FilipDominec/python-meep-utils: <NEEDS MAJOR UPDATE> Simulations of electromagnetic waves - easier scripting, postprocessing and field export · GitHub

Since the improvements in meep and its Python bindings in 2018/19, following scripts are rather obsolete. I recommend to refer to the (semi)official meep pages, e.g. https://meep.readthedocs.io/en/latest/ and http://www.simpetus.com/projects.html for up-to-date examples. Filip Dominec 2019

MEEP is a library of functions for numerical simulations of how electromagnetic waves propagate and interact with various structures; it is a finite-difference time-domain solver of the Maxwell equations. The simulation is defined by programming, with bindings to C/C++, Scheme, or Python; I chose to use python-meep as Python is a user-friendly language that makes simple simulations (relatively) simple, and really complex ones possible. One can also seamlessly integrate them with powerful Python modules as numpy, scipy, matplotlib and many others.

After I set up several different realistic simulations with python-meep, I noticed that much of the Python code for initialisation, material definition, processing and data output can be shared. I therefore moved such code in the meep_utils.py and meep_materials.py modules.

To demonstrate how to use them to simplify the simulation setup, I accompany these modules with several ready-to-use simulations of various typical problems. I believe the presented scripts can be a great starting point for anybody doing their research on photonic crystals, metamaterials, integrated photonics and nanophotonics, cavity resonators, waveguides, etc.

You are encouraged to clone this repository and to modify the examples to match your needs. I would be very happy if this project helps you with your thesis, homework or any publication. Do not hesitate to contact me if you need some advice, new functionality or if you find a bug.

Filip Dominec, filip.dominec@gmail.com, 2012 - 2016

Usually, everything you need to run an example is to change to its directory, and launch ./batch.sh. In a multiprocessing environment, it is recommended to launch it like export NP=4; ./batch.sh.

Uses scatter.py and effparam.py to retrieve the effective behaviour of a metamaterial using the Nichols-Ross-Weir (s-parameters) method. Some of these examples are scans through a parameter of the structure.

Runs scatter.py multiple times in frequency-domain, and then compares the results to the classical Fourier-transformed time-domain simulation

Using cdh.py, plot_cdh.py, computes and plots data for current-driven homogenization; compares them with those obtained from s-parameters

Sets up both the source and the monitor planes such that they have a growing phase in space (done simply by harmonic modulation of the source amplitude). This way, an oblique wave is excited and recorded. Using arccosine, the angle can be computed from our knowledge of the frequency and the transverse component of the wavevector. By several time-domain simulations with different transverse wavevectors, we can efficiently build a 2D map of angle- and frequency-dependent reflectance of a sample.

The simulation in cylindrical_cavity.py defines a metallic cylindrical cavity, excites the field by a short pulsed source, and analyzes the ringdown to search for all modes.

Then the data are processed by ringdown_analysis.py and a comparison of Fourier transform, filter-diagonalisation (harminv) method and the textbook analytic solution is plotted.

Optionally, by uncommenting the bottom half of example_ringdown_cylindrical_cavity/batch.sh, the ringdown analysis can be used to search for terahertz resonances in experimental transmission water vapour. Quite a good match is obtained, which means that harminv works as expected.

Uses plasmons.py: A small aperture in a thin metal sheet couples incident light to surface plasmons.

If the film is surrounded by two media with similar index of refraction, circular interference pattern can be observed between the symmetric and antisymmetric plasmon modes. A different (hyperbolic) interference pattern can be obtained when the plasmons are coupled by two holes.

• TODO add support for metal/diel substrate,
• and try to show the sym-asym interference

• detection of field behind the aperture, normalized against free reference
• anisotropic permittivity of the dielectric sphere

• TODO

• TODO , c.f. transfer-matrix

• TODO implement seamless 2-D support

• TODO implement nonlinearity, test out

• spdc.py - TODO

• Official website of MEEP: http://ab-initio.mit.edu/wiki/index.php/Meep
  Contains information on the FDTD algorithm and simulations in general, documentation of the MEEP functions. Examples are mostly in Scheme.

  • Since 2014, the MEEP source code is hosted at Github: https://github.com/stevengj/meep
  • Your questions may (or may not) be answered in the MEEP mailing list: meep-discuss@ab-initio.mit.edu,
    http://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/

• Website of the python-meep interface: https://launchpad.net/python-meep
  Provides some examples of how the python-meep functions can be used in scripts.

• I also write my own website on simulations: http://f.dominec.eu/meep/index.html
  Contains my experience with installation requirements and procedure, simulation performance, realistic definition of materials, data postprocessing etc.

