Molecular Foundry Photonics Toolkit

By Alexander S McLeod1, P. James Schuck1, Jeffrey B. Neaton2

1. University of California - Berkeley 2. Lawrence Berkeley National Laboratory

Simulate realistic 1, 2, or 3-dimension nano-optical systems using the FDTD method.

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Version 1.02w - published on 18 May 2015

doi:10.4231/D3959C85M cite this

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    Build novel structures From structure to simulation Visualize temporal evolution of electromagnetic fields Sample field values at different locations in space Visualize field values through time and space Compute frequency-resolved field distributions Generate movies of field distributions and easily scroll through a time or frequency range Visualize the spectral phase of electromagnetic fields Visualize using 3-D renderings in the time or frequency domains Analyze field power distributions with surface plots Compute the far-field scattering and absorption efficiency Compute frequency- and angularly-resolved radiation patterns Use realistic frequency-dependent material models



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= What is this tool? = The Molecular Foundry Photonics Toolkit is a simulation and analysis suite for nano-photonics and plasmonics. Built on the open-source finite-difference time-domain simulation software package MEEP (developed at MIT), this tool allows users to construct nano-optical systems, simulate them in action, then analyze their optical properties, all within the same easy-to-use NanoHUB graphical interface. Molecular Foundry PhotonicsTK is a MEEP/Python-based simulation and analysis suite for nano-optics research, developed jointly by the Theory Group and the Imaging/Manipulation and Nanofabrication Facilities at Lawrence Berkeley Laboratory's Molecular Foundry. = What can it do? = Molecular Foundry PhotonicsTK allows users to: * Construct complex nano-optical structures, complete with realistic frequency-dependent material properties. * Fully simulate the time-evolution of field distributions within structures using the MEEP FDTD code. * Visualize electric and magnetic fields, as well as derived quantities like near-field enhancement, charge and current densities, as well as Poynting vectors. * Post-process time-domain field data to obtain and visualize frequency-dependent field power distributions and phase. * Separately examine total, source, and scattered fields. * Compute far-field properties like scattering and absorption efficiencies, as well as angularly-resolved radiation patterns = Features: = * Several example simulation examples to get you started * Realistic frequency-dependent material models derived from literature data for noble metals, semiconductors, and other materials * Performs 1, 2, and 3-dimensional simulations at arbitrary spatio-temporal resolutions * Supports Bloch-periodic or quasi-infinite boundary conditions * Includes directed plane-wave and point/extended gaussian and continuous excitation sources * Produces MEEP input files for your simulation * Parallel execution of MEEP with multiple processors on several NCN remote computing clusters * Separately visualize the total, source, and scattered fields * Visualize field data with curves, surface plots, movies, and 3-D renderings * Automatic post-processing to obtain field spectra and far-field results * Automatic saving and loading of previously computed results * Load earlier simulation sessions to continue post-processing/analysis = How does it work? = Users are presented with four different modes of operation in this tool: Build a structure and generate input files for MEEP:: The tool takes the user's input, builds the desired structure and simulation configuration, and generates input files for MEEP. These files can be used to run the same simulation on the user's home computer/cluster using a personal installation of MEEP. Build a structure and visualize it ("dry run" the simulation):: The tool takes the user's input, builds the desired structure, and generates a 3-D visualization of the structure. This allows the user to verify they've successfully built the desired structure before proceeding with a full-fledged simulation. Build and simulate a new simulation configuration:: The tool takes the user's input describing the simulation geometry, settings, sources, and outputs, and executes a time-domain simulation. Simulations can be launched on the local NCN machines, or on a remote compute cluster for faster parallel execution on multiple processors. When the simulation is complete, the data is available for post-processing and visualization. Load and post-process/visualize completed simulations:: Previously executed simulations can be re-loaded, and their output data visualized in a variety of ways. Users can inspect slices of field data through time and space, or compute spectra of their data to analyze the frequency-response of their structures. Even compute far-field absorption/scattering efficiencies and radiation patterns! = How can I obtain this toolkit for research at my own facility? = The Molecular Foundry at LBNL is a user's facility for nano-science research. As such, the source code for the Molecular Foundry Photonics Toolkit is directly available to users of the Molecular Foundry. Please visit the Foundry's program overview page ( for further information about the user proposal process. = Features Coming Soon = * Anisotropic dielectric properties * Non-linear electric and magnetic susceptibility * User-defined material models * Automated construction of lattice objects * Photonic crystal band-structure calculations

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MEEP - The free finite-difference time-domain simulation software package (; H5Utils - Visualization utilities for HDF5 (; The Python programming language (; IPython - An interactive computing environment (; NumPy - Scientific computing for Python (; SciPy - Scientific and engineering tools for Python (; MatPlotLib - A Python plotting library (; BeautifulSoup - A flexible HTML/XML parser for Python (;


The Molecular Foundry Theory Group (; The Molecular Foundry Imaging and Manipulation Facility ( The Molecular Foundry Nanofabrication Facility (

Sponsored by

Lawrence Berkeley National Laboratory & The Molecular Foundry (


Ardavan F. Oskooi, David Roundy, Mihai Ibanescu, Peter Bermel, J. D. Joannopoulos, and Steven G. Johnson, “MEEP: A flexible free-software package for electromagnetic simulations by the FDTD method,” Computer Physics Communications 181, 687–702 (2010); V. A. Mandelshtam and H. S. Taylor, "Harmonic inversion of time signals," J. Chem. Phys. 107 (17), 6756-6769 (1997). Erratum, ibid. 109 (10), 4128 (1998).


A. McLeod, A. Weber-Bargioni, Z. Zhang, S. Dhuey, B. Harteneck, J. B. Neaton, S. Cabrini, and P. James Schuck, "Nonperturbative Visualization of Nanoscale Plasmonic Field Distributions via Photon Localization Microscopy," Phys. Rev. Lett. 106, 037402 (2011)

Cite this work

Researchers should cite this work as follows:

  • Alexander S McLeod; P. James Schuck; Jeffrey B. Neaton (2015), "Molecular Foundry Photonics Toolkit," (DOI: 10.4231/D3959C85M).

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