Select one or both of the Transport Mechanisms by checking the Advection and/or Diffusion boxes in the upper left part of the Experiment tab.

Check Simulate Diffusion to activate the computation of transport by diffusion. If the button is unchecked, the diffusivity is set to D0 = 0 in the advection-diffusion equation.

Check Simulate Advection to activate the computation of advective transport due to the fluid flow. If unchecked, the velocity of the fluid is zero, i.e. in the advection-diffusion equation, and therefore, the concentration field is transported by diffusion only. In this case, the Flow Boundary Conditions, the Flow Solver tab, and the Inflow Concentration are set inactive.

In the Simulated Time panel, the physical End Time of the simulation can be specified. The initial time is always zero. By clicking the Approximate End Time button, the End Time is automatically determined such that, for the specified average fluid velocity (defined in the Flow Boundary Conditions panel by Mean Velocity or by Flow Rate), most of the solute passes through the entire structure and a complete breakthrough curve is computed. When it is unclear how to choose the End Time, it is highly recommended that the Approximate End Time is used before starting the simulation. The approximation works best for high Péclet numbers, i.e., when advection dominates the transport.

The simulation time can be divided into intervals (so-called "time batches"), after which the concentration field and other information is written to disk. Define the Number of Batches. Depending on which time period should be more finely resolved, one of the following options can be chosen:

• Logarithmic: Time batches are large close to zero and small close to the end time.
• Linear: All time batches have the same size.
• Exponential: Time batch sizes are small close to zero and large close to the end time. This option is useful for scenarios that approach a stationary state.

In this panel, three Dimensionless Numbers are automatically estimated based on the entered parameter values, provided a structure is loaded. They give you an idea of how strongly advection and diffusion contribute to transport before the simulation is started. After the simulation, more precise values are listed in the report.

The Courant number quantifies the extent to which particles, molecules, or concentration fields are transported through the structure by advection during the simulation. For instance, if , then the solute (particles, molecules, or the concentration field) is advectively transported by the flowing solvent across half of the domain. The Courant number is defined as:

where is the characteristic velocity estimated from the flow boundary conditions, is the simulation time (which equals the End Time, given that the initial time is zero), and is the length of the structure in the through direction.

In contrast, the Fourier number quantifies the extent to which the solute (particles, molecules, or the concentration field) is transported through the structure by diffusion during the simulation. The Fourier number is defined as:

where is the characteristic diffusivity, taken as the maximum effective diffusivity across all existing materials.

Finally, the Péclet number is the ratio of advective transport to diffusive transport. A Péclet number of infinity implies purely advective transport, whereas a value equal to zero corresponds to purely diffusive transport. The Péclet number is defined as:

In the Transport Initial and Boundary Conditions panel, the initial concentration distribution in the structure and the Inflow Concentration can be defined. Inflow Concentration is only available if Simulate Advection is checked as otherwise the inflow boundary is not available.

When the check box next to Initial Concentration Field .hht File is checked, a concentration field can be loaded by clicking Browse. Through this option, an initial distribution of the solute in the structure can be defined. For each time batch, AddiDict automatically generates a *.hht file, so the output of a previous transport simulation can easily serve as the input for subsequent runs. Alternatively, *.hht files can be manipulated with Python scripting.

Under the Inflow Concentration, a concentration value that represents the amount of solute carried into the structure by the inflowing solvent fluid can be set. Currently, the distribution of one solute species can be simulated in a Transport Concentration Field simulation at a time.

In the Flow Boundary Conditions panel, either the Pressure Drop, the mean flow Velocity, or the Flow Rate can be defined. Note that this part of the dialog is accessible only if Simulate Advection is selected.

From the Flow PDE menu, you can specify the equations to be solved for computing the fluid flow field. The flow field is required to simulate the particle movements and trajectories or transport of the concentration field. (Navier-)Stokes equations describe fluid flow in structures containing only solid materials and pores. (Navier-)Stokes-Brinkman equations describe the flow through structures containing porous materials, solids, and pores. Use the Stokes equation when fluid velocities are slow or the viscosities are high, i.e. at low Reynolds numbers. The Navier–Stokes equation should be used for high fluid velocities when inertial effects cannot be neglected.

The used flow boundary conditions in X and Y direction are reported. For the Track Particles & Molecules command the boundary conditions in X and Y direction are set automatically to fit to the chosen boundary conditions for the particle movement:

• Reflective particle behavior leads to Symmetric flow boundary conditions.
• Periodic particle movement requires Periodic flow boundary conditions.

For the Transport Concentration Field and Adsorption commands the boundary conditions in X and Y direction are fixed to Symmetric.

The boundary condition in Z direction, can be Periodic, Symmetric, or VinPout. Please refer to the FlowDict user guide for more details. For the Track Particles & Molecules command, using the Stokes(-Brinkman) equation only allows for using Periodic or Symmetric boundary conditions, while the Navier-Stokes(-Brinkman) equation uses the VinPout boundary condition

Additionally, the Slip Length can be defined in the Flow Boundary Conditions panel. The Slip Length allows including sliding effects in the simulation. The default Slip Length of zero corresponds to a flow velocity of zero along the solid surface. A non-zero Slip Length simulates the sliding of the fluid along the structure’s solid parts, increasing the fluid mean flux and thus, the permeability. This option might be used when it is realistic for a given physical material, e.g., for gases when the mean free path is comparable to the pore size. The same slip length must be set for all materials in the structure. Find more details on the Slip Length here.

For the No-Slip boundary condition two additional options are available:

• Use Second Order No-Slip (default): This option sets the tangential velocity to zero at the center of the voxel surfaces and use a second order approximation of the velocity field.
• Use Sharp Corner: This option sets the tangential velocity to zero at the voxel corners.

Find more details on these settings in the FlowDict user guide.