[Meep-discuss] Using all parameters as named

2012-02-13 Thread Filip Dominec
Hi, I am learning to simulate electrodynamics in python-meep. I observed that very often people define a variable and then they pass its value to a function so that they know what each parameter means. Although this is surely better than just providing unnamed numbers, the correct pythonic way

Re: [Meep-discuss] Using all parameters as named

2012-02-13 Thread Filip Dominec
utodoc can be useful (see > http://www.swig.org/Doc1.3/Python.html#Python_nn69): > %feature("autodoc", "1"); > > I hope this helps, > > Regards, > Martin Fiers > > 2012/2/13 Filip Dominec : > > Hi, > > I am learning to simulate e

Re: [Meep-discuss] Using all parameters as named

2012-02-13 Thread Filip Dominec
include keyword arguments in > python-meep. > > Regards, > Martin Fiers > > > On 13-02-12 14:19, Filip Dominec wrote: >> These are good news! After writing the previous e-mail, I looked on how >> keyword arguments could be processed by the C++ code of the _meep.so &

[Meep-discuss] Python-meep: simulating metal structure in 3D

2012-02-14 Thread Filip Dominec
Can anybody point me to a minimum working example of simulating some metal structure in 3D using python-meep, please? The frequency lies around 1 THz, so I expect the gold fishnet is well described by its conductivity. (For optical frequencies, there is a nice guide at http://msdresearch.blogspot

Re: [Meep-discuss] Python-meep: simulating metal structure in 3D

2012-02-15 Thread Filip Dominec
me to some mistake, I will be happy as well. Thanks! Filip 2012/2/14, Filip Dominec : > Can anybody point me to a minimum working example of simulating some > metal structure in 3D using python-meep, please? > > The frequency lies around 1 THz, so I expect the gold fishnet is well > desc

[Meep-discuss] Define sphere in python-meep

2012-03-02 Thread Filip Dominec
Hi, does python-meep support definition of a sphere or similar 3D object? I can see that there is a "make sphere" command in Scheme-meep [http://ab-initio.mit.edu/wiki/index.php/Meep_Reference], but cannot find its counterpart in the python module. I would be very happy if somebody sent me a workin

[Meep-discuss] Harmin fails with "invalid argument to ZGEEV"

2012-03-04 Thread Filip Dominec
Hi all, I downloaded the 2D Harminv example [1] and modified it for 3D simulation of THz resonance in a tiny dielectric sphere. The simulation works well (there are two modes at 800 and 1500 GHz), but Harminv fails with: PHASE 2 : running the Harminv analysis on the probing point data. h

Re: [Meep-discuss] Harmin fails with "invalid argument to ZGEEV"

2012-03-04 Thread Filip Dominec
harminv C++ code. A quick workaround is to get along without SI units and rescale all constants to use high enough numbers. Filip On Sun, 4 Mar 2012 10:37:06 +0100 Filip Dominec wrote: > Hi all, I downloaded the 2D Harminv example [1] and modified it for 3D > simulation of THz res

[Meep-discuss] Wishlist: Variable grid density?

2012-03-07 Thread Filip Dominec
Hi all, I was thinking about how hard would it be to make MEEP use the grid with double (or quadruple) mesh density at some specified regions. In 3D simulations, the computation time grows with 4th power of the density. This makes it very hard to precisely simulate fine metallic structures (or str

[Meep-discuss] Measure flux as complex field amplitude, not intensity

2012-04-07 Thread Filip Dominec
time and only at the end it simply calculates R(f)=|r(f)|^2 and T(f)=|t(f)|^2. But I need to know the complex r(f), t(f) to calculate also the phase of the passing wave. Any hints are appreciated. Thank you in advance! Filip Dominec ___ meep-discuss

Re: [Meep-discuss] Measure flux as complex field amplitude, not intensity

2012-04-10 Thread Filip Dominec
h; shall I modify the Courant constant? Does anybody have any experience with this? Thank you! Filip 2012/4/9, Aaron Webster : > On Sun, Apr 08, 2012 at 12:42:33AM +0200, Filip Dominec wrote: >> Dear Meep users, >> I wrote a Python-MEEP simulation of a gaussian pulse passing through

Re: [Meep-discuss] Unstability of a long non-dispersive simulation (solved)

2012-04-13 Thread Filip Dominec
nator + PML = oscillation". Filip >> On Thu, Apr 12, 2012 at 12:00 PM, Filip Dominec >> wrote: >> >>> Dear Meep users, >>> today I am writing because I observed an unexpected behaviour of my >>> simple simulation: >>> A dielectric res

