Re: [Meep-discuss] integral of Poynting vector over a plane

2006-04-10 Thread Steven G. Johnson
On Mon, 10 Apr 2006, Steven G. Johnson wrote: Yes, that will work, although you will want to set force-complex-fields? in order that it give you the time average flux rather than a snapshot. Note, of course, that Re[E* x H], which is what flux-in-box computes, only gives the time-average flux

Re: [Meep-discuss] libctl installed in non-standard location

2006-04-12 Thread Steven G. Johnson
On Wed, 12 Apr 2006, David Leuenberger wrote: LDFLAGS=-L/home/eecs/dleuen/software/meeplibs/lib:/usr/lib CPPFLAGS=-I/home/eecs/dleuen/software/meeplibs/include:/usr/include This is not the syntax for LDFLAGS and CPPFLAGS. If you have multiple directories you use multiple -L or -I flags, not

Re: [Meep-discuss] source definition

2006-04-14 Thread Steven G. Johnson
On Fri, 14 Apr 2006, Qi Wu wrote: I would like to create several sources with related phase relationship. I want the first source to be a gaussian-src, and the second one is related to the first one by a phase factor exp(i * phi) where phi is a phase I know. Just use the amplitude property

Re: [Meep-discuss] E-field contrast

2006-04-17 Thread Steven G. Johnson
On Mon, 17 Apr 2006, Chad Husko wrote: I was wondering if there was a quick way to edit the color scale of the electric fields? I.e. can one modify the contrast so that weak (compared to an excitation, which I'm assuming the scale is normalized against) transmission signals are more visible?

Re: [Meep-discuss] Error when running Make check

2006-04-18 Thread Steven G. Johnson
On Tue, 18 Apr 2006, Fred Brossard wrote: I have installed all the components of meep on my Debian system... however when I run the make check i get the following during the test sequence: Strange, I have Debian stable (gcc 3.3.5) on x86 also, and I can't replicate your problem. In fact,

Re: [Meep-discuss] Differences between source Ez and Hz

2006-04-19 Thread Steven G. Johnson
On Wed, 19 Apr 2006, Andreas von Rhein wrote: Please have a look at the attached files. square.dat and square2.dat are calculated with eigen.ctl as given. Only difference is the M-Point. For square.dat I've chosen (vector3 0.5 0.5 0) and for the second (vector3 0.5 -0.5 0) So meep does

Re: [Meep-discuss] Problem with the collected flux shape.

2006-04-27 Thread Steven G. Johnson
On Thu, 27 Apr 2006, Florencio Garcia wrote: I'm trying (as an exercise) to calculate the reflectance and transmittance of a simple cubic lattice. I have a gaussian source, which is a 1x1 plane perpendicular to the Z direction. The frequency center is 0.5 and the fwidth is 0.8. However, when I

Re: [Meep-discuss] How to compute the extraction efficiency of spontaneous emission from slabs of photonic crystals

2006-04-27 Thread Steven G. Johnson
at the boundary of the block and the PML. Change the block size to, say, (size infinity infinity z). Cordially, Steven G. Johnson ___ 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 compute a band structure using C++

2006-05-01 Thread Steven G. Johnson
On Mon, 1 May 2006, Jun She wrote: I wrote, f.initialize_with_n_tm(4). Then I compiled the code and run the program. I saw, meep: cannot require a hp compoint in a 2D grid This function is for cylindrical coordinates only, and initializes the fields with a particular mode of a cylindrical

Re: [Meep-discuss] Fourier transform -- field profile at a fixed frequency

2006-05-22 Thread Steven G. Johnson
Although Meep computes Fourier transforms of field components in space internally, it doesn't currently give you an easy way to output this information, I'm afraid. (It is mainly used right now for computing flux spectra.) The Fourier transform of a region in space is computed when you all

Re: [Meep-discuss] Exciting the PCWG excited state in a nonlinear structure

2006-05-22 Thread Steven G. Johnson
On Mon, 22 May 2006, Chad Husko wrote: I'm interested in using the first excited state (odd) of a standard W1 Photonic Crystal Waveguide (PCWG). I'm trying to think of ways to excite that mode. Some caveats - I can't use symmetric excitations (I think) because I'm going to also include the

Re: [Meep-discuss] about flux variation along a straight waveguide with a continuous-src(df=0.1)

2006-05-29 Thread Steven G. Johnson
a continuous-src in order to compute flux spectra. Use a gaussian-src. You need to run long enough for the fields to have died away at the flux plane in order for the flux spectra to make sense. Cordially, Steven G. Johnson ___ meep-discuss mailing list

Re: [Meep-discuss] Arbitrary mu?

