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 in the particle momentum equation for the Tracer-based approach. For the Field-based approach the diffusivity is set to D0 = 0 in the advection-diffusion equation.

When using the Field-based approach, 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 and the Flow Solver tab 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 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.

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:

Select the Solver Framework, i.e., the approach that is used for simulating the adsorption reaction.

The Tracer-based approach releases clouds of molecular tracer particles for each batch. These tracer particles transport the concentration through the structure and are used to compute the adsorption reactions. This approach uses the Track Particles & Molecules command in AddiDict. When you select this option the Tracer Solver tab is activated.

The Field-based approach solves the reactive transport equation and directly yields volume fields for concentration and adsorption loading. This approach is based on the Transport Concentration Field command. When you select this option the Field Solver tab is activated.

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.