak, 02 Nov 2017 21:34
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