Re: [Meep-discuss] Conversion of E-field from meep units to V/m

2012-05-24 Thread Filip Dominec
w to get to > it. > > If you still don't understand the problem, I can send you some generated > data and the plots. > I would really appreciate if you could help me with this, cos I have to > finish my thesis in June and I stuck to this problem. > > Thank you again for yo

Re: [Meep-discuss] code divergence at gold resonance

2012-05-26 Thread Filip Dominec
Hi, I fighted with metal definition in meep, too. What I have observed is that there is a narrow region between conductivity too high (in Drude model it is polarizability at zero frequency) and conductivity too low. If the conductivity is too high, the system becomes unstable, usually creating a

Re: [Meep-discuss] field components and propagation direction of a volume source

2012-05-28 Thread Filip Dominec
Hi Ranjeet, as far as I remember from electrodynamics, the electric field in this case can generally have all components nonzero and the magnetic field will have Hz component zero. However, in the XY, YZ, ZX planes of symmetry of the source, the electric field and magnetic fields may have some com

Re: [Meep-discuss] Non-Convergence or Other Problem

2012-06-06 Thread Filip Dominec
Hi, Thomas, first of all, how does the flux observed change when you double the simulation time? Filip 2012/6/6, Thomas Butler : > Hi, > > I am currently having a problem with modeling a 1x1 micron SiO2 waveguide > sitting on a Si substrate. > With a gaussian pulse centered 1.55 microns at one end

Re: [Meep-discuss] Units conversion from natural units to meters, python meep

2012-06-13 Thread Filip Dominec
Hi, Rita, for my convenience, I personally decided to use 1) for all dimensions: the SI units (so my simulation volume dimension may be set e. g. to "10e-6", resolution is set to "1/1e-7" etc.), 2) for all time-related units: SI units rescaled by the speed-of-light (so the source frequency for gree

Re: [Meep-discuss] Issue using meep/meep-mpi on 64bit System

2012-06-25 Thread Filip Dominec
Hi, Nicolai, it seems to me to be this bug I reported in March: https://bugs.launchpad.net/python-meep/+bug/947884 I did not have time yet to investigate why it crashes. Filip 2012/6/25, Walter, Nicolai : > Hi everyone, > I have a weird problem using meep-mpi/meep on a 32-core,64gb RAM, 64bit > sy

Re: [Meep-discuss] How exactly do we use 3D?

2012-08-31 Thread Filip Dominec
The possibly simplest and least effective approach is to store whole 3+1D data from the simulation to a HDF5 file. One has to be careful that the file may grow really big (gigabytes...). After running the simulation, one can export the animated data using the e. g. similar commands (on Linux with

[Meep-discuss] Fwd: How exactly do we use 3D?

2012-08-31 Thread Filip Dominec
a) Use: h5ls MYFILE.h5 b) This depends on your geometry settings, but you may repeat exporting different slices from HDF, as well as you may put multiple meep.fields.output_hdf5() functions in the time stepping cycle. Once I would like to write a little howto on this topic... Filip P. S. Note that

Re: [Meep-discuss] about setting the pml

2012-09-04 Thread Filip Dominec
Hi, how would you describe the difference observed? Or, could you please upload the time-domain data from the simulation? F. One tip: I have always set the PMLs using one command, so I would believe that the X and Y PMLs could be overwritten by the Z PMLs. 2012/9/4, huang bo : > hi! everybody >

Re: [Meep-discuss] define and use of silver and gold

2012-09-26 Thread Filip Dominec
Dear Hossein, the permittivity of metals is a complex function of a nontrivial dependence of frequency. As far as I know, basically there is big negative real part and diverging imaginary part for low frequencies, few resonant bumps in the optical/UV region, and a limit of 1+0i for X-rays. If you

Re: [Meep-discuss] harminv underestimating resonance frequencies

2012-10-03 Thread Filip Dominec
image > files). If I could find the resonant mode I wanted, I would excite > with a narrower band source so we wouldn't see this (I think 2,3 > Laguerre-Gaussian) mode. > > Cheers, > > Devin > > On 3 October 2012 12:11, Filip Dominec wrote: > > Hi, could y

Re: [Meep-discuss] extinction spectra

2012-10-11 Thread Filip Dominec
Dear David, I have read your question also the first time you formulated it, but did not feel experienced enough to give a really good answer. However, as far as I can remember, the exctinction should be defined as -log(T), where T is intensity transmission. Both are usually a function of frequenc

Re: [Meep-discuss] extinction spectra

2012-10-16 Thread Filip Dominec
2012/10/16, Filip Dominec : > Hi, David, > I guess that the simulation you are performing probably uses > Bloch-periodic boundaries on both xy and zy faces. This simulates a > 2-dimensional, strictly periodic array of scattering spheres. Although > it is unrealistic, it should provi