2006-06-13 Thread Steven G. Johnson
We'd like to include mu at some point, for various reasons. It would be pretty easy to hack in support for a scalar mu. To simulate realistic negative-refractive materials, however, you really need to include material dispersion in the mu as well as in epsilon, and that would be more work.

Re: [Meep-discuss] libctl 3.0.1 problem

2006-06-21 Thread Steven G. Johnson
when you use the C compiler to link C++ code.) Maybe there is something strange in your environment variables? Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo

Re: [Meep-discuss] ma flux-region problem.

2006-06-24 Thread Steven G. Johnson
On Sun, 25 Jun 2006, K. Choi wrote: (define trans (add-flux fcen df nfreq ;X direction (make flux-region (center 3 0 ) (size 0 6 ) (direction X) (weight 1) ) (make flux-region (center -3 0 ) (size 0 6 ) (direction X) (weight -1) ) Hi, I looked into this, and add-flux is broken for

Re: [Meep-discuss] installing on cygwin

2006-07-28 Thread Steven G. Johnson
On Sun, 23 Jul 2006, Kang, Christopher wrote: I am having a problem installing Meep and h5utils on cygwin. I have compiled and installed BLAS, LAPACK, libctl, harminv, and HDF5. ./configure works for meep, but when I try to do make I get the following output: $ make make all-recursive

Re: [Meep-discuss] Configure failure in MPI build

2006-07-31 Thread Steven G. Johnson
On Fri, 28 Jul 2006, Cowan, Benjamin wrote: conftest.cc(11): error: namespace std has no member exit extern C void std::exit (int) throw (); using std::exit; Hmm, it looks like mpic++ requires a different declaration of std::exit than g++ on the same system? Perhaps you have more than one

RE: [Meep-discuss] Configure failure in MPI build

2006-07-31 Thread Steven G. Johnson
On Mon, 31 Jul 2006, Cowan, Benjamin wrote: In fact no file libgm.* is in any of these directories. Is libgm a library that should be included with the system or compiler? If so I could ask the unix admins here about it. I'm not sure what libgm is (Meep does not link to it explicitly), but

Re: [Meep-discuss] Forming a grating extending to infinity

2006-08-08 Thread Steven G. Johnson
On Tue, 8 Aug 2006, Ashifi wrote: grating). I think the question can simply be phrased as does MEEP permit setting periodic boundary conditions in one or two dimensions while having absorbing boundary conditions (PML) defined in the remaining computational area/volume? If so, could I possibly

Re: [Meep-discuss] How to define a bunch of random current sources?

2006-08-16 Thread Steven G. Johnson
On Thu, 17 Aug 2006, hb wrote: I have some qusetions: 1) How to write a loop? 2) The phases of the sources is random, but I have not find a function to generate random number. How to solve the problem? The answer to both your questions can be found at:

Re: [Meep-discuss] harminv gives no solutions

2006-08-16 Thread Steven G. Johnson
or whatever. By the way, your k points are wrong (they should vary *inversely* with a). Regards, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] PML implementation

2006-08-21 Thread Steven G. Johnson
have other advantages.) Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] when to stop the simulation

2006-08-22 Thread Steven G. Johnson
On Tue, 22 Aug 2006, Jun She wrote: If I want to calculate the flux, how many time steps enough? Why do you set f.time() nfreq / (freq_max-freq_min) / 2 here? Because of the uncertainty principle, the computation time must go inversely with the desired frequency resolution. In another

Re: [Meep-discuss] harminv gives no solutions

2006-08-22 Thread Steven G. Johnson
On Tue, 22 Aug 2006, Matt wrote: (output-epsilon) for this structure seems to give me a cross-section, possibly at z=0. I see a white square with a black circle where the metal rod should be. output-epsilon should give you a 3d dataset corresponding to the full structure. Probably you are

Re: [Meep-discuss] apparent violation of Poynting's theorem?

2006-08-22 Thread Steven G. Johnson
On Thu, 17 Aug 2006, G.J. Parker wrote: what i'm seeing is that R and T are NOT the same at each plane. in particular, at large frequencies, there is some spurious (?) oscillations in R T which depend on the position of the flux planes. since there is nothing but air between the various flux

Re: [Meep-discuss] what are the meanings of the parameters in the function do_harminv?

