PNNL

Abstract

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very im-portant for better understanding the ion dynamics in instrument development. Here, we present SimELIT (Simulator of Eu-lerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of mul-tiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational me-chanics applications), with a simple web-based graphic user interface (GUI) providing a means for user interaction to define the details of the cases of interest and run simulations. We present an overview of the architecture of SimELIT (containerized as a Docker image enabling easy execution of ion simulations without manual installation of any dependencies) and demon-strate its ability to run ion trajectory simulations. The Docker container of SimELIT, precompiled dependencies such as the OpenFOAM backend containing a suite of multiphysics solvers developed for ion trajectory simulations and the frontend web-based GUI, are detailed. We show a navigation interface to edit the configuration files of a simulation, and to perform and customize ion simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrody-namic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELITe) pro-vides two numerical solvers for ion trajectory simulations – (1) a Lagrangian particle tracker in vacuum and (2) an Eulerian ion density solver in static background gas in the presence of electrodynamic fields. A future version detailed in an upcoming manuscript, will include ion trajectories in electrohydrodynamic fields. The post-processing of the simulation data generated from SimELIT can be performed using ParaView, an open-source data visualization platform. In this manuscript, we describe the software architecture of SimELIT and demonstrate the computation of effective potentials of radio-frequency voltages in a rectilinear ion trap with and without a DC bias on the trapping electrodes. Also reported is the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). The results produced from SimELIT were compared with SIMION and theoretical estimates.