quadrupoleCollisionCellSim

Simulates a quadrupolar collision cell with hard sphere collisions between ions and background gas, space charge and variable electrode geometry given by SIMION potential arrays. The ions are accelerated into the collision cell which is filled with a collision gas. The ions are confined radially in a quadrupolar RF field.

Note

• The time step length is not adapted to the gas dynamic parameters of the hard sphere model model. For a valid modeling, the time step length should be significantly shorter than the mean time between ion-neutral collisions.

Simulation configuration description

sim_time_stepsion_start_geometry

Number of simulation time steps

record_modestring

Particle data record mode: Defines if a simple or an extended set of particle attributes is recorded in the trajectory files.

Valid modes are:

• full mode records

  • velocity

  • electric field acting on the particles and

  • space charge force acting on the particles

• simple records only the velocity

The recorded particle attributes are recorded as separated (\(x,y,z\)) components.

dtfloat

Time step length in seconds

trajectory_write_intervalinteger

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

space_charge_factorfloat

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

frequency_rffloat

Frequency of the RF trapping field in Hz.

V_rffloat

RF amplitude in V.

collision_gas_mass_amufloat

Molecular mass of the particles of the background gas in amu.

collision_gas_diameter_angstromfloat

Effective collision diameter of the particles of the background gas in angström.

background_gas_temperature_Kfloat

Isotropic temperature of the background gas in K.

background_gas_pressure_Pafloat

Pressure of the background / collision gas in Pa.

termination_modestring

Particle termination mode: Defines if simulated particles should be terminated or restarted when leaving the simulation domain or hitting an electrode.

Valid modes are:

• terminate Particles are terminated and not restarted

• restart Particles are restarted in their start zone

Note

Currently restart can not be used with an particle cloud start file, only with an particle start zone definition.

simulation_domain_boundariesvector of vector of floats

Defines the outer boundaries of the simulation domain around the coordinate system origin, where ions are terminated. Is defined as vector of three two component vectors, defining the minimum and maximum in the spatial dimensions:

[[x low, x high], [y low, y high], [z low, z high]]

Potential array / electric field configuration

The electrode geometry and the resulting electric potential is defined by SIMION potential arrays. Every potential array contains the potential distribution resulting from an individual electrode on a normalized potential and every other electrode on ground. The total potential is calculated by a linear combination of the individual normalized potentials.

Warning

The potential arrays are assumed to be generated with the fast adjustment feature of SIMION with the same physical extent, resolution and coordinate system origin.

potential_arraysVector of files paths

Paths to a set of potential potential arrays defining the geometry and the electric fields.

potential_array_scalefloat

Geometric scaling factor for the potential arrays.

dc_potentialsVector of float

Invariant (DC) potentials on the electrodes defined by the potential arrays in potential_arrays in V.

rf_potential_factorsVector of float

Factors defining the applied RF amplitude on the electrodes defined by the potential arrays in potential_arrays.

The applied voltage on the individual electrode is

\[U = U_{\text{DC}} + \cos(\omega \cdot t) \cdot V_{\text{RF}} \cdot F_{\text{RF}}\]

with

• \(t\) the current time in the simulation

• \(V_{\text{RF}}\) given by V_rf

• the angular frequency \(\omega\), given by \(2\pi\cdot\) frequency_rf

• \(F_{\text{RF}}\) given by rf_potential_factors.

Ion / simulated particle configuration

The particles to simulate can be defined in the simulation configuration file or a predefined particle ensemble can be used which is given as ion cloud file in CSV format.

Ion Cloud File

A predefined ion configuration can be specified by

ion_cloud_init_filefile path

Path to an ion cloud initialization / definition file

Ion definition in simulation configuration file

If no ion cloud file is used, the following configuration parameters define the ion ensemble to simulate:

n_ionsVector of integers

Number of ions of the ionic species defined by the the masses defined in ion_masses.

ion_massesVector of float

Ion masses in amu.

ion_chargesVector of float

Ion charges in elementary charges.

ion_collision_gas_diameters_angstromVector of float

Effective hard sphere collision diameters of the ionic species in angström.

ion_time_of_birth_range_sfloat

Time range in which ions are generated, in seconds. The specified number of ions are generated uniformly in this time range.

ion_direction_vectorVector of three floats

Initial direction of motion of the ions. This vector is only a direction vector, the initial velocity of the defined ions is set by ion_kinetic_energy_eV.

ion_kinetic_energy_eVfloat

Start energy of the ions in electronvolts, the initial ion velocity is in the direction of ion_direction_vector.

Ion start configuration

The initial positions of the simulated ions can be a cubic box with faces parallel to the spatial axes or a rotatable and translatable cylinder. The position of the ion start zone is defined by ion_start_base_position_m. This partameter defines the center of a box start zone or the position of the center of the bottom face of a cylinder start zone.

ion_start_geometryKeyword:[box, cylinder]

Sets the ion start geometry.

boxIon start zone is a box

The ion start zone is a cubic box with faces parallel to the spatial axes, randomly filled with particles. It is defined by

ion_start_box_size_m: Vector of three floats

Size of the box in x, y, z direction

ion_start_base_position_m: Vector of three floats

Position of the box center

cylinderIon start zone is a cylinder

The ion start zone is a rotatable and translatable cylinder. The cylinder is defined by

ion_start_radius_m: float

Radius of the cylinder in m.

ion_start_length_mfloat

Distance from bottom face of the cylinder to the top face of the cylinder (cylinder length).

ion_start_cylinder_normal_vector: Vector of three floats

Normal vector of the bottom face of the cylinder, defining the rotation of the cylinder. The normal vector is also the directon of the axis of rotational symmetry of the cylinder (e.g. [1,0,0] means the cylinder axis is parallel to the x-axis).

ion_start_base_position_m: Vector of three floats

Position of the center of the bottom face of the cylinder