* UDF [#sb525d43] - 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: (rheology, chain in shear flow) -- Electrolyte: (electrophoresis) ** List of variables in UDF for KAPSEL (input.udf) [#y1d5b4c6] ''constitutive_eq'': type: {Navier_Stokes, Shear_Navier_Stokes, 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 - 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)}; 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}; - Dielectric_cst: &color(blue){Dielectric constant of fluid}; - INIT_profile: &color(blue){''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: &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){Frequency of oscillatory electric field.}; ''object_type'': type: {spherical_particle, chain} 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)}; chain - Chain_spec[] -- Chain_spec[0] &color(blue){(0 meand 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)}; ''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, ''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, ''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 with attractive part, ''OFF:'' LJ without attraction (WCA potential), ''NONE:'' no pair potential at all}; - INIT_distribution: type: &color(blue){''uniform_random:'' randomly generate initial particle positions, ''random_walk:'' generate a initial chain configuration by random walk, ''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: &color(blue){Number of trial iteration to avoid bead-overlapping in the process of random walk}; : user_specify| -- Particles[] --- Particles[0] &color(blue){(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} &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}; ''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 - x: x-component of temporal particle position - y: y-component of temporal particle position - z: z-component of temporal particle position - v - x: x-component of temporal particle velosity - y: y-component of temporal particle velosity - z: z-component of temporal particle velosity ''resume'' - Calculation: {NEW, CONTINUE} &color(blue){''NEW:'' start a new simulation run, ''CONTINUE:'' restart continuing simulation run from the end of the previous run.};