FSILBM3D: Fluid-structure interaction solver based on Lattice Boltzmann method

Table of contents

• Installation
• Run solver
• Input file description
• Simulation control parameters
• Output file description
• License

Installation

Linux

Clone FSIBLM3D to a local machine,

git clone git@github.com:gaoak/FSILBM3D.git
cd FSILBM3D

To compile FSILBM3D in linux system, run

make

The executable file is FSILBM3D

The default compiler is intel fortran. To use a GNU gfortran compiler gcc, you need to change the first line in the Makefile

CMP = intel# intel,gcc

to

CMP = gcc# intel,gcc

Run solver

prepare work direcotry and input files

Copy input parameter file (inFlow.dat in examples), body mesh file (plate.dat in examples) and create or clean directories bash script (cleanfiles.sh in examples) to the work directory.

Create data folders in the work directory by running bash script (cleanfiles.sh)

for folder in DatBodySpan DatInfo DatBody DatFlow 
do
  if [[ -d $folder ]]; then
    rm -r $folder
    mkdir $folder
    echo Clear $folder
  else
    mkdir $folder
    echo Create $folder
  fi
done

for file in check.dat continue.dat log.* *.txt
do
  if [[ -e $file ]]; then
    rm $file
    echo Delete $file
  fi
done

Running on local linux machine

Run the solve using bash script

nohup /your/local/path/FSILBM3D/FSILBM3D &>log

Runing on the compute node

Submit the PBS script (2 threads for example)

#!/bin/sh 
#PBS -N LBM3D-Test
#PBS -e stderr.txt 
#PBS -o stdout.txt
#PBS -l nodes=1:ppn=2
#PBS -l walltime=1:59:00
#PBS -q CPU_Small
PBS_WDIR=`pwd`/FSILBM3D/FSILBM3D
PBS_ENAME=FSILBM3D
#########################################
echo Working directory is $PBS_O_WORKDIR
echo test is $PBS_O_HOST
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
cd $PBS_O_WORKDIR
$PBS_WDIR/$PBS_ENAME

Input file description

• inFlow.dat Simulation control parameters
• plate.dat Body mesh file
• cleanfiles.sh Bash script to create/clean output directories

Simulation parameters description

(A line starting with # indicates a comment)

• Parallel

  1. npsize : The core number used in the simulaion

• FlowCondition

  1. isConCmpt : Determining new simulation or continue simulaion

     • 0 : Calculate from the beginning
     • 1: Calculate from last time output

  2. numsubstep: Number of sub-steps for solid time-stepping solution

  3. timeSimTotal: Dimensionless total simulation time (time/Tref <= timeSimTotl)

  4. timeContiDelta: Dimensionless time interval for writing continue (continue.dat) which used for continue simulation

  5. timeWriteBegin: Dimensionless time to start fluid mesh (in DatFlow) and body mesh (in DatBody) writing

  6. timeWriteEnd: Dimensionless time to end fluid mesh (in DatFlow) and body mesh (in DatBody) writing (timeOutBegin should less than timeOutEnd)

  7. timeWriteFlow: Dimensionless time interval for fluid mesh (in DatFlow) writing

  8. timeWriteBody : Dimensionless time interval for body mesh (in DatBody) writing

  9. timeWriteInfo : Dimensionless time interval for post procesing information (such as force, velocity et. al. in DatInfo)

  10. Re: Dimensionless Reynolds Number

  11. denIn: Fluid density (Usually it's 1 )

  12. uvwIn: The given incoming Velocity $(U_\infty, V_\infty, W_\infty)$

      (determined by the velocity control parameters velocityKind)

  13. shearRateIn, velocityKind : the velocity control parameters

  • 0 : if velocityKind equals 0 , shearRateIn are the shear rate for incoming flow

    $U_\infty = U_{in} + 0 * shearRate(1) + y * shearRate(2) + z * shearRate(3)$

    $V_\infty = V_{in} + x * shearRate(1) + 0 * shearRate(2) + z * shearRate(3)$

    $W_\infty = W_{in} + x * shearRate(1) + y * shearRate(2) + 0 * shearRate(3)$

  • 1 : if velocityKind equals 2 , shearRateIn are the oscillatory parameter for incoming flow