Re: [Meep-discuss] [Python-meep] Build problems for MPI in Ubuntu 12.10

2012-11-26 Thread Filip Dominec
On Tue, 6 Nov 2012 14:15:43 -0600 Jeff Chiles wrote: > it seems that the program just executes two identical > copies of itself Hi, Jeff, this is easy: The script probably imports 'meep' by default, which has to be changed to 'meep_mpi'. I experimented with multiprocessing quite a lot and I mus

Re: [Meep-discuss] About error "invalid boundary absorbers for this grid_volume"

2012-11-27 Thread Filip Dominec
Hi, Mi, it seems to be just a little mistake in the units used for definition of the simulation. I always get this message when the PMLs are thicker than the simulation volume. F. > > 2012/11/15, Hongyi Mi : >> Dear All, >> >> I am trying to simulation a 2D structure with dimension about 50nm * >>

Re: [Meep-discuss] Python-Meep: Are there any equivalent functions?

2012-11-27 Thread Filip Dominec
Hi, * amp-function[function] should have its counterpart in the meep.amplitudeFactor() callback (see [1]) * probably answered in [1] as well (I am not sure), * sure, it is f.time(), where f = meep.fields(structure) * while (f.time() < sim_time): f.step(); do_something You may be interested in the s

Re: [Meep-discuss] misunderstanding in definition of gauss beam

2012-12-04 Thread Filip Dominec
Hi, Onder, I guess that the tilting trick on the aforementioned page is a good approximation for little angles. For higher angles of tilting, denoted by 'theta' here, a precise solution would require to: * stretch the source envelope by 1/cos(theta), * calculate k_x precisely as cotg(theta), * perf

Re: [Meep-discuss] PML reflection problem

2012-12-19 Thread Filip Dominec
low frequencies. > > > Best, > Ali > > > On Mon, Dec 17, 2012 at 1:47 PM, Filip Dominec wrote: > > > Hi, Ali, and all the MEEP users, > > first, I believe one should not place any material into the volume > > occupied by PML. However, what you report actua

Re: [Meep-discuss] Python meep-mpi version

2013-01-10 Thread Filip Dominec
Hi, I solved the same problem. I needed to make a symlink "/usr/include/meep" to "/usr/include/meep-openmpi" (See also http://fzu.cz/~dominecf/misc/meep/index.html, section "Installation".) Hope this helps, Filip 2013/1/10, Rita Ribeiro : > Hi, > > I am trying to install the meep-mpi version in UB

Re: [Meep-discuss] PML reflection problem

2013-01-10 Thread Filip Dominec
be interesting if a evanescent-wave-friendly (e. g. amplification-damping neutral) PML could be coded in MEEP in the future. I would be glad to read you thoughs! F. D. 2012/12/19, Filip Dominec : > Hi, Ali, > as I suggested, try to make a BIG spacing between your structure and the &g

Re: [Meep-discuss] MEEP-MPI

2013-01-14 Thread Filip Dominec
Hi, first of all a trivial question, do you import meep-mpi or just meep ? F. 2013/1/14, Rita Ribeiro : > Hi, > > I had installed python meep -mpi in Ubuntu 12.10 and when i execute the > command > > > mpirun -np 4 python name.py > > instead of getting one result i get 4. So each core is running

Re: [Meep-discuss] Setting conductivity

2013-01-18 Thread Filip Dominec
Hi, thanks to Shavkat and Martin, I made it work! The minimum code snippet is as such: class MyConductivity(meep.Callback): def __init__(self): meep.Callback.__init__(self) def double_vec(self, r): return 1e4 mc = MyConductivity() meep.set_COND_Callback(mc.__disown__()) s.s

Re: [Meep-discuss] segmentation fault in meep

2013-01-21 Thread Filip Dominec
Hi, first I would check if the "ošidka segmentovanija" (AKA segfault) persists when no harminv is used; second I would try to reduce the computation time. I had similar stability problem with long harminv runs: https://bugs.launchpad.net/python-meep/+bug/947884 Filip 2013/1/21, Alex : > I use Meep

[Meep-discuss] How to force the -fPIC option?

2013-02-05 Thread Filip Dominec
Dear MEEP users, I am trying to compile the latest version of python-meep with MPI support from scratch. First I compiled meep-mpi (against MPICH2). It works fine and meep-mpi supports multiprocessing; but when it comes to compilation of python-meep with the command "sudo ./make-mpi -I/usr/local/in

Re: [Meep-discuss] How to force the -fPIC option?

