AFMMeasure

The AFMMeasure step simulates an Atomic Force Microscopy (AFM) experiment, recording force-distance curves and other relevant data.

The output file format depends on the mode parameter:

Standard mode:

#Step                    X                    F
[step number]     [tip height]     [tip deflection force]

Where:

• Step is the simulation step number

• X is the tip height (tip position minus tip radius)

• F is the tip deflection force

Verbose mode:

#Step        ChipPos        TipPos    tipDeflection    tipForce    sampleForce    tipDeflectionForce
[step]       [chip z]       [tip z]    [deflection]    [tip Fz]    [sample Fz]    [deflection F]

Where:

• Step is the simulation step number

• ChipPos is the z-position of the AFM chip

• TipPos is the z-position of the AFM tip

• tipDeflection is the deflection of the tip from the chip position

• tipForce is the z-component of the force on the tip

• sampleForce is the z-component of the force on the sample

• tipDeflectionForce is the force due to tip deflection

All values are written in scientific notation with 24 character width for alignment.

---

• type: ExperimentMeasures, AFMMeasure

• parameters:

  • outputFilePath: string: Path to the output file

  • mode: string: Output mode, either “Verbose” or “Standard” (default: “Standard”)

  • tipType: string: Type name for AFM tip particles (default: “TIP”)

Example:

"afmMeasure":{
  "type":["ExperimentMeasures","AFMMeasure"],
  "parameters":{
    "intervalStep": 10000,
    "outputFilePath": "afm_data.dat",
    "mode": "Verbose",
    "tipType": "TIP"
  }
}

Note

This step requires an AFM interactor to be present in the simulation.

Tip

The “Verbose” mode provides detailed output including chip position, tip position, and forces, while “Standard” mode gives a more concise force-distance output.