Initial conditions

Here is a list of valid options for the initial_cond option in the configuration file:

• gaussian - Initialize all chemical species to be a 1D, 2D, or 3D Gaussian as appropriate for the model domain. Requires the following options for initial_cond_opts:

  • center_x, center_y, center_z - the center point of the Gaussian in the x, y, and z dimensions, given in meters. If the model is 1D, center_y and center_z may be omitted; likewise center_z may be omitted if the model is 2D.

  • width_x, width_y, width_z - the width of the Gaussian (its \(\sigma\)) in meters for the x, y, and z dimensions, respectively. Like the center coordinates, the y and z may be omitted if the model doesn’t include that dimension.

  • max - the maximum concentration, in molecules per cubic centimeter.

  In 1D that means that the initial concentrations of each species, \(A\) is given by:

  \[[A](x) = m_A \exp\left(-\frac{x - \mu_x}{2\sigma_x^2}\right)\]

  where \(m_a\) is the maximum given by the max option, \(\mu_x\) is center_x and \(\sigma_x\) is width_x