2013-02-06 Thread Filip Dominec
on fails on: ImportError: /usr/local/lib/python2.7/dist-packages/_meep_mpi.so: undefined symbol: _ZN3MPI3Win4FreeEv This is somehow related to the OpenMPI1.6 package I am using. I will try recompiling with another MPI package available in Ubuntu, such as OpenMPI or MPICH2. 2013/2/5, Filip Dom

[Meep-discuss] Meep 1.2 with python-meep 1.4.2?

2013-02-08 Thread Filip Dominec
Dear Meepers, I am sorry for being overly active in this mailing list, but this question is very simple: Has anybody succeeded running python-meep above MEEP 1.2? It can be built, but at my computer it always failed with "Unknown symbol" error when I tried to import the meep module. The older libm

Re: [Meep-discuss] FW: scheme meep to python meep

2013-03-11 Thread Filip Dominec
Hi, Fred, currently the python-meep interface does not have the convenient geometry-building function as scheme-meep does. (The reason is that the geometry is not implemented in meep itself, but in the libctl code, which is not processed by SWIG when building python-meep.) I think the most versati

Re: [Meep-discuss] how to install Meep on RedHat4 Linux Server

2013-03-28 Thread Filip Dominec
Hi, Valery, I spent some time trying to compile the newest version of MEEP with multiprocessing support, and the procedure is here: http://fzu.cz/~dominecf/misc/meep/index.html#install12 F 2013/3/28, Valery Kugel : > Folks, > > I would appreciate an advice on how to install MEEP on RedHat4 (or new

Re: [Meep-discuss] how to install Meep on RedHat4 Linux Server

2013-03-29 Thread Filip Dominec
I would be interested in your results. F. 2013/3/28, Valery Kugel : > Thank you Filip, > > do you think it will work in RH4 env? > > Valery > > - Original Message - > From: "Filip Dominec" > To: "Valery Kugel" > Cc: > Sent: Thursday, March 28,

Re: [Meep-discuss] clueless newbie

2013-04-02 Thread Filip Dominec
Hi, Jonathan, writing a scheme script and running it as: meep script.ctl is definitely the preferred way to run any but the simplest simulation. The meep examples seem to not to be included in the debian package, but they are enclosed with the meep source code, whose latest version may be dow

Re: [Meep-discuss] (no subject)

2013-04-08 Thread Filip Dominec
Hi, this is purely a mathematical question related to diffraction. Generally, if your source is ten times the wavelength, the output radiation divergence may be estimated to be one tenth of radian. So you have to make the source plane as big as possible. Another approach giving a precise plane wave

Re: [Meep-discuss] Calculating complex epsilon in MEEP 1.2

2013-05-15 Thread Filip Dominec
Hi, Kahli, few months ago, I needed to run some time-domain and frequency-domain simulations on the same structure, which contained dispersive materials. As MEEP does not accept dispersive model in frequency-domain computations yet, I had to compute the value of complex epsilon for each frequency m

Re: [Meep-discuss] Compiling C++ - undefined reference

2013-05-18 Thread Filip Dominec
Hi, Chris, it seems to me you are missing the MEEP header files. In my opinion, the best way would be to compile your simulations against the newest version of MEEP available. Its straightforward compilation procedure (for Debian/Ubuntu) is documented in the blue box at http://fzu.cz/~dominecf/misc

Re: [Meep-discuss] Porting MEEP to the Web

2013-05-21 Thread Filip Dominec
Hi, I did not know this project before. What would be the greatest benefits for the user? Would it not impact the performance too much? Filip 2013/5/21, Fernando Carvalho : > Hi everyone, > > Recently, Google Developers, at Google IO 2013, had announced PNaCl (Native > Client

Re: [Meep-discuss] make a source like a lamp

2013-05-23 Thread Filip Dominec
Dear Allesio, as far as I know, the random white light sources such as a lamp are rarely used in simulations. If one wants to obtain the broadband spectra, there is nothing more convenient than exciting one ultrashort pulse, possibly even half-cycle. However, it should be also possible to generate

Re: [Meep-discuss] Porting MEEP to the Web

2013-05-23 Thread Filip Dominec
verview > > > > On Wed, May 22, 2013 at 3:43 AM, Filip Dominec > wrote: > >> Hi, I did not know this project before. What would be the greatest >> benefits for the user? Would it not impact the performance too much? >> Filip >> >> 2013/5/21, Fernando C

Re: [Meep-discuss] Porting MEEP to the Web

2013-05-24 Thread Filip Dominec
with Physical simulations using NaCl, > but I'm no expert in this technology. > We can discuss issues with Google developers which are very supportive, if > you got interested in the project. > I can't port MEEP to this technology by myself, but with some help, I think &g

Re: [Meep-discuss] Get (n, k) for a frequency from a dispersive material.