2006-08-24 Thread Steven G. Johnson
On Thu, 24 Aug 2006, Jun She wrote: What are the meanings of the parameters (spectral_density, rel_err_thresh, rel_amp_thresh, amp_thresh) in the function do_harminv? They correspond to the -d, -e, -a, and -A options of the harminv program. 'man harminv' for more info.

Re: [Meep-discuss] band diagram of the photonic crystal slab

2006-08-25 Thread Steven G. Johnson
On Fri, 25 Aug 2006, Jun She wrote: When I updated MEEP to version 0.10, I found that I couldn't calculate the band diagram of the photonic crystal slab. I can't get any mode after do_harminv. The program I wrote is ok under MEEP-0.9. That's strange; could you tell me more about your

Re: [Meep-discuss] what is the meaning of A in function add_volume_source?

2006-08-27 Thread Steven G. Johnson
It is a function of position (relative to the center of the source volume) that multiplies the amplitude. This allows you to specify non-constant amplitude profiles. On Mon, 28 Aug 2006, Jun She wrote: What is the meaning of A in function add_volume_source? void add_volume_source(component

Re: [Meep-discuss] make check fails in version 0.10

2006-08-28 Thread Steven G. Johnson
On Mon, 28 Aug 2006, Heiner Matthias wrote: I just installed the latest version of meep (0.10). When I did make check, Meep passed nearly all the tests, but in 2D_convergence.dac the following error occurs. Can you do make distclean ./configure --enable-debug make

Re: [Meep-discuss] Re: [MayaVi-users] isosurface config hangs on inf dimension (fwd)

2006-08-28 Thread Steven G. Johnson
Thanks, that's good to know. I should probably patch h5tovtk to take care of this. I would suggest that you remove infs and nans from the data before you use VTK/MayaVi. ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu

Re: [Meep-discuss] Simulation worked in 0.9, blows up in 0.10?

2006-08-28 Thread Steven G. Johnson
On Mon, 28 Aug 2006, Bryce Meredig wrote: Have there been syntax changes in any of the program's features (especially dispersive materials, since that's what I'm doing) that require changes to old .ctl files? No, there haven't been any syntax changes to dispersive materials. The main

Re: [Meep-discuss] output-png+h5

2006-08-28 Thread Steven G. Johnson
On Mon, 28 Aug 2006, Chad Husko wrote: I tried the new command output-png+h5 and it will only output the h5 files. I thought the syntax was the same as the output-png command. Is there something else I'm missing? Whoops, this is a bug. It will be fixed in the next release, but for now you

Re: [Meep-discuss] errors while running 'make check' for version 0.10

2006-08-28 Thread Steven G. Johnson
On Mon, 28 Aug 2006, Andre Charbonneau wrote: I managed to compile and install the latest version of Meep (0.10) on my cluster. But when I try to run 'make check', I get the following error after a while. (I tried with the 'enable-debuggin' switch but still get the same results): Does the

Re: [Meep-discuss] failed to install meep-0.10

2006-08-28 Thread Steven G. Johnson
On Tue, 29 Aug 2006, Jun She wrote: I tried to install meep-0.10 into our cluster. Four nodes is ok. However, one node shows: /usr/lib/libc_nonshared.a(elf-init.oS)(.gnu.linkonce.t.__i686.get_pc_thunk.bx+0x0): In function `__i686.get_pc_thunk.bx': : multiple definition of

Re: [Meep-discuss] plotting

2006-08-31 Thread Steven G. Johnson
On Thu, 31 Aug 2006, matt wrote: Which tools were used to make holey-wvg-bands.png? matlab? gnuplot? ooffice? That figure was created in Matlab. xmgrace is a nice free plotting tool that is also quite flexible. ___ meep-discuss mailing list

Re: [Meep-discuss] error when using meep 0.10

2006-09-04 Thread Steven G. Johnson
On Sat, 2 Sep 2006, opthan zju wrote: meep: error on line 494 of h5file.cpp: file data is inconsistent size for subsequent processor Make sure HDF5 is compiled with MPI support, as the parallel HDF5 output otherwises uses something of a hack that can be unreliable if you have many processors

Re: [Meep-discuss] questions on run-k-points and harminv

2006-09-04 Thread Steven G. Johnson
On Thu, 31 Aug 2006, matt wrote: For a 2d periodic square lattice structure, with lattice constant a, what is the correct meep k-point list which corresponds to the boundary of the Brillouin zone? I guessed the following, but wasn't sure about units: (define k-points (list (vector3 0 0 0)

Re: [Meep-discuss] how to call harminv from FORTRAN in Linux/windows

2006-09-07 Thread Steven G. Johnson
understanding. The simplest thing is to just output comma-delimited text from your Fortran program, and then analyze it with the stand-alone harminv program. Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http