    $U_\infty = U_{in} + shearRate(1) * cos(2 * pi * shearRate(2) * time + shearRate(3) * pi / 180)$

    $V_\infty = V_{in}$

    $W_\infty = W_{in}$

  14. VolumeForceIn,VolumeForceAmp,VolumeForceFreq,VolumeForcePhi : Parameters for Volume Force

      According to the NS equation :

      $rho * Du/Dt = rho * f_x - dp/dx$

      The volume force is calculated as following:

      $volumeForce(1) = VolumeForceIn(1) + VolumeForceAmp * sin(2 * pi * VolumeForceFreq * time + VolumeForcePhi)$

      $volumeForce(2) = VolumeForceIn(2)$

      $volumeForce(3) = VolumeForceIn(3)$

  15. TrefType: Determining the definition of reference time

      • 0 : Caculated by referece length and reference velocity

        $Tref = Lref / Uref$

      • 1 : Caculated by the maximum frequency of the bodies

        $Tref = 1 / max(frequency)$

      • else : The input value Tref in parameter file inflow.dat

  16. UrefType: Determining the definition of reference velocity

      • 0 : X-incoming flow velocity : $U_\infty$

      • 1 : Y-incoming flow velocity : $V_\infty$

      • 2 : Z-incoming flow velocity : $W_\infty$

      • 3 : Incoming flow velocity magnitude : $\sqrt{U_\infty^2 + V_\infty^2}$

      • 4 : The velocity amplitude only for velocityKind 2 : $|shearRateIn(1)|$

      • 5 : Flapping frequency velocity : $L f$

      • 6 : Maximum plunging velocity : $2\pi f a$

      • 7 : Twice maximum plunging velocity used by Park et al. (2017) PoF : $2\pi f a * 2$

      • else : The input value Uref in parameter file inflow.dat

  17. ntolLBM: Maximum number of iterations for the LBM method

  18. dtolLBM: Error tolerance for the LBM method

  19. interpolateScheme: Interpolate Scheme for multi-block communication.

      • 1 : Linear interpolation.

      • 2 : Third-(boundary) and fourth-order(inner) mix interpolation.

• FluidBlocks

  1. nblock: Number of fluid grid partitions
  2. ID: The ID of fluid grid
  3. iCollideModel: Determines the LBM model used in simualtion
     • 1 : SRT : Single Relaxation Time
     • 2 : TRT : Double Relaxation Time
     • 3 : MRT : Multiple Relaxation Time
     • 11 : SMAG-SRT: Single Relaxation Time With Smagorinsky Model
     • 12 : Regular-SRT: Regularised Single Relaxation Time
     • 13 : ELBM-SRT: Single Relaxation Time In ELBM
     • 14 : WALE-SRT: WALE Single Relaxation Time
     • 15 : Vremann-SRT: Vremann Single Relaxation Time
  4. offsetOutput: The computation domain moves with first body if this equals 1
  5. isoutput: Outputting the relative flow grid and body, i.e. in the moving frame of reference, if this equals 1
  6. xDim,yDim,zDim: Number of nodes in the x, y, and z directions of the fluid block
  7. dh: For uniform grid dh=dx=dy=dz
  8. xmin,ymin,zmin: Starting position of the fluid block
  9. boundaryConditions(1:6) (xmin,xmax,ymin,ymax,zmin,zmax): Boundary conditions parameters on six directions
     • 0: Fluid boundary conditions
     • 101: Dirichlet boundary condition (velocity equal to a specified value)
     • 102: Dirichlet boundary condition (The value of velocity at the boundary is not a fixed constant, but a non-uniform distribution of function values)
     • 103: First order extrapolation boundary conditions
     • 104: Second-order extrapolation boundary conditions
     • 201: Fixed wall(full way bounce back)
     • 202: Moving wall, only for the top and bottom boundaries $(ymin, ymax)$
     • 203: Fixed wall(half way bounce back, good choice for turbulent in LES compute)
     • 301: Periodic Boundary(For the son block, the xDim/yDim/zDim should have have one more layer than the father block)
     • 302: Symmetric boundary
  10. params: Pending Parameters

