RMPCDMD
Functions/Subroutines
chemotactic_cell.f90 File Reference

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Functions/Subroutines

program chemotactic_cell
 Model a chemotactic experiment in a microfluidic channel. More...
 
subroutine flag_particles
 
subroutine change_species
 
subroutine concentration_field_cylindrical
 
subroutine buffer_particles (particles, edges)
 
subroutine compute_rho_xy
 

Function/Subroutine Documentation

subroutine chemotactic_cell::buffer_particles ( type(particle_system_t), intent(inout)  particles,
double precision, dimension(3), intent(in)  edges 
)

Definition at line 813 of file chemotactic_cell.f90.

subroutine chemotactic_cell::change_species ( )

Definition at line 699 of file chemotactic_cell.f90.

program chemotactic_cell ( )

Model a chemotactic experiment in a microfluidic channel.

In this simulation, an inlet (x=0) is fed with A and S fluid species in the lower and upper halves in the y direction, respectively. A constant accerelation is applied in the x direction and walls in the z direction confine the flow, leading to a Poiseuille velocity profile.

The colloid is a passive sphere, an active sphere or a dimer nanomotor.

Parameters
gmagnitude of acceleration
buffer_lengthlength of the inlet buffer
max_speedmaximum velocity of profile to initialize the velocities
probabilityprobability of reaction
alphaangle of collision
store_rho_xystore the xy density of solvent particles on a grid
store_rho_xy_zbounds in z for the slice of rho_xy to store (2 elements)
dimersimulate a dimer nanomotor (boolean, else it is a single sphere)
N_typeassign N species to the single sphere (boolean, else it is a C sphere)
Llength of simulation box in the 3 dimensions
rhofluid number density
TTemperature. Used for setting initial velocities and for wall thermostatting.
dlength of rigid link
N_in_frontplace N sphere in front (higher x), for the dimer nanomotor
tauMPCD collision time
N_MDnumber MD steps occuring in tau
N_loopnumber of MPCD timesteps
colloid_samplinginterval (in MD steps) of sampling the colloid position and velocity
steps_fixednumber of steps during which the colloid is fixed (only when buffer_length>0)
equilibration_loopsnumber of MPCD steps for equilibration (only when buffer_length=0)
sigma_Cradius of C sphere
sigma_Nradius of N sphere
track_y_shiftshift of the track in the y direction with respect to Ly/2
epsilon_Cinteraction parameter of C sphere with both solvent species (2 elements)
epsilon_Ninteraction parameter of N sphere with both solvent species (2 elements)

Definition at line 40 of file chemotactic_cell.f90.

subroutine chemotactic_cell::compute_rho_xy ( )

Definition at line 843 of file chemotactic_cell.f90.

subroutine chemotactic_cell::concentration_field_cylindrical ( )

Definition at line 751 of file chemotactic_cell.f90.

subroutine chemotactic_cell::flag_particles ( )

Definition at line 678 of file chemotactic_cell.f90.