UDF †

  • UDF is a text file. One can browse and edit it using a text editor, but it.can be more easily handled with "Gourmet". See the manuals below for general information on UDF.
  • In the case of UDF used for KAPSEL, one must first choose the type of problem you want to simulate by selecting "constitutive_eq" from list below.
    • Navier_Stokes: (sedimentation, diffusion, coagulation)
    • Shear_Navier_Stokes: (rheology, chain in shear flow)
    • Electrolyte: (electrophoresis)
↑

List of variables in UDF for KAPSEL (input.udf) †

constitutive_eq: type: {Navier_Stokes, Shear_Navier_Stokes, Electrolyte}

Navier_Stokes

  • DX: Girid width (this is the unit of length)
  • RHO: Density of fluid
  • ETA: Viscosity of fluid
  • kBT: Temperature of dispersion
  • alpha_v: Scaling factor for fluctuating force (translation)
  • alpha_o: Scaling factor for fluctuating torque (rotation)

Shear_Navier_Stokes

  • DX: Girid width (this is the unit of length)
  • RHO: Density of fluid
  • ETA: Viscosity of fluid
  • kBT: Temperature of dispersion
  • alpha_v: Scaling factor for fluctuating force (translation)
  • alpha_o: Scaling factor for fluctuating torque (rotation)
  • External_field: type: {DC, AC}: Steady shear (DC) or Oscillatory shear (AC)
DC
  • shear_rate: Shear rate (DC)
AC
  • shear_rate: Max shear rate (AC)

Electrolyte

  • DX: Girid width (this is the unit of length)
  • RHO: Density of fluid
  • ETA: Viscosity of fluid
  • kBT: Temperature of dispersion
  • Dielectric_cst: Dielectric constant of fluid
  • INIT_profile: Uniform: use uniform ionic densities as initial state. Poisson_Boltzmann: use optimal ionic densities as initial state by solving Poisson-Boltzman Eq. for a given initial particle configuration in advance to start simulation.
  • Add_salt: type: salt: salt is added, saltfree: no salt is added
salt
  • Valency_positive_ion: Valency of positive ions
  • Valency_negative_ion: Valency of negative ions
  • Onsager_coeff_positive_ion: Onsager transport coefficient of positive ions
  • Onsager_coeff_negative_ion: Onsager transport coefficient of negative ions
  • Debye_length: Debye screening length This causes the corresponding salt concentration to be specified automatically.
saltfree
  • Valency_counterion: Valency of counter ions
  • Onsager_coeff_counterion: {Onsager transport coefficient of counter ions
  • Electric_field: type: ON: apply external electric field, OFF: no external electric field
    • ON: type: DC: apply steady electric field, AC: apply oscillatory electric field
    DC
    • Ex: Intensity of electric field in x-direction
    • Ey: Intensity of electric field in y-direction
    • Ez: Intensity of electric field in z-direction
    AC
    • Ex: Max intensity of electric field in x-direction
    • Ey: Max intensity of electric field in y-direction
    • Ez: Max intensity of electric field in z-direction
    • Frequency: Frequency of oscillatory electric field.

object_type: type: {spherical_particle, chain}

spherical_particle

  • Particle_spec[]
    • Particle_spec[0]: (0 means the 1st component)
      • Particle_number: Number of particles
      • MASS_RATIO: Density of particle / density of fluid
      • Surface_charge: Valency of particles (total charge carried by a single particle in unit of electron charge)

chain

  • Chain_spec[]
    • Chain_spec[0] (0 meand the 1st component)
      • Beads_number: Number of beads in a single chain
      • Chain_number: Number of chains in a simulation box
      • MASS_RATIO: Density of beads / density of fluid
      • Surface_charge: Valency of beads (total charge carried by a single bead in unit of electron charge)

A_XI: Thickness of the particle-fluid boundary

A: Radius pd particles or beads

gravity

  • G: Gravitational acceleration
  • G_direction: Select the direction in which gravity is applied from -X , -Y , -Z.

EPSILON: Energy unit of Lennard-Jones potential

LJ_powers: {12:6, 24:12, 36:18}: &color(blue){Set of power exponents of the Lennard-Jones potential};

mesh

  • NPX: Defines the size of simulation box in x-direction as Lx=2^NPX
  • NPY: Defines the size of simulation box in y-direction as Ly=2^NPY
  • NPZ: Defines the size of simulation box in z-direction as Lz=2^NPZ

time_increment: type: auto: set delta_t automatically, manual: set delta_t manually

auto

  • factor: Set delta_t = factor * min [ rho/(eta k_max^2), 1/(k_B T Gamma_a k_max^2)],

manual

  • delta_t: Set delta_t manually

switch

  • ROTATION: ON: solve rotational motion of particles properly, OFF: no rotational motion of particles
  • HYDRO_int: Set Correct (other options are obsolete)
  • Stokes: Set with advection (other options are obsolete)
  • LJ_truncate: ON: LJ with attractive part, OFF: LJ without attraction (WCA potential), NONE: no pair potential at all
  • INIT_distribution: type: uniform_random: randomly generate initial particle positions, random_walk: generate a FCC lattice configuration and give random deviations from the lattice points, FCC: place particles on a FCC lattice, BCC: place particles on a BCC lattice points, user_specify: Set initial particle positions and velocities manually
random_walk
  • iteration: Unused?
user_specify
  • Particles[]
    • Particles[0] (0 means properties of the 1st particle. If you want to inclease/decrease the number of particles, select "Edit" menu -> "Add Array Elements"/"Delete Array Elements" to change the number of "Particles[]" box. Modify also "Particle_number" in "object_type" section to be consistent.) 
      - R
  - x:  &color(blue){x-component of initial particle position};
  - y:  &color(blue){y-component of initial particle position};
  - z:  &color(blue){z-component of initial particle position};
- v
  - x:  &color(blue){x-component of initial particle velocity};
  - y:  &color(blue){y-component of initial particle velocity};
  - z:  &color(blue){z-component of initial particle velocity};
FIX_CELL
  • x: {ON, OFF} Set ON to avoid the drift of center of gravity in x-direction
  • y: {ON, OFF} Set ON to avoid the drift of center of gravity in y-direction
  • z: {ON, OFF} Set ON to avoid the drift of center of gravity in z-direction

boundary_condition: type: &color(blue){Set full_periodic (other options are obsolete)}

z_dirichlet

  • wall_velocity_x: Unused?
  • wall_velocity_y: Unused?
  • wall_velocity_z: Unused?

output

  • GTS: Number of intervals between data saving
  • Num_snap: Number of data saving. Total number of simulation step is GTS * Num_snap.
  • AVS: {ON, OFF} Set ON if AVS data is needed. Huge disk space is used if ON.
ON
  • Out_dir: Name of subdirectory in which AVS data is saved. Make subdirectories ./"Out_dir" and ./"Out_dir"/avs in advance to run KAPSEL.
  • Out_name: Set a name of AVS field data file "Out_name".fld
  • File_Type: Select a file format of AVS data from BINARY or ASCII
  • UDF: Set ON

E: Unused??

t: Present time

Particles[] There is no data in this section in input UDF. Temporal particle positions and velocities are stored here in restart and output UDF.

  • Particles[] 
    - R
  - x: 
  - y: 
  - z: 
- v
 - x: 
 - y: 
 - z:

resume

  • Calculation: {NEW, CONTINUE} NEW: start a new simulation run, CONTINUE: restart continuing simulation run from the end of the previous run.