- The added line is THIS COLOR.
- The deleted line is THIS COLOR.
* UDF for KAPSEL (version 3.0) [#sbf148c5]
- 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.
-- English: &ref(Tutorial/udf_spec_eng.pdf);
-- Japanese: &ref(Tutorial/UDF_Spec_jpn.pdf);
- 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: (dynamics in shear flow, rheology)
-- Shear_Navier_Stokes_Lees_Edwards: (dynamics in shear flow, rheology)
-- Electrolyte: (electrophoresis)
- Older versions of UDF(v2.0,v2.1) must be converted to UDF(v3.0). Use &ref(convert.py); to be consistent with KAPSEL(v3.0). This script needs &ref(input_3.00.udf); and &ref(define_3.00.udf); additionally to old input_2.00.udf to be converted and define_2.00.udf used in it. In the following example, input_2.00.udf is converted to input_new.udf.
> ls
> convert.py define_2.00.udf define_3.00.udf input_2.00.udf input_3.00.udf
> python convert.py input_2.00.udf input_new.udf
** List of variables in UDF for KAPSEL (input.udf) [#y1d5b4c6]
''constitutive_eq'': type: {Navier_Stokes, Shear_Navier_Stokes, Shear_Navier_Stokes_Lees_Edwards,Electrolyte}
Navier_Stokes
- DX: &color(blue){Girid width (this is the unit of length)};
- RHO: &color(blue){Density of fluid};
- ETA: &color(blue){Viscosity of fluid};
- kBT: &color(blue){Temperature of dispersion};
- alpha_v: &color(blue){Scaling factor for fluctuating force (translation)};
- alpha_o: &color(blue){Scaling factor for fluctuating torque (rotation)};
Shear_Navier_Stokes&br;(This type implements shear flow with zigzag shape.)
- DX: &color(blue){Girid width (this is the unit of length)};
- RHO: &color(blue){Density of fluid};
- ETA: &color(blue){Viscosity of fluid};
- kBT: &color(blue){Temperature of dispersion};
- alpha_v: &color(blue){Scaling factor for fluctuating force (translation)};
- alpha_o: &color(blue){Scaling factor for fluctuating torque (rotation)};
- External_field: type: {DC, AC}: &color(blue){Steady shear (DC) or Oscillatory shear (AC)};
: DC|
-- shear_rate: &color(blue){Shear rate (DC)};
: AC|
-- shear_rate: &color(blue){Max shear rate (AC)};
-- Frequency: &color(blue){Alternating frequency of shear flow};
Shear_Navier_Stokes_Lees_Edwards&br;(This type implements shear flow with Lees-Edwards periodic boundary condition.)
- DX: &color(blue){Girid width (this is the unit of length)};
- RHO: &color(blue){Density of fluid};
- ETA: &color(blue){Viscosity of fluid};
- kBT: &color(blue){Temperature of dispersion};
- alpha_v: &color(blue){Scaling factor for fluctuating force (translation)};
- alpha_o: &color(blue){Scaling factor for fluctuating torque (rotation)};
- External_field: type: {DC, AC}: &color(blue){Steady shear (DC) or Oscillatory shear (AC)};
: DC|
-- shear_rate: &color(blue){Shear rate (DC)};
: AC(unpopulated)|
-- shear_rate: &color(blue){Max shear rate (AC)};
-- Frequency: &color(blue){Alternating frequency of shear flow};
Electrolyte
- DX: &color(blue){Girid width (this is the unit of length)};
- RHO: &color(blue){Density of fluid};
- ETA: &color(blue){Viscosity of fluid};
- kBT: &color(blue){Temperature of dispersion};
- alpha_v: &color(blue){Scaling factor for fluctuating force (translation)};
- alpha_o: &color(blue){Scaling factor for fluctuating torque (rotation)};
- Dielectric_cst: &color(blue){Dielectric constant of fluid};
- INIT_profile:
-- &color(blue){''Uniform:'' use uniform ionic densities as initial state.};
-- &color(blue){''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: &color(blue){''salt:'' salt is added, ''saltfree:'' no salt is added};
: salt|
-- Valency_positive_ion: &color(blue){Valency of positive ions};
-- Valency_negative_ion: &color(blue){Valency of negative ions};
