This file Cote_et_al_2022_ReadMe.txt was updated on 2022-06-02 by Bryan M Cote
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GENERAL INFORMATION
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1. Title of Dataset:
Supporting Data for Surface Structure Dependent Circular Dichroism in Single and Double Gyroid Metamaterials
2. Author Information:
Principal Investigator Contact Information
Name: Vivian E. Ferry
Institution: University of Minnesota
Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455
Email: veferry@umn.edu
ORCID: https://orcid.org/0000-0002-9676-6056
Associate or Co-investigator Contact information
Name: Christopher J. Ellison
Institution: University of Minnesota
Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455
Email: cellison@umn.edu
ORCID: https://orcid.org/0000-0002-0393-2941
Associate or Co-investigator Contact Information
Name: Bryan M. Cote
Institution: University of Minnesota
Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455
Email: cote0058@umn.edu
Associate or Co-investigator Contact Information
Name: William R. Lenart
Institution: University of Minnesota
Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455
Email: wlenart@umn.edu
3. Date of data collection range: (YYYY-MM-DD) 2021-07-27 - 2022-03-27
4. Geographic location of data collection (where was data collected?):
Simulations were conducted on the Ferry Group Workstation, located in 421 Washington Ave SE, as well as on The Minnesota Supercomputer Institute. Both a part of the University of Minnesota, Twin-Cities Campus.
5. Information about funding sources that supported the collection of the data:
This research was supported by a grant from the National Science Foundation through MRSEC award DMR-1420013.
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SHARING/ACCESS INFORMATION
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Recommended citation for the data: William, Lenart R; Ellison, Christopher J; Ferry, Vivian E; Cote, Bryan M. (2022). Supporting data for Surface Structure Dependent Circular Dichroism in Single and Double Gyroid Metamaterials. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/fp2j-xr45.
1. Licenses/restrictions placed on the data: CC0 1.0 Universal
2. Links to publications that cite or use the data: https://doi.org/10.1002/adom.202200363
3. Links to other publicly accessible locations of the data: N/A
4. Links/relationships to ancillary data sets: N/A
5. Was data derived from another source? No
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DATA & FILE OVERVIEW
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1. File List
Files are organized by the gyroid's orientation. All 39 .mat require MATLAB to open. The data was collected using Lumerical FDTD solutions Release 2021 R2 and processed on MATLAB R2021a. The .mat files follow the same naming convention.
Example: 220109_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0_RTA.mat
Jan-09-2022 simulation date
Single gyroid
65 nm periodicity
Silver infill
100 oriented
m = +0.9 (positive enantiomer, ~20 vol% infill)
4 unit cells thick
The gyroid's top surface was terminated at tau_{100} = 0
A. Files that end in _RTA contain:
Right (RCP) and Left-handed circularly polarized (LCP) reflection (R), transmission (T), and absorption (A) data. The absorption data was also used to calculate the circular dichroism (CD) and Kuhn's dissymmetry factor (g). The datasets have dimensions [length(Wvlgth), length(tau)].
B. Files that end in _Fields contain:
E2_LCP, E2_RCP: Intensity enhancements of incident circularly polarized light in the near-field of the gyroid metamaterial (|E|^2/|E_0|^2). The datasets have dimensions [length(x), length(y), length(z), length(Wvlgth_EM)].
E2_LCP_int, E2_RCP_int: Integrated intensity enhancements down the depth of the gyroid metamaterial (E2_LCP_int(x,lambda) = int(E2_LCP(x,y,z,lambda))dA/int(1)dA). The datasets have dimensions [length(x), length(Wvlgth_EM)].
idx: Spatially resolved complex refractive index in the near-field of the gyroid metamaterial. The dataset has dimensions [length(x), length(y), length(z)].
C. File 210924_SingleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_EM_tau0pt30_Pabs.mat contains:
Pabs_LCP, Pabs_RCP: Lumerical datasets of the spatially resolved absorption in the near-field of the gyroid metamaterial.
Pabs_LCP_reshape, Pabs_RCP_reshape: Spatially resolved absorption in the near-field of the gyroid metamaterial. The datasets have dimensions [length(x), length(y), length(z)].
Pabs_LCP_int, Pabs_RCP_int: Integrated absorption down the depth of the gyroid metamaterial. The datasets have dimensions [length(x)].
Pabs_LCP_cumulative, Pabs_RCP_cumulative: Cumulative integrated absorption down the depth of the gyroid metamaterial. The datasets have dimensions [length(x)].
2. Relationship between files: Each folder contains the 3D models (.stl files) of the gyroids used in the Lumerical FDTD simulations. The simulation results were then processed and saved as .mat files.