Re: [Meep-discuss] reintroducing units in meep

2006-09-09 Thread Steven G. Johnson
interactive? to true at the end. Correct these problems, and you should see what you expect. Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] Trapezoid objects

2006-09-13 Thread Steven G. Johnson
On Wed, 13 Sep 2006, Lorem Ipsum wrote: is there an easy way of defining trapezoids or triangles in the geometry? Currently I do this by subtracting tricky blocks of air from other tricky blocks of some material but it is a bit tedious. In two dimensions you can use a cone object, since only

Re: [Meep-discuss] how to keep two sources energy equal?

2006-09-14 Thread Steven G. Johnson
On Thu, 14 Sep 2006, hbchen wrote: I am trying to put a same source in two different structures, then compare the influence of the two structures to the source. So, I need to keep the two total energies to be equal and calculate two flux. Is the total energy equal in the two situations(in

Re: [Meep-discuss] frequency spectra for arbitrary grid points

2006-09-15 Thread Steven G. Johnson
is proportional to the field at a single point. Cordially, Steven G. Johnson ___ 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 keep two sources energy equal?

2006-09-15 Thread Steven G. Johnson
On Fri, 15 Sep 2006, hbchen wrote: I only want to compare the output efficiency( namely the Poynting vector) in certain direction. What should I do? You have to define what you mean by output efficiency. ___ meep-discuss mailing list

Re: [Meep-discuss] (meep::fields::add_dft_pt)

2006-09-21 Thread Steven G. Johnson
On Thu, 21 Sep 2006, matt wrote: If you're using run-k-points on a unit cell, you want to be able to tell how many time steps is long enough until the characteristic modes have settled. For this purpose, it would be nice to watch an animation of the DFT evolution for a given field point.

Re: [Meep-discuss] Installing problem

2006-09-29 Thread Steven G. Johnson
On Fri, 29 Sep 2006, hbchen wrote: I want to install meep on SGI-irix6.5. Firstly, I should install readline package on it. After using ./configure command (there is no problem), I use make. Then the computer screen show: cc ERROR: file does not exist: readline.c. However, I found that

Re: [Meep-discuss] meep memory usage

2006-09-29 Thread Steven G. Johnson
On Fri, 29 Sep 2006, João Luis Silva wrote: The grid will be 1000x1000. At each point we need to know a double value, so it's approximately 7.6 MB per field. However the real memory consumption is around 87 MB. Meep definitely is a bit liberal about memory usage, although my first estimate

Re: [Meep-discuss] Re: meep memory usage

2006-09-30 Thread Steven G. Johnson
On Sat, 30 Sep 2006, João Luis Silva wrote: I found the problem: When dispersive media is used, the memory related to the dispersive media is not split by the nodes, but every node has a full copy of the fields. In my real problem I use a Sellmeier formula for silica Yikes, this is indeed a

Re: [Meep-discuss] Scheme vs C++ Interface

2006-10-08 Thread Steven G. Johnson
On Sun, 8 Oct 2006, Robert Bicknell wrote: I've been using the Scheme interface to meep and have been thinking about switching to the C++ interface. Are there any fundamental reasons not to do this ? It seems that there are more examples and documentation for the Scheme interface. Will the c++

Re: [Meep-discuss] How to separate the incident and reflected fields using C++ interface?

2006-10-10 Thread Steven G. Johnson
On Tue, 10 Oct 2006, Jun She wrote: As MEEP tutorial shows, computing reflection spectra is a bit tricky because we need to separate the incident and reflected fields. When we using ctl interface, we can save the Fourier-transformed fields from the normalization run and load them, negated. How

Re: [Meep-discuss] integration function

2006-10-11 Thread Steven G. Johnson
On Wed, 11 Oct 2006, Andreas von Rhein wrote: After calling the run function I would like to integrate over a plane. For testing I've chosen the whole computation area (defined by default). e.g. I like to integrate the Ey-component: (define (get-field-point2 where what) (get-field-point what

Re: [Meep-discuss] Electric field units

2006-10-11 Thread Steven G. Johnson
On Wed, 11 Oct 2006, João Luis Silva wrote: the nonlinear coefficient n2 in um^2/W as described on the web page. My length unit is the um, so all is OK so far. My question is what are the units of the electric field, so I know what to pass to the (amplitude A0) of the gaussian-src. Assuming

