run_style nufeb command

Syntax

run_style nufeb keyword values ...

one or more keyword/value pairs may be listed

group-ID = ID of the group atoms to apply the fix to

diffdt value = time step for diffusion and chemical processes (default: 1.0e-3 s)
difftol value = stopping tolerance for diffusion and chemical processes (1.0e-6 kg/m3)
diffmax = maximum # of iterations for diffusion and chemical processes (default: -1)
pairdt = time step for physical processes (default: 1.0e-8 s)
pairtol = stopping pressure tolerance for physical processes (default: 1.0 N/m2)
pairmax = maximum # of iterations for physical processes (default: -1)
profile = file_name, print performance info to file
screen = yes or no, print additional diffusion and pressure information to screen (default: yes)
initdiff =  yes or no, solve diffusion during initialisation (default: yes)

Examples

#--- examples/biofilm-heterotroph ---#

run_style nufeb diffdt 1e-4 difftol 1e-6 pairdt 1e-2 pairtol 1 pairmax 1000 diffmax 5000

Description

Choose the style of time integrator used for a NUFEB simulation. The procedure of the integration is shown below:

Run for N biological steps and for each iteration, do:
    1. change to biological timestep
    2. solve biological processes
    3. change to physical timestep pairdt
    4. solve physical processes until reaching pairtol or pairmax
    5. change to biological timestep
    6. solve post-physical processes
    7. change to diffusion timestep diffdt
    8. solve diffusion and chemical processes until reaching difftol or diffmax
    9. change to biological timestep
    10. solve reactor processes
    11. output results

The model processes are operated sequentially and they are on different timescales. The coupling between the multiple timescales relies on the pseudo steady-state approximation and the frozen state. For example, when a threshold pressure (step 4) or a steady state substrate concentration (step 8) is reached, the system is assumed to remain unchanged (frozen state) until the next biological step.

The biological processes (step 2) update the biological attributes of the particles (mass, diameter, type, etc). The corresponding timestep and the maximum number of biological steps are defined by the LAMMPS commands timestep* and run*, respectively. Thus, the total simulation time is calculated as bio_timestep * bio_steps.

The physical processes (step 4) apply the Verlet algorithm to update the physical attributes of the particles (velocity, force, position, etc). The algorithm involves a sub-loop using the timestep of pairdt. The keywords pairtol and pairmax determine the criterion to stop the Verlet integration. pairtol defines a threshold pressure, assuming that the system reaches a mechanical relaxed state when the total pressure is below the value. pairmax defines the maximum number of physical iterations. The procedure moves to step 5 when the Verlet sub-loop reaches the specified maximum number, regardless of the current system pressure.

The post-physical processes (step 6) update particle or grid attributes that need to be considered after solving the physical processes. A typical example is fix nufeb/diffusion_coeff. The command updates diffusion coefficient at each grid based on its occupied particles. Therefore, a physically relaxed system is required in order to accurately calculate the values.

The chemical processes (step 8) are solved on a Marker-And-Cell (MAC) uniform grid (see grid style) using a diffusion solver. The chemical attributes of each grid (concentration, pH, reaction rate, etc) are updated during each diffusion iteration. The keywords difftol and diffmax determine the criterion for stopping the diffusion and all other chemical processes. pairtol defines a threshold substrate concentration used to evaluate whether the system reaches a steady state substrate concentration. diffmax is the maximum number of diffusion iteration.

The reactor processes (step 10) update the attributes of the large-scale system (reactor) to which the microscale IbM simulation box is connected (e.g, via dirichlet boundary condition). Example attributes include bulk solute concentration (nufeb/reactor/solute_balance), bulk gas concentration (nufeb/reactor/gas_balance), and boundary layer position (nufeb/boundary_layer).

The profile keyword outputs the performance of each IbM process module to a file. When the screen keyword is enabled, additional diffusion and pressure information is displayed in the terminal after each biological step. When the initdiff keyword is activated, the diffusion solver will be triggered during the simulation initialisation stage. This allows for the updating of substrate concentration before addressing the biological processes.