3. Additional related data collected that was not included in the current data package: Lumerical FDTD simulation files.
4. Are there multiple versions of the dataset? N
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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data:
The FDTD simulations in this report were performed using commercial software provided by Lumerical FDTD solutions (Release: 2021 R2). The gyroid structures were added to the FDTD software by importing a gyroid 3D model as defined by Equation 4 in the main text. Coordinate rotations were applied to the gyroid model to align the desired crystallographic orientation along the +x direction prior to import. A circularly polarized light source, aligned to the +x direction, was added to the simulation by combining two linear polarized light sources with polarization and phase shifts of ±90°. The top surface of the gyroid was defined as the surface closest to this circularly polarized source. A uniform 1 nm meshing was applied over the entire gyroid metamaterial and extended a/sqrt(h^2+k^2+l^2) on either side of the gyroid. Periodic boundary conditions were used on boundaries parallel to the light propagation while absorbing PML boundaries were used parallel to the termination plane and perpendicular to light propagation. The PML boundaries consisted of 12 layers of the predefined steep angle profile within Lumerical’s software.
The absorbance of the gyroid metamaterials under each incident polarization was calculated using the gyroid’s reflectance and transmittance spectra: A=1–R-T. The optical response to unpolarized light was calculated by averaging of the left- and right-handed circularly polarized light simulation results:
<|E|^2>=(|E_{LCP}|^2+|E_{LCP}|^2)/2.
The gyroid network structures are defined using the following analytical equation for the gyroid’s surface:
sin(2*pi*x/a)cos(2*pi*y/a)+sin(2*pi*y/a)cos(2*pi*z/a)+sin(2*pi*z/a)cos(2*pi*x/a) = m
where a is the periodicity of the gyroid, which is set to 65 nm in this study, and m is a parameter such that 0<|m|<sqrt(2). The magnitude of m controls the volume fraction of the network domain. In this work, two different fill fractions are considered: |m|=0.9, which generates single gyroid domains of approximately 20 vol%, and |m|=1.2, which has a decreased fill fraction of ≈10 vol%. The sign of m is also used to determine the single gyroid network’s handedness. The modeled gyroid metamaterials are assumed to consist of Ag networks in air, with the refractive index of Ag described by a Lorentz–Drude–Debye fit to complex refractive index data from Palik. To investigate all possible surface groups along a particular crystallographic direction, a termination coordinate, τhkl, is utilized in a manner similar to Dolan et al. but expanded for use along any crystallographic direction within a cubic crystal system. The termination coordinate is defined as the distance from the crystallographic origin to the terminating plane along the direction of light propagation in units of structural periodicity, and is summarized by:
tau_{hkl} = x/a*sqrt(h^2+k^2+l^2)
where x is the distance from the plane (hkl) to the termination plane in the direction [hkl]. The termination coordinate is related to the corresponding, terminating Miller plane by dividing the orientation direction by the termination coordinate. Termination coordinates of τ=0 and 1 are identical. For example, [100] oriented gyroids with τ_{100}=0 or 1 have (100) termination planes, a [110] oriented gyroid with τ_{110}=0.5 has (220) termination planes, and a [111] oriented gyroid with τ_{111}=0.25 has (444) termination planes.
2. Methods for processing the data:
Data processing utalized combination of Lumerical's and MATLAB's built-in programs.
The gyroids' reflection and transmission were calculated using Lumerical's 'transmission' command. The spatially resolved electric field intensity enhancements were extracted from the simulations using Lumerical's 'getelectric' command. Spatially resolved absorption calculations utalized Lumerical's advanced absorption analysis group. More information about the analysis group can be found at: https://support.lumerical.com/hc/en-us/articles/360034915693-Calculating-absorbed-optical-power-Higher-accuracy. All other variables (spatial coordinates, refractive indices, frequencies, tau) were extracted from the FDTD simulation using Lumerical's 'getdata' or 'getnamed' commands. The variables were then saved to .mat files using the command 'matlabsave'.
The data was then further processed and visualized in MATLAB. The termination and spectrally resolved CD was plotted using MATLAB's 'imagesc' command. Area integrations for E2_LCP_int and E2_RCP_int were calculated using 'Integrate_E2.m' and utilized MATLAB's 'trapz' command. Pabs_LCP_int, and Pabs_RCP_int were calculated in a similar manner. The cumulative absorption was then calculated by using MATLAB's 'cumtrapz' command on the integrated absorption data. Lastly, the gyroid models with the electric field intensity enhancement cross sections (e.g. Figure 5a) were generated using 'GyroidFieldProfiles.m' which used spatially resolved refractive index data and the 'isosurface' and 'isocaps' commands, to define the gyroid volume, and the 'slice' command, to generate plot the electric field intensity enhancement cross sections.
3. Instrument- or software-specific information needed to interpret the data: MATLAB
4. Standards and calibration information, if appropriate: N/A
5. Environmental/experimental conditions: N/A
6. Describe any quality-assurance procedures performed on the data:
Convergence testing was performed to ensure accurate simulation results. These included convergence tests on Lumerical's auto-shutoff value, as well as mesh density tests. Furthermore, the broadband simulations were broken into two wavelength ranges (200-600 nm and 600 - 1500 nm) and combined in post-processing to prevent the simulated polarization state from diverging from circular polarization.
7. People involved with sample collection, processing, analysis and/or submission:
Simulations were developed, ran, and analyzed by Bryan M. Cote
The manuscript was written by Bryan M. Cote with editing assitance from Vivian E. Ferry, Christopher J. Ellison, and William R. Lenart.