• License: GPLv2, http://www.gnu.org/licenses/gpl-2.0.html

The scripts require working python-meep environment, recommended compilation procedure is supplied in the python-meep-install.py script which is hosted here: https://github.com/FilipDominec/python-meep-install

Some scripts use the matplotlib's binding for LaTeX for nicer plots. You may either install the dependencies using sudo apt-get install -y texlive-latex-extra dvipng, or modify the scripts to avoid using the latter.

The procedure is tested on Debian-based Linux distributions. You may have to manually modify it if your system differs. Please read the script for details.

• meep_utils.py - the main module with routines useful for python-meep simulations
• meep_materials.py - module containing realistic definition of materials used
• README.md - this file
• LICENSE - General Public License
• metamaterial_models.py - different metamaterial models (that can be shared by other scripts)
• plot_scan_as_contours.py - if multiple simulations are run as a parametric scan, this allows to present all results in a single contour plot
• harminv_wrapper.py - allows to simply use filter diagonalisation method from Python

• terminate called after throwing an instance of 'Swig::DirectorMethodException', and simulation fails with an ugly call trace
  • Perhaps you left some run-time error in the structure definition: The eps() method is a callback, so a runtime error will not be handled by Python's usual "friendly" report of where the error is. To test this function prior to running MEEP's callback, put meep_utils.testmaterials() at the end of the model's initialization, which will help to obtain a reasonable Python report to find the problem.
  • If meep_utils.testmaterials() did not help, check other possible callback routines.
  • Make sure to never set the eps variable within the AbstractMeepModel class, since this name is reserved for MEEP callback.
• Simulation hard-crashes during model initialization with the 'memory not mapped' error (observed with Matplotlib 1.5.1 on Ubuntu 16.10)
  • This happens at the point when matplotlib tries to plot the permittivity spectrum, and to place a label at some high-frequency position like 10^16
  • I reported this error here matplotlib/matplotlib#6984; the solution is in installing a newer fixed version of matplotlib. I suggest picking the freshest one from git: http://matplotlib.org/faq/installing_faq.html#source-install-from-git
  • One little annoyance is that uninstalling the original python-matplotlib package one also has to uninstall paraview. Compile the new version, then install paraview back and everything will be fine.
• Simulation aborts with lorentzian unstable although the medium passed the meep_utils.testmaterials() function
  • The compiled-in check for Lorentzian stability in MEEP is overly prudent; it sometimes aborts a simulation that would be completely stable. You may either change the material model as MEEP suggests.
  • I consider this to be just an unfixed bug, see also the discussion NanoComp/meep#12. So even better is to change the MEEP source code to bypass the abort in function lorentzian_unstable in src/susceptibility.cpp and recompile it. My branch of MEEP does it.
• The time-domain simulation aborts when I try to define a material with a negative permittivity
  • The frequency-independent part of permittivity (i.e. permittivity without Lorentzian oscillators) in the time-domain solver can never be defined negative. In fact its minimum value is roughly 0.87 by default, this number is determined by the Courant factor used. For mathematical discussion, see NanoComp/meep#12. If you need a medium with negative permittivity, resort to the frequency-domain solver, or define a proper Drude-Lorentz model.
• The frequency-domain simulation does not converge when I try to define a material with a negative permittivity
  • The frequency-domain usually fails to converge in the infrared or optical range, where permittivity of metals is a small negative (complex) number. Defining the same metals in microwave simulations appears fine and converges. This situation is somewhat hard to compute with MEEP; you may try to reformulate your problem using Lorentz-Drude model and run a time-domain simulation with a narrow-band source.
  • Changing the resolution or running few time-domain steps before running frequency-domain solver may also help.
• AttributeError: 'unicode' object has no attribute 'shrink'
  • Try disabling LaTeX in Matplotlib.
• HDF5-DIAG: Error detected in HDF5 (...) unable to open file:w
  • perhaps you try to export the fields twice to the same file?
• ValueError: width and height must each be below 32768
  • this seems like a bug in certain versions of Matplotlib, try disabling labels

• Exported figures show no fields and are black
  • This means that infinite values or not-a-numbers ("NaN") resulted from the simulation. This is perhaps due to simulation being unstable for some reason. If you use the AmplitudeMonitorPlane objects, you will automatically get the amplitudes_time_domain.png plot for diagnostics. It should show whether the fields are exponentially growing instead of decaying.
• The simulation seems to be stable, but no valid data are plotted - the results seem rather random
  • Did you use the same polarisation (field-component) of the source and detectors, etc.? If not, you obviously get numerical noise from normalization of tiny values by other tiny values. Check the order of magnitude for the source duration and simulation. Make sure the source has broad enough spectrum to cover all frequencies of interest.
• Using AmplitudeMonitorPlane, the retrieved transmission or reflection is over unity
  • If this happens in the form of characteristic "ringing" in spectra around narrow resonances, it may often be due to spectral leakage. Prolonging the simulation time or using a lossy medium usually helps.
  • Make sure to check the time-domain exported fields if they decay in exponential manner as they should, or do something unexpected.
• Frequency-domain and time-domain results are different
  • In fact, the results were different by few percent when I made comparisons, and I do not know why.
  • Either the frequency-domain solver did not converge correctly, or the time-domain solver had to modify the material definition to make the simulation stable. In either case, read the simulation printouts what happened.