Re: [Meep-discuss] There is no destructor in the Class dft_flux

2006-10-12 Thread Steven G. Johnson
On Thu, 12 Oct 2006, Jun She wrote: There is no destructor in the Class dft_flux. Is it a bug? No, it's intentional. The dft_chunks are removed when the fields are deallocated, so there should be no memory leak. If I added a ~dft_flux destructor, however then there is a chance that it

[Meep-discuss] please help convince DARPA that MPB, Meep, etc. are useful

2006-10-13 Thread Steven G. Johnson
, finding papers that employ MPB is not a problem.) Feel free to forward this email to any MPB/Meep user you know of who might not be on the mailing list. Thanks for your support! Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu

Re: [Meep-discuss] Meep installation problems: please help

2006-10-13 Thread Steven G. Johnson
/stable you could have libctl-2.2 in /usr/lib, which would cause the error you saw.) Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] Version 0.10 installation error on Cygwin

2006-10-13 Thread Steven G. Johnson
On Fri, 13 Oct 2006, Min Yan wrote: My aforementioned installation problem on Cygwin can be overcome by following the suggestion from Mischa Megens. There were also a couple of fellows wrote to me checking if I got over the problem. So this might be useful to those who have to stick to a Cygwin.

Re: [Meep-discuss] There is no destructor in the Class dft_flux

2006-10-13 Thread Steven G. Johnson
On Thu, 12 Oct 2006, Jun She wrote: When I do 3D simulation, I meet a problem when the program want to free the memory. If you can send me a minimal C++ file (all extraneous calculations removed, but it should still compile) that demonstrates the problem, I'll see if i can reproduce the

Re: [Meep-discuss] parallel meep/ print output

2006-10-14 Thread Steven G. Johnson
On Sat, 14 Oct 2006, Andreas von Rhein wrote: I like to compute self defined functions depending on field-variables (Ex, Ey, etc.) and finally print them on stdout. But sometimes the output interferes with the meep-ping output. What do you mean by meep-ping? I print the results of

Re: [Meep-discuss] Re: Electric field units

2006-10-16 Thread Steven G. Johnson
On Mon, 16 Oct 2006, João Luis Silva wrote: I thought I was specifying the electric field, not the current (oops!). So I used flux-in-box passing a plane perpendicular to the wave. However, with real field no averaging will be done, and (flux-in-box ...) cannot be used as a step function. So I'm

Re: [Meep-discuss] Problem with Bragg multilayer...

2006-10-17 Thread Steven G. Johnson
than it does in vacuum. This is a real physical effect, having to do with the difference in the local density of states.) Regards, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman

Re: [Meep-discuss] epsilon function (c vs. libctl)

2006-10-17 Thread Steven G. Johnson
On Tue, 17 Oct 2006, matt wrote: Increasing the resolution should minimize the errors you describe, so let's try changing the resolution of the example from 20 to 80. Note that the comparison you posted was incomplete, because you didn't show the differences for a resolution of 20 to see

Re: [Meep-discuss] is there a way to specify a PML region inside?

2006-10-19 Thread Steven G. Johnson
On Thu, 19 Oct 2006, G.J. Parker wrote: i would like to place blocks of PML inside of the simulation region (not just next to a boundary). is that possible? is it advisable? This is not currently possible, sorry. Can you explain why you would want to do this?

Re: [Meep-discuss] configure error on Cygwin

2006-10-19 Thread Steven G. Johnson
On Wed, 18 Oct 2006, Guo, Shy-Hauh wrote: Environment: CYGWIN_NT-5.1 Error message: C++ complier cannot create executables I have Visual studio installed on the same computer, and it should be included in PATH (as shown below), so there should be C++ complier available on my computer. I don't

Re: [Meep-discuss] strange MEEP transmittance/reflectance problem

2006-10-23 Thread Steven G. Johnson
On Sat, 21 Oct 2006, Erik Nelson wrote: I'm trying to compute transmission and reflection spectra for a 3D opal of SiO2 (n=1.45) sphere's infilled with Si (n=3.5), however the intensity of the reflectance spectrum has values from 0 to almost 3.5 and the transmittance spectrum intensity ranges

Re: [Meep-discuss] is there a way to specify a PML region inside?