The manuscript was submitted by Vivian E. Ferry.
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Directory Structure
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| Cote_et_al_2022_ReadMe.txt
| GyroidFieldProfiles.m
| Integrate_E2.m
+---100
| 100_Gyroid_m-0pt9.stl
| 100_Gyroid_m0pt9.stl
| 220107_SingleGyroid_a65_Ag_100_m-0pt9_4cells_RTA.mat
| 220107_SingleGyroid_a65_Ag_100_m0pt9_4cells_RTA.mat
| 220109_SingleGyroid_a65_Ag_100_m-0pt9_4cells_tau0pt125_RTA.mat
| 220109_SingleGyroid_a65_Ag_100_m-0pt9_4cells_tau0_RTA.mat
| 220109_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0pt125_492nm_Fields.mat
| 220109_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0pt125_RTA.mat
| 220109_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0_Fields.mat
| 220109_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0_RTA.mat
| 220327_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0pt125_Additional_Fields.mat
| 220327_SingleGyroid_a65_Ag_100_m0pt9_4cells_tau0_Additional_Fields.mat
|
+---110
| 110_Gyroid_m-0pt9.stl
| 110_Gyroid_m0pt9.stl
| 210727_SingleGyroid_a65_Ag_110_m-0pt9_4sqrt2cells_tau0pt3_Fields.mat
| 210727_SingleGyroid_a65_Ag_110_m-0pt9_4sqrt2cells_tau0pt8_Fields.mat
| 210727_SingleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_tau0pt3_Fields.mat
| 210727_SingleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_tau0pt8_Fields.mat
| 210910_SingleGyroid_a65_Ag_110_m0pt9_0pt25sqrt2cells_tau0pt30_Fields.mat
| 210924_SingleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_EM_tau0pt30_Pabs.mat
| 211008_SingleGyroid_a65_Ag_110_m0pt9_VaryThickness_tau0pt30_RTA.mat
| 211217_DoubleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_RTA.mat
| 211217_SingleGyroid_a65_Ag_110_m-0pt9_4sqrt2cells_RTA.mat
| 211217_SingleGyroid_a65_Ag_110_m0pt9_4sqrt2cells_RTA.mat
| 220105_SingleGyroid_a65_Ag_110_m0pt9_0pt25sqrt2cells_tau0pt30_RTA.mat
|
+---111
| 111_Gyroid_m-1pt2.stl
| 111_Gyroid_m0pt9.stl
| 111_Gyroid_m1pt2.stl
| 211217_Gyroid_a65_Ag_111_m-1pt2_2sqrt3cells_RTA.mat
| 211217_Gyroid_a65_Ag_111_m0pt9_2sqrt3cells_RTA.mat
| 211217_Gyroid_a65_Ag_111_m1pt2_2sqrt3cells_RTA.mat
| 211230_Gyroid_a65_Ag_111_m1pt2_2sqrt3cells_tau0pt125_737nm_Fields.mat
| 211230_Gyroid_a65_Ag_111_m1pt2_2sqrt3cells_tau0pt25_864nm_Fields.mat
| 211230_Gyroid_a65_Ag_111_m1pt2_2sqrt3cells_tau0pt375_723nm_Fields.mat
| 211230_Gyroid_a65_Ag_111_m1pt2_2sqrt3cells_tau0_850nm_Fields.mat
| 220118_Gyroid_a65_Ag_111_m0pt9_2sqrt3cells_tau0pt59_735nm_Fields.mat
| 220118_Gyroid_a65_Ag_111_m0pt9_2sqrt3cells_tau0pt67_729nm_Fields.mat
|
+---211
| 211217_Gyroid_a65_Ag_211_m-0pt9_2sqrt6cells_RTA.mat
| 211217_Gyroid_a65_Ag_211_m0pt9_2sqrt6cells_RTA.mat
| 211230_Gyroid_a65_Ag_211_m0pt9_2sqrt6cells_tau0pt78_700nm_Fields.mat
| 211_Gyroid_m-0pt9.stl
| 211_Gyroid_m0pt9.stl
|
\---Defects
110_Gyroid_m0pt9.stl
220105_Gyroid_a65_Ag_110_m0pt9_4sqrt2x1xsqrt2cells_1-10StrutRemoved_RTA.mat
220105_Gyroid_a65_Ag_110_m0pt9_4sqrt2x1xsqrt2cells_110StrutRemoved_RTA.mat
220105_Gyroid_a65_Ag_110_m0pt9_4sqrt2x1xsqrt2cells_All110StrutRemoved_RTA.mat
220105_Gyroid_a65_Ag_110_m0pt9_4sqrt2x3x3sqrt2cells_1-10StrutRemoved_RTA.mat
220126_Gyroid_a65_Ag_110_m0pt9_4sqrt2x2x2sqrt2cells_1nmRMS_5nmSigma_RTA.mat
220126_Gyroid_a65_Ag_110_m0pt9_4sqrt2x2x2sqrt2cells_5nmRMS_5nmSigma_RTA.mat