• Python's tracebacks are double printed, and their lines are randomly mixed.
  • Run the simulation in single process if you need clear debugging messages.
• Simulation gives correct results, but at the end complaints that mpirun has exited ... without calling "finalize"
  • This is harmless. I did not find any way to prevent the message in python-meep.
• Simulation writes about 'epsilon averaging' although I did not explicitly enable it.
  • This appears to be a little bug of python-meep; no matter what it writes, the averaging is probably off anyway

• scatter.py, cdh and others should output sim_param in the header (moreover CDH has weird header!!)

• move Kx, Ky out of the model parameters

• put the models into separate module

• sync harminv from its module with meep_utils, and remove from the latter

• effparam.py does not cope with "plot_freq_max=None" anymore? -- fix

• why I do not see interference of sym/asym plasmons in the example? wrong metal model!

• plot_contour to read any column from direct sim output / effparam

• [ ]

• stability of metals - try to increase 'gamma' until it goes unstable; map the parameter!

• from scipy.misc import imsave; imsave('../docs/static/tutorial-epsilon.png', -N.rot90(epsilon)) ?

• Use average_field_function instead of my own averaging!

• use synchronize_fields() instead of shifting H(t) ? - benchmark

• test averaging on SRR

• test the Fresnel inversion algorithm on dispersive dielectric slabs

• fix the stupid SWIG bug: http://sourceforge.net/donate/?user_id=246059#recognition

• resonant modes extraction via HarmInv, done in a branched file

• optimize the structure using D.E (http://inspyred.github.com) or CMA-ES

• mode separation on the user-defined ports

• add examples (tests / case study?):

  • waveguide-splitter
  • metamaterial parameters of dielectric sphere in wire mesh
  • a split-ring resonator and current-driven homogenisation
  • surface-plasmons
  • surface-plasmons on thin-metal
  • thin-gold-film-transmission
  • plasmonic resonance in gold nanoparticles
  • resistive-metal strips
  • extraordinary transmission
  • Kerr nonlinearity and self-focusing
  • scattering SNOM microscope
  • oblique-wave fabry-pérot resonances, comparison with analytic solution
  • resonances in cylinder cavity, application of harminv and comparison with analytic
  • modeling spontaneous parametric down-conversion

• check what functionality is available on Windows (could add the procedure to compile python-meep for Win)

  • probably no run_bash call will work - slice export will fail on Windows?

• currently, the materials are composed into a structure only for the permittivity (static value + Lorentzians), shall we do this also for permeability? And for nonlinear effects etc.?

• compress video with something like: ffmpeg -i input -c:v libx264 -preset veryslow -qp 0 output.mkv

• solve the following message Progress 0.90 of expected total 107 s CMD: cd 'SphereWire_comment=TiO$_2$ spheres only_resolution=5.000e-06_radius=3.000e-05'; h5tovtk 'EPS_at_t0.000e+00.h5:eps' '-t 0' -o 'EPS_at_t0.000e+00.vtk' CMD: cd 'SphereWire_comment=TiO$_2$ spheres only_resolution=5.000e-06_radius=3.000e-05'; rm 'EPS_at_t0.000e+00.h5' Traceback (most recent call last): File "../../scatter.py", line 113, in eps1=getattr(model, 'mon1eps', 1), eps2=getattr(model, 'mon2eps', 1)) ## enable monitors inside dielectrics File "/home/filip/python-meep-utils/meep_utils.py", line 902, in get_s_parameters Ex1, Hy1, Ex2, Hy2 = map(lambda x: np.append(x, np.zeros(target_len - len(Ex1))), (Ex1, Hy1, Ex2, Hy2)) File "/home/filip/python-meep-utils/meep_utils.py", line 902, in Ex1, Hy1, Ex2, Hy2 = map(lambda x: np.append(x, np.zeros(target_len - len(Ex1))), (Ex1, Hy1, Ex2, Hy2)) TypeError: 'numpy.float64' object cannot be interpreted as an index