UDF for KAPSEL (version 2.10) †
- 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)
- Shear_Navier_Stokes_Lees_Edwards: (rheology, chain in shear flow)
- Electrolyte: (electrophoresis)
List of variables in UDF for KAPSEL (input.udf) †
constitutive_eq: type: {Navier_Stokes, Shear_Navier_Stokes, Shear_Navier_Stokes_Lees_Edwards,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)
- Frequency: Alternating frequency of shear flow
Shear_Navier_Stokes_Lees_Edwards
(This type implements Lees-Edwards periodic boundary conditions for fluid fields under shear flow.)
- 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(unpopulated)
- shear_rate: Max shear rate (AC)
- Frequency: Alternating frequency of shear flow
Electrolyte
- 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)
- 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: Alternating 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 without attraction (WCA potential)
- OFF: LJ with attractive part
- NONE: no pair potential at all
- INIT_distribution: type:
- uniform_random: randomly generate initial particle positions
- random_walk: add some deviations to a perfect FCC lattice
- FCC: place particles on FCC lattice
- BCC: place particles on a BCC lattice
- user_specify: Set initial particle positions and velocities manually
- (If object_type = chain, all the above options are omitted and initial chain configurations are generated by self-avoided random walk unless user_specify is selected.)
- random_walk
- iteration: Number of trial iteration to avoid bead-overlapping in the process of random walk
- user_specify
- Particles[]
- (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: x-component of initial particle position
- y: y-component of initial particle position
- z: z-component of initial particle position
- v
- x: x-component of initial particle velocity
- y: y-component of initial particle velocity
- z: 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
- pin: type:
-
- If you want to inclease/decrease the number of pined particles, select "Edit" menu -> "Add Array Elements"/"Delete Array Elements" to change the number of "pin[]" and "pin_rot[]" box.
boundary_condition: type: 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
E: Unused
t: Present time
Particles[] There is no data in this section of input UDF. Temporal particle positions and velocities are stored here in restart and output UDF.
resume
- Calculation: {NEW, CONTINUE}
- NEW: start a new simulation run
- CONTINUE: restart continuing simulation run from the end of the previous run.