2013-05-24 Thread Filip Dominec
Hi, Oscar, this is rather straightforward. The dielectric function used by MEEP is given by the well-known Lorentz formula. (I have verified it numerically, but this is a bit longer to explain.) In Python, I use the following function for the material. As an example I will give the SiO2 definition

Re: [Meep-discuss] Get (n, k) for a frequency from a dispersive material.

2013-05-24 Thread Filip Dominec
And I forgot to add that n = real(sqrt(eps)) k = imag(sqrt(eps)) F. D. ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] organic material in meep

2013-06-04 Thread Filip Dominec
Dear Gholamhosain, the permittivity has to be established from experimental (or quantum-mechanical) sources, see for instance http://xplqa30.ieee.org/ielx5/5503869/6055237/6004802/html/img/6004802-fig-2-large.gif This graph may be easily converted to numerical data using Engauge or similar program

[Meep-discuss] Amplitude monitor plane for MEEP 1.3

2013-06-12 Thread Filip Dominec
Dear MEEP developers and users, in our team, we employ MEEP to solve various problems and it is very useful. However, now and then we encounter some important functions to be missing. Most of them may be somehow written in Python code, but they would be the most efficient if hard-coded in the C++ s

[Meep-discuss] FDTD packages convergence

2013-06-12 Thread Filip Dominec
Dear all, this is an additional thought following my previous e-mail. Many interesting functions have been already implemented in different free FDTD codes. Just few examples of "special capabilities": * MEEP implements interesting physics and frequency-domain solver, * EMTL uses sub-pixel smoothin

[Meep-discuss] New feature: band-pass source

2013-06-19 Thread Filip Dominec
Dear MEEP users, let me share a little code snippet with you. Sometimes it happens that one wants to run a FDTD simulation with a broadband source, which however avoids some frequencies. A single gaussian source is not useful in such case, as its spectrum has always broad wings. Composing the sourc

Re: [Meep-discuss] New feature: band-pass source

2013-06-19 Thread Filip Dominec
Just for comparison, these are some spectra recorded using the old Gaussian source: http://fzu.cz/~dominecf/misc/meep/img/ampli_debug_gaussian.png The structure couples to the low frequencies and induces ugly artifacts by spectral leakage. And here are those obtained using the band source with wid

Re: [Meep-discuss] add-field, save-field, load-field, etc.

2013-06-21 Thread Filip Dominec
Hi, John, other people have asked a similar question and I am afraid it is not implemented yet. It is one of the features I proposed to implement in the mail few weeks ago: http://permalink.gmane.org/gmane.comp.science.electromagnetism.meep.general/4959 However, I did not get any reply so far, the

Re: [Meep-discuss] Fw: question about meep

2013-07-09 Thread Filip Dominec
Dear Lin, for better illustration of what actually happens, could you generate the images again with the source shifted downwards, e. g. to 1/4 of the picture height? Thanks, Filip 2013/7/9, nw...@mail.sim.ac.cn : > > > > > > > > Dear meep users > > I'm a student of CAS(Chinese Academy of Scie

Re: [Meep-discuss] How to set frequency and fwidth

2013-09-20 Thread Filip Dominec
Hi, Rui, I also always need to compute it from the basics. 25 nm corresponds to 0.25 units, therefore one unit corresponds to 1e-7 m, 400 nm is roughly 700 THz in reality, therefore you would rescale the frequency to 700e12 * 1e-7 = 7e7, but MEEP defines speed of light as 1 instead of 3e8 m/s, so

Re: [Meep-discuss] refractive index of silicon

2013-09-21 Thread Filip Dominec
consumes CPU time! Some remarks on the materials in MEEP and FDTD stability is also here: http://fzu.cz/~dominecf/misc/meep/#mat_mod Regards, Filip Dominec On Fri, 20 Sep 2013 15:55:50 -0700 Rui La wrote: > Dear meep users, > > I want to study the short wavelength light(300-700nm) pr

Re: [Meep-discuss] Near-field radiation between two parallel plates in MEEP

2013-11-27 Thread Filip Dominec
Dear Farhad, I must admit that maybe I do not fully understand your question, but anything is predicted by Maxwell equations should be possible in MEEP. In many cases my computations required MEEP to take into account the non-radiative electric or magnetic fields (such as when building a split-r

Re: [Meep-discuss] Designing inclined geometry

2013-12-04 Thread Filip Dominec
Dear Prem, as far as I know, this task would require either 1) to build the desired structure by overlapping a big (potentially infinite) number of overlapping blocks, or 2) load the structure pixel-by-pixel either from a data file, or from a mathematical expression. I spent several days implementi

Re: [Meep-discuss] (no subject)

