Post-Processing

plasmonX provides a command-line tool called plasmonX_analysis for post-processing output data generated from simulations.

This tool extracts and visualizes information from the compressed .tar.gz output file.

Basic usage:

plasmonX_analysis.py -i input_file.tar.gz -w WHAT [options]

After execution, a post_process_input_file folder is created.

Required arguments

• -i or --input_file: path to the .tar.gz archive produced by plasmonX.

• -w or --what: type of analysis to perform. Valid values:

  • xyz: export atomic/tesserae positions in XYZ format

  • pqr: export atomic charges for a given frequency (available for \(\omega\text{FQ}\) and BEM)

  • field: export induced electric field (3D or 2D plots)

  • density: export induced charge density (available \(\omega\text{FQ}\) and \(\omega\text{FQ}F\mu\))

Optional arguments

Option	Description	Allowed Values	Default
-n, --num_ex_freq	Number of frequencies to process	Integer	–
-freq	Explicit list of frequencies (in eV)	Comma-separated floats	–
-min_freq	Start of frequency range (eV)	Float	–
-max_freq	End of frequency range (eV)	Float	–
-step	Frequency step (eV)	Float	–
-plane	Plane to slice data (2D plot)	xy, xz, yz	–
-n_plane	Number of planes	Integer	10
-step_plane	Distance between planes (Ang)	Float	1.0
-start	Start coordinate for slicing (Ang)	Float	0.0
-field_dir	Field direction for plotting	x, y, z, all	all
-volume	Enable volume integration	Flag	–
-nx_points	Number of grid points in X direction	Integer	200
-ny_points	Number of grid points in Y direction	Integer	200
-nz_points	Number of grid points in Z direction	Integer	200
-min_grid	Min corner of 2D/3D grid (x,y,z)	String (comma-separated)	–
-max_grid	Max corner of 2D/3D grid (x,y,z)	String (comma-separated)	–
-offset_grid	Padding around structure (Ang)	Float	10.0
-format_grid	Format of output files	cube, plt	cube
-separate_q_mu	q and mu contributions [what=density]	Flag	–
-omp	Number of OpenMP threads	Integer	Max available
-mem	Available memory (GB)	Float	Max available

Field

• -n or --num_ex_freq: Number of external frequencies to analyze. Required when extracting field or density data

• -freq or --frequencies: Manually specify a comma-separated list of frequencies (in eV)

• -min_freq, -max_freq, -step: Define a uniform frequency grid. These are used as an alternative to -freq

• -field_dir: Direction of the external electric field inducing the density or the field

2D plot

• -plane: Select the slicing plane for visualization of induced density/field. When requested a folder planes/ will be created containing .csv files, png plots, and py python scripts to produce the plots

• -n_plane: Number of parallel planes to generate

• -step_plane: Distance between planes in Angstorm

• -start: Starting coordinate for slicing the system

Grid

• -nx_points : number of points in X direction

• -ny_points : number of points in Y direction

• -nz_points : number of points in Y direction

• -offset_grid : Extends the grid around the nanostructured system (default: ±10.0 Angstrom in all directions)

• -format_grid : Defines the file format for output grid data

• -min_grid, -max_grid: User-defined grid by setting the minimum and maximum coordinates in all directions. For 2D plots, define the min. and max. coordinates for the 2 required axis in -plane

Effective Volume & Area

• -volume: Enables the calculation of effective volume and area in a thin slab of volume V and thicknes h to analyze the induced field localization. To be combined with a user-defined grid, possibly with a large number of points.

  The code performs the following integrals according to Nanolett 2015, 15, 3410 :

  \[\begin{split}V^{\text{eff}} = \int_V \frac{|\mathbf{E}_{\text{ind}}(x, y, z)|^2}{|\mathbf{E}^{\text{max}}_{\text{ind}}|^2} \, dV \\ A^{\text{eff}} = \frac{1}{h} \int_V \frac{|\mathbf{E}_{\text{ind}}(x, y, z)|^2}{|\mathbf{E}^{\text{max}}_{\text{ind}}|^2} \, dV\end{split}\]

Resource management:

• --omp: Number of OpenMP threads to use for parallelization. If not specified, uses all available threads.

• --mem: Amount of memory (in GB) available for the analysis. If not set, uses all system-available memory.

Examples

• XYZ extraction

  plasmonX_analysis.py -i results.tar.gz -w xyz
  

  This will create a results.xyz file

• Field plots on XY plane

  plasmonX_analysis.py -i results.tar.gz -w field -n 1 -freq 1.58 --plane xy --start 0.0 --step_plane 0.5 -field_dir x
  

  This will create a folder planes/xy containing 10 .csv, .png, .py for the selected planes (from 0.0 to 4.5 Angstrom)

• Extract charge densities for specific frequencies

  plasmonX_analysis.py -i results.tar.gz -w density -n 3 -freq 1.2,2.4,3.6 -nx_points 100 -ny_points 100 -nz_points
  

  This will produce six .cube files with real and imaginary charge distributions at the selected frequencies.

• Field plots on XY plane

  plasmonX_analysis.py -i results.tar.gz -w field -n 1 -freq 1.58 -volume -min_grid=-5.0,-5.0,-1.0 -max_grid=5.0,5.0,1.0
  

  This will produce a .cube file for the field calculated in the selected volume, and will calculate the effective volume and area (considering h = 2.0 Ang in the Z direction)