• SolidBody

  1. IBPenaltyalpha : Velocity correction parameter of the penalty function in the IBM method

  2. alphaf : Parameter for correcting torsion in the mass matrix

  3. NewmarkGamma, NewmarkBeta: Parameters of the Newmark method

  4. dampK, dampM : Stiffness damping K, mass damping M

  5. dtolFEM, ntolFEM : Maximum number of iterations and error tolerance for the FEM method

  6. nFish : Total number of the solid bodies

  7. nfishGroup : Numbers of the solid bodies type

  8. isKB : Determining the kind of parameters of the flexible bodies

     • 0 : KB, KS(Bending Stiffness, Stretching Stiffness)
     • 1 : EmR, TcR (Elastic Modulus Ratio, Characteristic Time Ratio)

  9. fishnum (fishGroup) : The number of the solid bodies in the specific type

  10. numX,numY,numZ : Number of arrangements of multiple bodies in the x, y, and z directions

  11. FEmeshName(iFish) : The name of the body mesh file in the specific type

  12. iBodyModel(iFish) : Choose for the body models

      • 1: rigid body
      • 2: flexible body

  13. iBodyType(iFish) : Type of virtual object

  14. isMotionGiven : Degrees of freedom in six directions

  15. denR(iFish) : Density ratio $(rho_b * h / rho_f * L)$, where $L$ is the virtual plate thickness

  16. psR(iFish) : Poisson ratio

  17. Freq(iFish) : The flapping frequence for flexible bodies

  18. firstXYZ : The initial position of the first point of the bodies

  19. deltaXYZ : If there are more than one bodies in a type, deltaXYZ determines the interval between front and rear solids

  20. initXYZVel : The given initial translatory velocity for the flexible body and the given translational velocity for the rigid body.

  21. XYZAmpl, XYZPhi : Parameters for body flapping

      • $XYZ = XYZAmpl * dcos(2.0 * pi * Freq * time + XYZPhi)$

  22. AoAo, AoAAmpl, AoAPhi : Parameters for body rotation

      • $Theta = AoAo + AoAAmpl * dcos(2.0 * pi * Freq * time + AoAPhi)$

• ProbingFluid

  1. fluidProbingNum: The number of data detection points in flow field
  2. fluidProbingCoords : The coordinates of detection points

• ProbingSolid

  1. solidProbingNum: The number of data detection points in bodies
  2. solidProbingNode: The serial number of each detection points in the specific body

Output file description

• Output files and directories

1. DatBody : Folder of body results
2. DatBodySpan : Folder of spanwise-extension body results
3. DatFlow : Floder of flow field results
4. DatInfo : Floder of force and power et. al. results
5. Check.dat : Parameters record file for checking
6. continue.dat : Results record file for continue calculating

• Files in DatInfo description

1. FishAngular.plt
   • AoA : The deflection angle of the body $(y2-y1)/(x2-x1)$;
   • Ty-TH : Height difference between the first and last points $(y2 - y1)$
   • Hy : y Coordinate of the first point $(y1)$
   • Ty : y Coordinate of the last point $(y2)$
2. FishPower.plt : The power information of the bodies
   • Ptot : Px + Py + Pz
   • Px,Py,Pz : Output power calculated by ($force * velcity$)
3. FishEnergy.plt : The energy of the bodies
   • E_s : Streching strain energy
   • E_b : Bending strain energy
   • E_p : Total strain energy calculated by (E_s + E_b)
   • E_w : Kinetic energy
   • E_t : total energy calculated by (E_p + E_w)
   • E_k : Output energy calculated by ($E_k = E_k + t * ptot$)
4. FishForce.plt :The forces exerted on the bodies
5. FishNodeBegin.plt : The information of the first point of the bodies
6. FishNodeCenter.plt : The information of the center point of the bodies
7. FishNoEnd.plt : The information of the last point of the bodies
8. FishNodeMean.plt : The average information of the all points of the bodies