parameters.txt

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# DICE Parameter Configuration - compatible with DICE Version 1.X
# Last updated: Dec 4, 2023
# GitHub Repository: https://github.com/thiebes/DICE

# Instructions:
# - Modify values in the format: 'setting name': value,
# - Include the comma at the end of each line.
# - Comments (text following #) are ignored by the program.
# - Uncomment a setting by removing the # at the beginning.
# - Only one option per choice should be active (uncommented).
# - Save changes before running the program.
# - For detailed setting explanations, see the README at the GitHub link above.
##################################################################

{
    ### Filename ###
    'filename slug': 'example',  # Prefix for exported data filenames.

    ### Number of runs ###
    'number of runs': 1000,       # How many iterations of the simulation to run.

    ### Units ###
    'length unit': 'micrometer',  # Options: 'micrometer', 'angstrom', etc.
    'time unit': 'nanosecond',    # Options: 'nanosecond', 'picosecond', etc.

    ### Nominal diffusion and lifetime parameters ###
    # Provide either diffusion length OR both diffusion coefficient and lifetime:
    'nominal diffusion length': 0.1,
    # 'nominal diffusion coefficient': 0.01, 
    # 'nominal lifetime (tau)': 1, 

    ### Initial profile parameters ###
    # Initial profile width (choose one):
    'FWHM_0': 1,                  # Full Width at Half Maximum.
    # 'sigma_0': 0.4032,           # Standard deviation.

    # Initial amplitude and mean:
    'amplitude_0': 1,             # Initial amplitude.
    'mean_0': 0,                  # Initial mean.

    ### Noise parameter ###
    # Choose one:
    'noise value': 0.02,           # Standard deviation of noise.
    # 'estimate noise from data': 'example_profile.csv'

    ### Spatial axis parameters ###
    'spatial width': 5,           # Spatial width across entire x-axis of profiles (units parameterized above).
    'pixel width': 100,           # Pixel width across entire x-axis of profiles.

    ### Time axis parameters ###
    # Choose one:
    'time range': [0, 1, 10],     # Format: [start, stop, steps].
    # 'time series': [1,3,5,10,15,25,60,100],

    ### Diffusion coefficient proximity threshold ###
    'proximity level': 0.5,       # Threshold for diffusion estimate analysis.

    ### Plot image parameters ###
    'image type': 'png',         # Options: 'jpg', 'png', 'svg', 'tif'.
    'image width': 8.5,          # Width in cm. 
    'image height': 5,           # Height in cm. 
    'image dpi': 300,            # Resolution in DPI. 
    'image font size': 8,        # Font size in points.
    'image tick length': 6,      # Axis tick length in points.
    'image tick width': 2,       # Axis tick width in points.
    'image numbins': 35,         # Number of histogram bins.
    'image x_lim': None,         # X-axis limits. Default if None: 3 sigma.

    ### Performance settings ###
    'retain profile data': False, # Retaining profile data can be memory-intensive.
    'multiprocessing': True,      # Enable/disable parallel processing.

}