-- Onsager_coeff_positive_ion: &color(blue){Onsager transport coefficient of positive ions};
-- Onsager_coeff_negative_ion: &color(blue){Onsager transport coefficient of negative ions};
-- Debye_length: &color(blue){Debye screening length This causes the corresponding salt concentration to be specified automatically.};
: saltfree|
-- Valency_counterion: &color(blue){Valency of counter ions};
-- Onsager_coeff_counterion: &color(blue){{Onsager transport coefficient of counter ions};
- Electric_field: type: &color(blue){''ON:'' apply external electric field, ''OFF:'' no external electric field};
-- ON: type: &color(blue){''DC:'' apply steady electric field, ''AC:'' apply oscillatory electric field};
:: DC|
--- Ex: &color(blue){Intensity of electric field in x-direction};
--- Ey: &color(blue){Intensity of electric field in y-direction};
--- Ez: &color(blue){Intensity of electric field in z-direction};
:: AC|
--- Ex: &color(blue){Max intensity of electric field in x-direction};
--- Ey: &color(blue){Max intensity of electric field in y-direction};
--- Ez: &color(blue){Max intensity of electric field in z-direction};
--- Frequency: &color(blue){Alternating frequency of oscillatory electric field.};
''object_type'': type: {spherical_particle, chain, rigid}
spherical_particle
- Particle_spec[]
-- Particle_spec[0]: &color(blue){(0 means the 1st component)};
--- Particle_number: &color(blue){Number of particles};
--- MASS_RATIO: &color(blue){Density of particle / density of fluid};
--- Surface_charge: &color(blue){Valency of particles (total charge carried by a single particle in unit of electron charge)};
--- janus_axis: select {'NONE', 'X', 'Y', 'Z'}: &color(blue){janus axis in body_fixed frame};
--- janus_propulsion: select{'OFF', 'TUMBLER', 'SQUIRMER', 'OBSTACLE'}:
--- janus_force: x, y, z: &color(blue){self-propulsion force};
--- janus_torque: x, y, z: &color(blue){self-propulsion torque};
--- janus_slip_vel: &color(blue){Slip velocity coeff B1};
--- janus_slip_mode: &color(blue){Blake squirmer mode B2/B1};
chain
- Chain_spec[]
-- Chain_spec[0] &color(blue){(0 means the 1st component)};
--- Beads_number: &color(blue){Number of beads in a single chain};
--- Chain_number: &color(blue){Number of chains in a simulation box};
--- MASS_RATIO: &color(blue){Density of beads / density of fluid};
--- Surface_charge: &color(blue){Valency of beads (total charge carried by a single bead in unit of electron charge)};
--- janus_axis: select {'NONE', 'X', 'Y', 'Z'}: &color(blue){janus axis in body_fixed frame};
rigid
- Rigid_spec[]
-- Rigid_spec[0] &color(blue){(0 means the 1st component)};
--- Beads_number: &color(blue){number of beads in a chain};
--- Chain_number: &color(blue){number of chains};
--- MASS_RATIO: &color(blue){mass density ratio chain/solvent};
--- Surface_charge: &color(blue){surface charge of colloid};
--- Rigid_motion: select {'fix','free'}: &color(blue){fix=forced motion, free=non-forced motion};
--- Rigid_velocity: x, y, z: &color(blue){speed of translation ### fix only ###};
--- Rigid_omega: x, y, z: &color(blue){angular velocity ### fix only ###};
''A_XI'': &color(blue){Thickness of the particle-fluid boundary};
''A'': &color(blue){Radius pd particles or beads};
''gravity''
- G: &color(blue){Gravitational acceleration};
- G_direction: &color(blue){Select the direction in which gravity is applied from ''-X'' , ''-Y'' , ''-Z''.};
''EPSILON'': &color(blue){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: &color(blue){Defines the size of simulation box in x-direction as Lx=2^NPX};
- NPY: &color(blue){Defines the size of simulation box in y-direction as Ly=2^NPY};
- NPZ: &color(blue){Defines the size of simulation box in z-direction as Lz=2^NPZ};