2014-01-06 Thread Filip Dominec
implemented in MEEP successfully so even this can be done. The article touches a quite interesting topic, by the way. Best wishes, Filip Dominec 2014/1/6, FARHAD KAZEMI : > Dear all, > > I would like to model the radiation transfer between two plates > separated by nano-gap in which we h

Re: [Meep-discuss] (no subject)

2014-01-06 Thread Filip Dominec
t how can I include the effects of > temperature on the emission of the EM wave from a surface with a finite > temperature? > > Thank you again. sorry if my message is long. > > Farhad > > > > On Monday, January 6, 2014 5:50 PM, Filip Dominec > wrote: > > D

Re: [Meep-discuss] Gaussian pulses in Meep

2014-02-07 Thread Filip Dominec
Dear Simon, I think your conjectures are all correct. The pseudo-gaussian spectral profile (I guess the spectrum is more precisely ~ f*exp[-(f-fcen)**2 / fwidth**2] or something like that) requires a gaussian time evolution of the source. The cutoff defines sharp edges in time when the source start

Re: [Meep-discuss] wave guide coupling

2014-02-13 Thread Filip Dominec
simple task. If there is coupling of freely propagating wave to any waveguide, the task becomes a bit more complicated and a sketch of your geometry would be needed. Best regards, Filip Dominec 2014-02-13 16:44 GMT+01:00, ISAAC MATERE : > Hi meep users > am trying to come up with a script for

Re: [Meep-discuss] silica dispersion model

2014-02-26 Thread Filip Dominec
Dear Pablo, I plot the Lorentz model for silica at http://fzu.cz/~dominecf/misc/eps/#SiO2 The page also contains the numerical data for the Lorentzian oscillators, along with additional information about the sources and application of the data. Hope this helps, Fillip 2014-02-26 13:14 GMT+01:00,

Re: [Meep-discuss] meep mpi harminv problem

2014-03-13 Thread Filip Dominec
Hi, it appears to me that harminv may not use the MPI synchronisation at its end. If this is the case, it could result in a race condition, when one instance of harminv ends the multithreaded program, while the second one is still running. I suggest to add some field-manipulating function at the

Re: [Meep-discuss] Meep frequency snapshots and near to far field transform

2014-03-28 Thread Filip Dominec
Dear Arthur, thank you for sharing your code! I cloned your source, downloaded the meep 1.2.1 sources and copied your files over the original directory. Then I used my old compilation procedure on Ubuntu [1] to compile meep and rebuilt the python-meep interface. The new functions of snapshot() an

Re: [Meep-discuss] meep-mpi doesn't print anything in terminal

2014-04-10 Thread Filip Dominec
Dear Ehsan, on Linux, you can use the 'tee' command: mpirun -np 8 meep-mpi test.ctl| tee test.out Did it help? Filip 2014-04-10 8:39 GMT+02:00, Ehsan Saei : > Dear all, > > I try to run a ctl file using meep-mpi on a ubuntu machine with the > following command line: > > mpirun -np

Re: [Meep-discuss] Doubt about concept of flux spectrum in MEEP

2014-04-14 Thread Filip Dominec
Another option would be to define an amplitude-recording-plane: for instance, knowing the Ex-field and Hy-field, one can easily separate the amplitudes of both forward- and backward-propagating waves along the z-axis. The usual scattering problems with properly absorbing boundaries then require onl

Re: [Meep-discuss] Doubt about concept of flux spectrum in MEEP

2014-04-15 Thread Filip Dominec
the Fourier-transformed fields in the same cross-section. > This is certainly do-able to implement (at least for dispersionless > materials). > > On Apr 14, 2014, at 5:21 PM, Filip Dominec wrote: > >> This is true - I mostly simulate the behaviour of an infinite periodic >> arr

Re: [Meep-discuss] why the energy spectrum radiated by a point source doesn't match with the spectrum of source itself?

2014-04-22 Thread Filip Dominec
May it be attributed to that the radiated field is a derivative of the current, so that high-frequency components are enhanced compared to the lower frequency ones? Or is it a more complicated deviation? Regards, Filip 2014-04-22 16:01 GMT+02:00, Ehsan Saei : > Dear Steven and MEEP users, > > I si

Re: [Meep-discuss] why the energy spectrum radiated by a point source doesn't match with the spectrum of source itself?