2006-10-23 Thread Steven G. Johnson
On Sun, 22 Oct 2006, G.J. Parker wrote: there may not be a critical reason. originally i was thinking it could shape the spatial incoming spectral pulse. i can do the same thing, i think, using metal blocks. Or you could use the amplitude function of the source to make the source current

Re: [Meep-discuss] BLAS and LAPACK

2006-10-23 Thread Steven G. Johnson
On Sun, 22 Oct 2006, Guo, Shy-Hauh wrote: For those who have been able to install MEEP under Cygwin, would you please let me know what I should do with BLAS and LAPACK? As far as I know, I have LAPACK from the Math library in Cygwin, but the optimized BLAS is hardware dependent. However, I

Re: [Meep-discuss] Magitudes of induced currents and conducting media

2006-10-26 Thread Steven G. Johnson
On Tue, 24 Oct 2006, Dr Chris Stevens wrote: how to extract a plot of field versus distance from my source ? Output the field into an hdf5 file (e.g. pass output-efield-z to run) and then read it into your favorite plotting program. Matlab can read HDF5 files directly with the hdf5_read

Re: [Meep-discuss] Bloch periodic boundaries

2006-10-27 Thread Steven G. Johnson
On Fri, 27 Oct 2006, Loïc Le Guyader wrote: Suppose the computation cell size is L in the X direction. I want to say that this cell is in fact a unit cell and that I have a periodicity of L in the X direction, I do then: (set! k-point (vector3 1 0 0)) (set! ensure-periodicity true) If this is

Re: [Meep-discuss] Gaussian source

2006-10-30 Thread Steven G. Johnson
On Sun, 29 Oct 2006, Loïc Le Guyader wrote: Another thing that I don't understand is that when you specify the frequency of a gaussian source, it actually as a different frequency. In the attached ctl file, frequency is set to 0.15, but the transmitted flux in air shows 0.1636 ! You didn't

Re: [Meep-discuss] Bloch periodic boundaries

2006-10-30 Thread Steven G. Johnson
On Sun, 29 Oct 2006, Loïc Le Guyader wrote: Damn ! Ok so what is the solution then to have a periodic structure in 2 directions only ? Is it correct to set k-point and then put a pml-layers in the direction where we don't want periodicity ? For example I want periodicity Absolutely. You

Re: [Meep-discuss] install meep-0.10

2006-10-30 Thread Steven G. Johnson
On Mon, 30 Oct 2006, hbchen wrote: Dear Steven: (1) I tried to install Meep 0.10 on cluster, and was stoped by the following errors at make step: anisotropic_averaging.cpp:20: `sphere_quad' undeclared (first use this function) sphere_quad should be defined in sphere-quad.h, which is

Re: [Meep-discuss] meep-mpi runtime error

2006-11-02 Thread Steven G. Johnson
On Wed, 1 Nov 2006, °­ÈñÁø wrote: I had installed parallel Meep.   I got some error message when I execute sample code on 2 processor. Remove the output-epsilon command from your .ctl file, to see if it is a problem with the HDF5 output. If that fixes the problem, probably you need to

Re: [Meep-discuss] Very slow computation for complex dielectrics

2006-11-02 Thread Steven G. Johnson
On Tue, 31 Oct 2006, Dr Chris Stevens wrote: am still playing with this complex dielectric issue. I am running two ctl files listed below. The first, sea_fake.ctl runs in about 75s having only real dielectrics ie water with zero conductiivty. The second which simulates the same situation but

Re: [Meep-discuss] Arbitrary shape.

2006-11-02 Thread Steven G. Johnson
On Tue, 31 Oct 2006, David Domenech wrote: As I read on this discuss list you've talked about create arbitrary shapes by using the material-function subclass. Could you give me any hint to use that class?? I'm trying to do a parabolic horn. But I don't have any idea what kind of arguments must

Re: [Meep-discuss] periodic visualization of meep field output

2006-11-03 Thread Steven G. Johnson
On Fri, 3 Nov 2006, matt wrote: Using meep, I calculate the fields in a unit cell of a periodic structure. For visualization of modes, it would be nice to see the pattern in an array of several cells. I thought perhaps mpb-data would work on meep h5 output, as described in the mpb data

Re: [Meep-discuss] Fwd: MPB modal field pattern as source in Meep

2006-11-06 Thread Steven G. Johnson
On Sun, 5 Nov 2006, Simone Sugliani wrote: This is my first post and I would thank Steven Johnson and ab-initio MIT group for their great work. I'm trying to simulate an optical graded index waveguide in order to obtain some useful project parameters. I have calculated the modal behaviour of

[Meep-discuss] Re: calculation with symmetry

2006-11-06 Thread Steven G. Johnson
On Sun, 5 Nov 2006, Zhichao Ruan wrote: Many thanks for your help. I understand how to setup a Hx source oriented on the z=0 to excite the even Hx field about z. Now i have another question, can i use the Hx source, which is not oriented on z=0 but with the (phase 1), to excite the odd Hx