''time_increment'': type:
- &color(blue){''auto:'' set delta_t automatically};
- &color(blue){''manual:'' set delta_t manually};
auto
- factor: &color(blue){Set delta_t = factor * min [ rho/(eta k_max^2), 1/(k_B T Gamma_a k_max^2)],};
manual
- delta_t: &color(blue){Set delta_t manually};
''switch''
- ROTATION:
-- &color(blue){''ON:'' solve rotational motion of particles properly};
-- &color(blue){''OFF:'' no rotational motion of particles};
//- HYDRO_int: &color(blue){Set ''Correct'' (other options are obsolete)};
//- Stokes: &color(blue){Set ''with advection'' (other options are obsolete)};
- LJ_truncate:
-- &color(blue){''ON:'' LJ without attraction (WCA potential)};
-- &color(blue){''OFF:'' LJ with attractive part};
-- &color(blue){''NONE:'' no pair potential at all};
- INIT_distribution: type:
-- &color(blue){''uniform_random:'' randomly generate initial particle positions};
-- &color(blue){''random_walk:'' add some deviations to a perfect FCC lattice};
-- &color(blue){''FCC:'' place particles on FCC lattice};
-- &color(blue){''BCC:'' place particles on a BCC lattice};
-- &color(blue){''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: &color(blue){Number of trial iteration to avoid bead-overlapping in the process of random walk};
: 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: 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
- q
- q0: 0th-component of initial quaternion
- q1: 1st-component of initial quaternion
- q2: 2nd-component of initial quaternion
- q3: 3rd-component of initial quaternion
- omega
- x: x-component of initial angular velocity
- y: y-component of initial angular velocity
- z: z-component of initial angular velocity
: FIX_CELL|
-- x: {ON, OFF} &color(blue){Set ON to avoid the drift of center of gravity in x-direction};
-- y: {ON, OFF} &color(blue){Set ON to avoid the drift of center of gravity in y-direction};
-- z: {ON, OFF} &color(blue){Set ON to avoid the drift of center of gravity in z-direction};
: pin: type:|
-- &color(blue){''NO:'' do not pin any particles};
-- &color(blue){''YES:'' pin specified particles};
- pin[]
- pin[0]: Index of the 1st particle to be transitionally pined.
- pin_rot[]
- pin_rot[0]: Index of the 1st particle to be rotationally pined.
:: 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: &color(blue){Set ''full_periodic'' (other options are obsolete)};
//
//z_dirichlet
//- wall_velocity_x: &color(blue){Unused};
//- wall_velocity_y: &color(blue){Unused};
//- wall_velocity_z: &color(blue){Unused};
''output''
- GTS: &color(blue){Number of intervals between data saving};
- Num_snap: &color(blue){Number of data saving. Total number of simulation step is GTS * Num_snap.};
- AVS: {ON, OFF} &color(blue){Set ''ON'' if AVS data is needed. Huge disk space is used if ON.};
: ON|
-- Out_dir: &color(blue){Name of subdirectory in which AVS data is saved. Make subdirectories ./"Out_dir" and ./"Out_dir"/avs in advance to run KAPSEL.};
-- Out_name: &color(blue){Set a name of AVS field data file "Out_name".fld};
-- File_Type: &color(blue){Select a file format of AVS data from ''BINARY'' or ''ASCII''};
- UDF: &color(blue){Set ''ON''};
''E'': &color(blue){Unused};
''t'': &color(blue){Present time};
''Particles[]'' &color(blue){There is no data in this section of input UDF. Temporal particle positions and velocities are stored here in restart and output UDF.};
- Particles[]
- R
- R_raw
- v
- q
- omega
- f_hydro
- torque_hydro
- f_slip
- torque_slip
''resume''
- Calculation: {NEW, CONTINUE}
-- &color(blue){''NEW:'' start a new simulation run};
-- &color(blue){''CONTINUE:'' restart continuing simulation run from the end of the previous run.};