2014-04-22 Thread Filip Dominec
This appears exactly as the result of the said effect. The good point is that the gaussian source shape is reasonably preserved upon differentiation, so you may pre-compensate it by "fcen=0.40". Or, if you have tighter requirements on the source, you may use the newly implemented feature of band-so

Re: [Meep-discuss] Zero Amplitude source

2014-04-24 Thread Filip Dominec
Hi, you can probably set the source cutoff to 0 (http://ab-initio.mit.edu/wiki/index.php/Meep_Reference#source). (But I must admit that I do not understand the purpose to do this.) F. 2014-04-23 22:13 GMT+02:00, James Green : > Dear MEEP users, > > Does anyone have any idea about how to make a ga

Re: [Meep-discuss] Meaning of Complex fields in hd5 files

2014-04-28 Thread Filip Dominec
Hi, jayv, the real and imaginary fields should be the same except for that the imaginary part if shifted by 1/4 of its period. Thus computing the modulus of the complex fields you get a smooth, non-oscillating function, describing the magnitude of the field amplitude. I think you can disregard the

Re: [Meep-discuss] Drude material in MEEP

2014-04-28 Thread Filip Dominec
Dear Allen, If I correctly understand your question, the Drude model can be approximated by the polarisation coming from a Lorentz oscillator with as extremely low resonance frequency. General approach is to select a realistic plasma frequency (for instance, omega_p := 2*pi*3.64e15 rad/s for alumin

Re: [Meep-discuss] Drude material in MEEP

2014-04-29 Thread Filip Dominec
Dear Allen, surely the best guide for defining the Lorentzian model for materials in MEEP is http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial/Material_dispersion where also a working example is presented. I must apologize for the statement that you have to use a low-frequency Lorentzian oscil

Re: [Meep-discuss] PML overlapping dispersive material

2014-05-07 Thread Filip Dominec
Hi, Sophia, from my personal experience, the dispersive material can overlap with PML in the simulations. The question of stability under such conditions may be quite hard, though. You probably have to find out by trying which parameters are stable - and which not. Regards, Filip 2014-05-07 12:07

Re: [Meep-discuss] Read refractive index data from file

2014-05-13 Thread Filip Dominec
If I correctly understand your question, you wish to define material properties as an arbitrary function of frequency. This is generally not possible in FDTD, see e.g. http://ab-initio.mit.edu/wiki/index.php/Dielectric_materials_in_Meep Filip 2014-05-13 19:07 GMT+02:00, Charalampos Mavidis : > Hel

Re: [Meep-discuss] Permittivity of Silicon

2014-05-19 Thread Filip Dominec
Dear Thomas and all, I wrote most of my thoughts on the referred page; while sometimes the discrete Lorentzian oscillators suffice to precisely describe the dielectric function in the frequency range of interest, the optical spectra of semiconductors are usually of the harder cases. You can manual

Re: [Meep-discuss] Beam splitters in meep?

2014-05-26 Thread Filip Dominec
Hi, as a simplest approach, I would suggest to reduce the 'sigma' parameter of the metal, first. It should allow the transmission to be adjusted even in the case of a low resolution. Filip 2014-05-26 7:06 GMT+02:00, jayv : > I need some beam splitters with varying T/R ratios, and I've had some > s

Re: [Meep-discuss] (no subject)

2014-06-12 Thread Filip Dominec
NSHA#". The capitals look like shouting, and the hashmarks look like something as banging your fist on the table before and after saying it... Regards, Filip Dominec 2014-06-12 18:01 GMT+02:00, #SHAMPY MANSHA# : > Dear Steven and other Meep users, > > I am doing a simulation in whic

Re: [Meep-discuss] real metal material

2014-06-19 Thread Filip Dominec
uge positive imaginary part, it is a inductance-free conductor with tiny resistivity, again --> PEC. Complex infinity has no sign. Hope this helps, Filip Dominec IOP ASCR, Prague 2014-06-19 14:07 GMT+02:00, Weiner John : > Dear meep users and experts: > > I am really stuck, and I need your

Re: [Meep-discuss] Multiple wavelengths and light direction

2014-06-19 Thread Filip Dominec
Hi, 1) spectrum: although the gaussian source with frequency around (1/1.55) would give an approximate result, you probably want to use the band_src_time which is described here: http://fzu.cz/~dominecf/misc/meep/index.html#bandsource I am going to contribute the code to github today. 2) If you wi

Re: [Meep-discuss] Complex transmission and reflection coefficients

2014-07-14 Thread Filip Dominec
Hi, Joshua, I am not sure if it will be helpful to you, but two years ago I wrote a similar simulation of complex scattering coefficients (reflection+transmission) from a SRR or any other metamaterial unit cell. The codes are in python-meep and are publicly available at https://github.com/FilipDom

Re: [Meep-discuss] Part of PML

2014-08-17 Thread Filip Dominec
Hi, Sophia, as far as I know, it is possible to overlap any material with PML. The PML condition however applies for the whole boundary, so it can not be defined in its part only. Note I had some numerical stability issues when the PML was defined on one axis only while the other boundaries were p