Re: [Meep-discuss] material dispersion

2006-11-11 Thread Steven G. Johnson
On Fri, 10 Nov 2006, Loïc Le Guyader wrote: original patch posted by Steven, this does reduce memory requirements when using Lorentzians. i have no problems using five Lorentzians w/ Note that the patch referenced in this post reduces the memory requirements for dispersive materials on

Re: [Meep-discuss] a minor mistake

2006-11-12 Thread Steven G. Johnson
On Mon, 13 Nov 2006, Jun She wrote: http://ab-initio.mit.edu/wiki/index.php/Meep_Introduction#Maxwell.27s_equations Last sentence, MPB supports simulation in cylindrical coordinates: see Cylindrical coordinates in Meephttp://ab-initio.mit.edu/wiki/index.php/Cylindrical_coordinates_in_Meep . I

Re: [Meep-discuss] Geometry Oddity

2006-11-13 Thread Steven G. Johnson
On Mon, 13 Nov 2006, Ashifi wrote: Thanks for the feedback Steven. I tried a few things over the weekend. Resolution = 1e8 should give me 1e8 pixels per meter, or 1 pixel = 1e-8 meters which would sufficiently resolve the 18 micron thick copper plate. Setting the resolution to 1e8 gives the

Re: [Meep-discuss] the thickness of the PML

2006-11-13 Thread Steven G. Johnson
On Mon, 13 Nov 2006, Jun She wrote: If the frequence is very low, i.e. 0.1, in other words, the wavelength is 10, do I need to set the thickness of the PML layer to be 5? I don't know if it needs to be 5, but in general for longer wavelengths you'll need thicker PML. Steven

Re: [Meep-discuss] PCB simulation question

2006-11-13 Thread Steven G. Johnson
On Mon, 13 Nov 2006, Pieter G wrote: Are MEEP actually the right choice for this kind of problem (I think so!)? Do you know of any other project (OSS) that might be better suited to my problem? Or even technical articles that discuss this subject. First, I should say that my own research deals

Re: [Meep-discuss] -Q option for harminv

2006-11-13 Thread Steven G. Johnson
On Mon, 13 Nov 2006, Changsoon Kim wrote: I am calculating a band structure for a photonic crystal slab, and the results do not show some of high frequency leaky guided modes. I was wondering whether there is a way to set -Q option for harminv from a *.ctl file. It is possible, by calling

Re: [Meep-discuss] Geometry Oddity

2006-11-13 Thread Steven G. Johnson
On Tue, 14 Nov 2006, Ashifi wrote: All the files in the examples directory run fine, except bend-flux.ctl. It complains about an error in opening an HDF5 file. That's because you have to run its normalization case first, as explained in the tutorial. The file attached gave me the error I

Re: [Meep-discuss] How can I apply the source to study the resonant point defect modes of PC slabs!

2006-11-16 Thread Steven G. Johnson
. at (0.1234,0.4567,0). That way you will be sure to excite all of the modes, unless you are extremely unlucky. Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep

Re: [Meep-discuss] error when I call sh autogen.sh

2006-11-30 Thread Steven G. Johnson
On Thu, 30 Nov 2006, Jun She wrote: I want to modify some MEEP code and add some classes into the MEEP. I used darcs to download the MEEP source files. Then I run sh autogen.sh. Unfortunately, I am failed. src/Makefile.am:12: bad macro name [EMAIL PROTECTED]@_la_SOURCES' Probably you need to

Re: [Meep-discuss] How to plot the inset for the resonant mode?

2006-12-24 Thread Steven G. Johnson
-sys.matlab newsgroup for more information. Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Re: [Meep-discuss] output-hfield-r and output-hefield-p

2007-01-15 Thread Steven G. Johnson
On Sun, 14 Jan 2007, Huazhong Wang wrote: in my 2D simulation with TM (Ez) source, I want to calculate output-hfield-r and output-hefield-p. after running, meep didn't create .h5 files. but when I calculate output-hfield-x and output-hfield-y, the results are right. who could help me find the

Re: [Meep-discuss] Requiring -malign-double flag while compiling C++ program

2007-01-15 Thread Steven G. Johnson
On Fri, 12 Jan 2007, [EMAIL PROTECTED] wrote: Unfortunately the compiled program always ended up with a segmentation fault.. The programs seem to run perfectly well when I change the command to the following. g++ -malign-double `pkg-config --cflags meep` foo.cpp -o foo `pkg-config --libs meep`

Re: [Meep-discuss] command: output-field-function name cs func.

