PyMeepPlasmonics

Free and open-source code package designed to perform PyMEEP FDTD simulations applied to Plasmonics.

About

PyMeepPlasmonics is a freely accesible FDTD-MEEP implementation that contains code modules and routine scripts that allow for serial and parallel Plasmonics simulations to be run both in personal computers and clusters.

PyMeepPlasmonics allows to perform Finite-Differences Time-Domain (FDTD) simulations, where a certain domain is discretized both in space and time in order to simulate the electromagnetic response in time by advancing step-by-step the electromagnetic field evaluated in each and every position or node. It uses a free and open-source FDTD implementation called MIT Electromagnetic Propagation (MEEP). MEEP has been cited in many scientific publications and it holds a Python library that offers great flexibility and versatibility while allowing users to create customized scripts and routines.

PyMeepPlasmonics aims to apply PyMEEP FDTD simulations to the nanoscale and it is particularly focused in studying the optical properties of metallic nanoparticles (NPs). It has four fully equiped routines that configure and perform simulations to extract, analyse and save data both in time-domain (direct electromagnetic field calculations) and in frequency domain (indirect scattering cross section calculations).

In order to build these routines, several code modules are used, each and every one of them highly documented. By calling functions from these modules and combining them with other famous scientific packages such as numpy or matplotlib, PyMeepPlasmonics should be able to present you with a whole spectrum of possibilities that will help you build your own Plasmonics or Nanophysics simulations.

Installation

Ubuntu

A series of simple instructions can be followed to install the required packages in Ubuntu 20.04 LTS or any newer Ubuntu OS.

The steps are slightly different whether you intend to run MEEP simulations using serial execution or parallel execution. If you have not decided yet, by following the instructions below you can actually have two Anaconda environments installed at the same time, one intended for serial execution and the other one for parallel execution.

Serial execution

First, install the Miniconda distribution.
You might need to activate Anaconda from an Ubuntu terminal by using the command conda init.
You can then create a Conda environment for MEEP using the command conda create -n mp -c conda-forge pymeep.
To start using the environment you will need to activate it by using conda activate mp.
Additional packages you might want to install using conda install or pip install include h5py for HDF files management, resource for monitoring resources such as RAM consumption and imageio for making gifs.
It might also come in handy installing Spyder for interactive serial execution and it is highly recommended to install click for console serial execution.

Parallel execution

First, install the Miniconda distribution.
You might need to activate Anaconda from an Ubuntu terminal by using the command conda init.
You can then create a Conda environment for MEEP using the command conda create -n pmp -c conda-forge pymeep=*=mpi_mpich_*.
To start using the environment you will need to activate it by using conda activate pmp.
Additional packages you might want to install using conda install or pip install include h5py for HDF files management, resource for monitoring resources such as RAM consumption and imageio for making gifs.
It is highly recommended to install click for parallel serial execution.

Windows

As required by MEEP, an Ubuntu OS will be necessary, so if you wish to work in Windows you will need a virtual machine or similar. Up to date, only Ubuntu has been used to execute PyMeepPlasmonics simulations, so saddly you will need to find out how to install it yourself.

Usage

First, you need to configure your system's setup. The suggested way to do this is to use the automatic setup provided by PyMeepPlasmonics. To do this, you will need to follow these steps:

Open a terminal and go to your repository's directory by running cd my\route\to\PyMeepPlasmonics.
Activate the Anaconda environment by using a line such as conda activate mp (serial) or conda activate pmp (parallel).
Call the module v_save as an executable file by using the command python v_save.py.
Follow the instructions in the screen:
- First, indicate a nickname for your current PC and system.
- Then, make sure the detected route to the repository is correct.
- Finally, choose a path to a folder where the results will be saved.
A configuration file named "SystemDirectories.txt" will have been created at your repository's folder and you will be ready to go.

Once you have finished, you will be able to open, inspect and execute those scripts that are already created to perform FDTD-MEEP Plasmonics simulations. Hopefully they will provide you with the results you are looking for. If not, they will surely provide you with enough examples to build your own simulation :)

Licence

Free open-source code developed as part of a Master Thesis Project in Physics.

FDTD Applications To The Nanoscale: Photonics & Plasmonics Through MEEP

Development by Valeria R. Pais, DF, FCEyN, UBA

Direction by Prof. Dr. Fernando D. Stefani, Applied Nanophysics Group, CIBION, CONICET

0xinfty / pymeepplasmonics Goto Github PK