Re: [Meep-discuss] monochromatic source

2014-08-25 Thread Filip Dominec
Hi, Farhad, generally both the continuous and the narrow-band-gaussian sources are good choices. Note however that for mathematical reasons a source short in time will always have a broad spectrum. Spectral selectivity has to be paid with computation time. Fortunately, the Fourier transform of a g

Re: [Meep-discuss] Units in Meep

2014-11-10 Thread Filip Dominec
I am convinced that it would be more convenient if MEEP allowed one to use the true SI units. (Thanks to the terahertz time-domain spectroscopy, I can directly compare data from simulation and from our laboratory.) The current approach of normalized units is however just a formal complication and i

Re: [Meep-discuss] Dispersive anisotropic media

2014-11-19 Thread Filip Dominec
ence, Pilani > > On Wed, Nov 19, 2014 at 9:04 PM, Filip Dominec > wrote: > >> Dear Rajath, >> it pretty much looks like missing- or incompatible version of libhdf. >> Have you tried the compilation procedure from this site? >> http://fzu.cz/~dominecf/meep/index.h

Re: [Meep-discuss] Scaling - dielectric-epsilon, metal-copper, lattice/resolution and Symmetry

2014-11-24 Thread Filip Dominec
Dear Steve, 1) Use the value of 2.3. The static permittivity is invariant to scaling. 2) If you wanted to model realistic copper, with scaling of 1:1e6, you would have to feed MEEP with values normalized to the scaling (1e6) and also by the speed of light (2.998e8). For instance, the physical Lore

Re: [Meep-discuss] Scaling - dielectric-epsilon, metal-copper, lattice/resolution and Symmetry

2014-11-25 Thread Filip Dominec
If my current run is successful I want to calculate forces > around the outside of the modeled resonate cavity. I am hopeful that > Meep can detect forces caused by evanescent wave momentum and if so, I > will be a long way ahead of game. I appreciate your continued support. > > S

Re: [Meep-discuss] Slow calculation with meep parallelisation

2014-12-02 Thread Filip Dominec
, I tried multiprocessing on single node too. And the problem persists. > Is it a common problem with meep multiprocessing? > > Thanks and Regards, > Ratnesh > > -Original Message- > From: Filip Dominec [mailto:filip.domi...@gmail.com] > Sent: Tuesday, December 02, 2014 3:41 P

Re: [Meep-discuss] meep and python-meep on OS-X

2015-02-10 Thread Filip Dominec
Thank you, Glenn, great job. I will be happy to add a link to your post! Filip ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] how to define a invariable complex refractive index?

2015-02-10 Thread Filip Dominec
Dear Liu, from the principle of FDTD computation, there is no other way how to define complex refractive index than to include dispersion. Either you may introduce a Drude term (conductivity), or some high-frequency Lorentzian. More details are here: http://ab-initio.mit.edu/wiki/index.php/Material

Re: [Meep-discuss] Puzzling results for reflection spectrum

2015-02-10 Thread Filip Dominec
Hi, if you properly divide the reflected amplitude by the incident amplitude, the reflection of a linear system should indeed be the same, independent of the source duration and spectrum. If it is not, one possible cause may be that you clip the time record while the source was still running, or th

Re: [Meep-discuss] Gaissian Distribution of Phase

2015-02-10 Thread Filip Dominec
Hi, currently I do not have the example you mention, but surely you can make a focused beam from an oblique beam, by introducing a *quadratic* term into the imaginary part of the exponential that defines the source amplitude. If you wish to build a focused *gaussian* beam, you will also wish to mod

Re: [Meep-discuss] Error while using perfect-metal

2015-02-11 Thread Filip Dominec
Dear Jim, this seems to be a result of instability, resulting in saturated (i.e. infinite or NaN) values as you suggest. To verify this, you may shorten the simulation until you get some image that is not plain black. As a matter of fact, the instability does not occur instantly, but it takes it se

Re: [Meep-discuss] help for calculation of transmission and reflection of photnic crystals slabs

2015-02-17 Thread Filip Dominec
Hi, Saeid, your task has been perhaps done by somebody else, please take a look at https://timsaucer.wordpress.com/2013/04/30/building-l3-photonic-crystal-cavity-in-meep-1-finding-mode/, http://comments.gmane.org/gmane.comp.science.electromagnetism.meep.general/10, http://osdir.com/ml/science.elect

Re: [Meep-discuss] Seeking advice for measuring transmission spectra

2015-02-18 Thread Filip Dominec
Dear John, I can not confirm not deny your approach is correct. I use another way to get the incident/transmitted/reflected fields from a structure in free space. Most importantly, it provides also the phase information, and also allows to get all the reflection and transmission coefficients in si

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