2007-01-15 Thread Steven G. Johnson
On Thu, 11 Jan 2007, Huazhong Wang wrote: i am trying to use command: output-field-function name cs func). i don't know what means of name. i think it is just a name of a dataset. but i couldn't make this command run. meep responded me that the name in my code is unbound variable. who can give

Re: [Meep-discuss] i want to take out the Ex at point (0 0 0) after running

2007-01-15 Thread Steven G. Johnson
On Fri, 12 Jan 2007, Huazhong Wang wrote: i want to take out the Ex at point (0 0 0) after running. my code is below: ... (define (myfun Ex) (get-field-point Ex (vector3 0 0 0))) ... (run-util 100 (at-end (output-field-function Ex (list Ex) myfun)) ) ... but meep stops running, its response

Re: [Meep-discuss] Can I use MEEP software to get the coupling and field distribution?

2007-01-15 Thread Steven G. Johnson
regions of space, so you can use that to determine how efficiently your source couples into, say, a photonic-crystal waveguide compared to, say, empty space. Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab

Re: [Meep-discuss] who has a better method with less computing time to calculate Hx along a line?

2007-01-15 Thread Steven G. Johnson
(volume (center 0 0 0) (size 2 0 0)) output-hfield-x))) will output the Hx field along a line of length 2 from (-1 0 0) to (1 0 0). Cordially, Steven G. Johnson ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab

Re: [Meep-discuss] problem with (at-time T...)

2007-01-15 Thread Steven G. Johnson
On Mon, 8 Jan 2007, Mischa Megens wrote: meep meep (reset-meep) meep (run-until 10 .. (at-time 5 .. (lambda (x) (display time: ) (display (meep-time)) (newline)) .. ) .. ) This is not correct: your step function should take no arguments, i.e. it should be (lambda () ...) and

Re: [Meep-discuss] Re: 4. How to define a metal has the epsilon 12 - 5i, for example?

2007-02-08 Thread Steven G. Johnson
On Sat, 20 Jan 2007, Son-Geun Kang wrote: I really want to know if MEEP can simulate lossy material. If it's possible, how to? Yes, you would define it as a dispersive material (which allows you to include any desired set of absorption resonances).

Re: [Meep-discuss] Segmentation fault on Itanium2

2007-02-08 Thread Steven G. Johnson
On Sat, 20 Jan 2007, Bill Chen wrote: I meet a problem when run meep in my Itanium2 machine (Suse9 os),   radius 1, height 1e+20, axis (0, 0, 1)   dielectric constant epsilon = 1 Halving computational cell along direction y time for set_epsilon = 0.157944 s ---

Re: [Meep-discuss] dispersive material

2007-02-08 Thread Steven G. Johnson
On Thu, 25 Jan 2007, xqhuang wrote: Dear Steven and others, When I calculate the dispersive material, why the output of the structure are all black? In this case, are there any ways to see the field patterns of the dispersive material?Thanks in advance! Possibly something is blowing up? Or

Re: [Meep-discuss] local density of state

2007-02-08 Thread Steven G. Johnson
On Sat, 27 Jan 2007, Changsoon Kim wrote: I am interested in calculating a Green's function of a photonic crystal and from that, a local density of state, by exciting a photonic crystal structure with a point source that has a Gaussian temporal shape and then comparing its Fourier transform

Re: [Meep-discuss] using in-volume to plot 3d cylinder

2007-02-08 Thread Steven G. Johnson
On Wed, 31 Jan 2007, MUHAMMAD Amin wrote: I have used the cylinderical coordinates to make use of circular symmetry. Now for the output hdf5 i want to plot the whole cylinder instead of slice in the cylinder. i know the in-volume is the meep feature for this issue but i dont know how to use it.

Re: [Meep-discuss] change resolution

2007-02-08 Thread Steven G. Johnson
On Wed, 31 Jan 2007, 구 석모 wrote: I want to make resolution different by location For example, make resolution 40 at cell (0 0) , and 20 elsewhere How can I do that? Meep does not currently support nonuniform spatial resolution, sorry.___

Re: [Meep-discuss] Making 3D movies with meep results

2007-02-08 Thread Steven G. Johnson
On Fri, 2 Feb 2007, Ashifi wrote: I performed a 3D simulation and I have the results as h5 files. I would like to know if it is possible to make a movie out of the files, looking at the whole 3D volume. I can look at the output of each time step in 3D using MayaVI, but I'm not sure how I can see

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