Focus¶

simfs_fcs evaluates a foucs function on a stream of molecular coordinates.

Signature¶

$ simfs_fcs [list] [exi|det] [gauss|alpha|efield] < params.json > log.json

list : don’t run, only parse parameters
exi|det : choose excitation or detection mode (default: excitation)
gauss|alpha|efield : choose focus funcition (default: gauss)

Parameters¶

Mode:

excitation.json¶

Parameters of simfs_fcs exi

Object Properties:
	input (string) – Coordinate input filename output (string) – Flux density output filename power (float) – Excitation power in Watt wavelength (float) – Excitation wavelength in m focus (object) – Focus function parameters

detection.json¶

Parameters of simfs_fcs det

Object Properties:
	input (string) – Coordinate input filename output (string) – Detection efficiency output filename focus (object) – Focus function parameters

Kind:

gauss.json¶

Additional foucus parameters of simfs_fcs gauss

Object Properties:
	waist_x (float) – \(\frac{1}{e^2}\) waist in x of gauss focus. waist_y (float) – \(\frac{1}{e^2}\) waist in y of gauss focus. waist_z (float) – \(\frac{1}{e^2}\) waist in z of gauss focus.

alpha.json¶

Additional foucus parameters of simfs_fcs alpha

Object Properties:
	waist_xy (float) – \(\frac{1}{e^2}\) waist in xy of alpha focus. waist_z (float) – \(\frac{1}{e^2}\) waist in z of alpha ocus.

Example params.json¶

Gaussian excitation: simfs_fcs gauss exi < params.json

{
    "focus": {
        "waist_x": 2e-07,
        "waist_y": 2e-07,
        "waist_z": 8e-07
    },
    "input": "__coordinates__",
    "output": "__focus__",
    "power": 1e-10,
    "wavelength": 4.88e-07
}

Gaussian detection: simfs_fcs gauss det < params.json

{
    "focus": {
        "waist_x": 2e-07,
        "waist_y": 2e-07,
        "waist_z": 8e-07
    },
    "input": "__coordinates__",
    "output": "__focus__"
}

Alpha excitation: simfs_fcs alpha exi < params.json

{
    "focus": {
        "waist_xy": 2e-07,
        "waist_z": 8e-07
    },
    "input": "__coordinates__",
    "output": "__focus__",
    "power": 1e-10,
    "wavelength": 4.88e-07
}

Alpha detection: simfs_fcs alpha det < params.json

{
    "focus": {
        "waist_xy": 2e-07,
        "waist_z": 8e-07
    },
    "input": "__coordinates__",
    "output": "__focus__"
}

Notes¶

Excitation focus function evaluate a photon flux density, according to a total power level. Detection functions are normalized to values between 0 and 1.