reactiveQITSim

Ion trajectory simulation in an ideal Quadrupole Ion Trap (QIT) considering chemical reactions of the simulated ions.

The field definition and basic theory is the same as in QITSim. In addition to the trajectory integration considering space charge and hard sphere background gas collisions, chemical reactions are simulated with RS. Since the simulation is coupled to RS, most of the particle parameters are defined in the RS reaction system file referenced in reaction_configuration.

The application allows different reaction types (static, temperature dependent, etc.) in the chemical kinetics simulation. Particularly, collision based reactions can be simulated: For this reaction type, possible reaction events takes place, when ions collide with neutral background gas particles in the hard sphere collision simulation.

Simulation configuration description

sim_time_stepsinteger

Number of simulation time steps

trajectory_write_intervalinteger

Interval, in time steps, between writes to the trajectory result file.

concentrations_write_intervalinteger

Interval, in time steps, between the writes of the species concentration.

fft_write_intervalinteger

Interval, in time steps, between samples for the FFT result file, which records a simulated transient for Fourier transformation.

fft_modeKeyword:[off, unresolved, mass_resolved]

Selects the mode in which the FFT result file is written. The FFT result records the average velocity of the simulated particle ensemble in the z direction as an approximate induced mirror charge on the cap electrodes.

off: FFT analysis is switched off, no FFT file is written
unresolved: The FFT transient signal is calculated from the whole simulated particle ensemble. This is the signal which would be detectable in a physical experiment.
mass_resolved: The FFT transient signal is recorded for every ionic species, with distinct molecular mass, separately. This allows to see individual transients for the species.

dtfloat

Time step length in seconds

n_ionsVector of integers

Number of particles of the discrete chemical substances defined in the reaction configuration. The order in this vector is the same as the order of discrete substances defined in the reaction configuration.

Example: If the [SUBSTANCES] block in the reaction configuration is

[SUBSTANCES]
Cl_1 discrete 19 1 3.57e-4  4.00000000e-10
Cl_2 discrete 37 1 2.76e-4  5.17391304e-10
Cl_3 discrete 55 1 2.35e-4  6.07659574e-10

the n_ions vector [100, 50, 10] will initalize the simulation with 100 particles of Cl_1, 50 of Cl_2 and 10 of Cl_3.

start_width_mfloat

Ions are initialized randomly within a cubic box around the trap center. This is the edge length of this box in m.

background_temperature_Kfloat

Temperature of the background gas in K.

space_charge_factorfloat

Multiplication factor for particle-particle interaction (space charge).

max_ion_radiusfloat

Maximum radius a simulated particle can have before it is terminated in the simulation, in m.

Chemistry and background gas configuration

reaction_configurationfile path: Path to a RS configuration file, defining the chemical reaction system for the simulation.

The interaction between the simulated ions and the neutral background gas is simulated with hard sphere collisions. The background gas can be a mixture of individual components.

collision_gas_namesVector of strings: Names of the background gas components.

Note

Due to the coupling to the chemical reaction model, the background gas componentes have to exist as isotropic components in the RS configuration.
collision_gas_masses_amuVector of float: Molecular masses of the particles of the background gas mixture components in amu.
collision_gas_diameters_angstromVector of float: Effective collision diameters of the particles of the background gas components in Angström.
partial_pressures_Pavector of float: Partial pressures of the individual components of the background gas mixture in Pascal.

Warning

There is no check if the reaction configuration and the parameters specified here are physically and chemically consistent. One has to check if the speciefied system is actually possible.

Trap geometry configuration

geometry_modeKeyword:[default, scaled, variable]

Selects trap geometry mode. The trap geometry defines the electric field in the trap and is defined by the ring electrode radius r_0 and the cap distance z_0.

defaultDefault trap with \(r_0= 10 \text{mm}\)

The default geometry is a typical small commerical QIT with \(r_0 = 10 \text{mm}\) and \(z_0 = 7 \text{mm}\) which is approximately (within 2%) fulfilling the ideal relationship \(r_0^2 = 2 z_0^2\).

scaledScaled default trap

The default trap geometry scaled by a factor geometry_scale:

geometry_scalefloat: Geometric scaling factor for a scaled default trap.

variableVariable geometry

Fully variable geometry, \(r_0\) and \(z_0\) can be configured freely:

r_0: float: \(r_0\) in meter.
z_0: float: \(z_0\) in meter.

Trap field configuration

f_rffloat: Frequency of the RF trapping field in Hz.

Trap field RF voltage

The RF trap field voltage can be static or can be ramped during the simulation.

Static field mode:

rf_Vfloat: Ground to peak trap field amplitude in V.

Ramped field mode:

rf_ramp_start_Vfloat: Ground to peak field amplitude at the start of the amplitude ramp, in V.
rf_ramp_stop_Vfloat: Final ground to peak field amplitude at the end of the amplitude ramp, in V.
rf_ramp_waiting_timestepsinteger: Number of time steps to wait on rf_ramp_start_V before starting the amplitude ramp.

Ion excitation field

The trapped ions can be excited by an bipolar field applied to the cap electrodes.

excite_mode : Keyword:[off, rect_pulse, waveform, continuous_sine]

Selects the ion excitation mode.

offNo excitation
No bipolar field is applied at all.

rect_pulseRectangular excitation pulse
Applies a rectangular excitation pulse to the cap electrodes at the beginning of the simulation. The amplitude of the pulse is defined by excite_potential, the duration is defined by

excite_pulse_lengthfloat
Length of the excitation pulse in seconds.

waveformExcitation with sampled waveform
Applies an excitation with a given sampled waveform read from a waveform file.

excite_waveform_csv_fileFile path
File path to a file with a sampled excitation waveform.

The waveform file contains one sample per time step and is not looped, it is replayed only once at the begin of the simulation run. The sampled waveform is assumed to be normalized, the waveform data is multiplied with “excite_pulse_potential” to calculate the applied excitation potential.

This file path is relative to the simulation run configuration file.

continuous_sineContinuous sinusoidal excitation
Applies a continuous sinusoidal excitation on the cap electrodes with a frequency which is a fraction of the main RF frequency. The ground to peak amplitude of the applied excitation field is defined by excite_potential.

The frequency is defined by

excite_divisorfloat
Frequency divisor. The excitation field frequency is the main trap field RF frequency devided by this devisor.

excite_potentialfloat: Excitation potential / excitation scaling multiplicator. See excite_mode for details.