Commit 1d2dfd56 authored by ylan's avatar ylan
Browse files

[peb-mesh] add peb11k mesh

- This is not stable for Re10k, but still good enough for scaling tests.
parent fd3171f9
## 11145 (non-touching) pebbles in a cylinder (Last updated: Jun. 12, 2020)
cyl11145 N, Version 3.0, E3,575,076
This mesh is not very stable for Re10k. There is (at least) a known location having high distorted Cell.
Run dt=5e-4 is fine for the first 14000 steps.
After that dt=4e-4 will have CFL too high stop at 14000+5996th step (time=9.99800000e+00)
We never manage to run over an convection unit
This is a better mesh using improved techniques developed within last few months.
Please note that the improvement has not finished.
- New features:
- A more robust and cleaner code with lots of user intreface improvement
- Add Taubin smoothing before edge collapse
- Switch to a passive tessellation if the first attempt didn't do well.
- Add local optimization for better performance.
- dump co2 directly
- DEM results from project chrono on nurburg gpu
- Fix some bugs as well
- Geometry and BC:
- Sphere distribution: flat-free
- Sphere radius = 1.0 (Wall)
- Cylinder radius = 40.672 (SYM), (convert SYM to Wall in usr file)
- Zbot of the cylinder = 14.655 (Outflow)
- Ztop of the cylinder = -12.627 (Inflow)
- We use dimless scale to run Re10000 with vz=1.0
- Case files:
- .re2, a curved (projected at lx1=3) hex20 re2 mesh, converted by a hex20 rea: xn3.rea+reatore2, R\_peb=1.0
```
xyz min -40.672 -40.672 -12.627
xyz max 40.672 40.672 14.655
mesh metrics:
GLL grid spacing min/max : 3.67E-04 3.32E-01
scaled Jacobian min/max/avg: 1.52E-02 9.97E-01 3.65E-01
aspect ratio min/max/avg: 1.06E+00 6.06E+01 1.27E+01
```
- Manage to run to time=7.0 with dt=5e-4 and the follow commit of NekRS
```
commit c26b570af4a85e8ef8425b7e7057f0926f5aaace
Author: Stefan Kerkemeier <stefanke@jlselogin2.ftm.alcf.anl.gov>
Date: Fri Aug 7 12:06:07 2020 +0000
add missing file and fix gsh for scalars
```
- peb.11k.dat, locations of the pebble centers under R\_peb=1.0
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
// Boundary conditions
/* wall 1, inflow 2, outflow 3, x-slip 4, y-slip 5, z-slip 6 */
void insVelocityDirichletConditions3D(bcData *bc)
{
bc->uP = 0.0;
bc->vP = 0.0;
bc->wP = 1.0;
}
void insVelocityNeumannConditions3D(bcData *bc)
{
}
void cdsDirichletConditions3D(bcData *bc)
{
bc->sP = 0.0;
}
void cdsNeumannConditions3D(bcData *bc)
{
bc->sF = 1.0;
}
// Stabilized outflow (Dong et al)
void insPressureDirichletConditions3D(bcData *bc)
{
const dfloat iU0delta = 10.0;
const dfloat un = bc->uM*bc->nx + bc->vM*bc->ny + bc->wM*bc->nz;
const dfloat s0 = 0.5 * (1.0 - tanh(un*iU0delta));
bc->pP = -0.5 * (bc->uM*bc->uM + bc->vM*bc->vM + bc->wM*bc->wM) * s0;
}
[OCCA]
backend = CUDA
deviceNumber = 0
[GENERAL]
#verbose = true
polynomialOrder = 7
startFrom = r7.fld
stopAt = numSteps
numSteps = 20000
dt = 4.0e-4
timeStepper = tombo2
extrapolation = subCycling
subCyclingSteps = 2
writeControl = TIMESTEP
writeInterval = 1000
filtering = hpfrt
filterWeight = 200
filterModes = 2
[PRESSURE]
#preconditioner = semg_amg
#amgSolver = parAlmond
#galerkinCoarseOperator = yes
residualTol = 1e-04
[VELOCITY]
#solver = pcg+block
boundaryTypeMap = inlet, outlet, wall, wall
density = 1.0
viscosity = -5000.0
residualTol = 1e-06
#[TEMPERATURE]
#solver = none
#boundaryTypeMap = inlet, outlet, insulated, flux
#rhoCp = 1.0
#conductivity = -100
#residualTol = 1e-06
#[SCALAR01]
#solver = none
[BOOMERAMG]
#coarsenType = 10
#interpolationType = 6
#smootherType = -1
#iterations = 2 # testing
#strongThreshold = 0.25
#nonGalerkinTol = 0.1
//
// nekRS User Defined File
//
#include <math.h>
#include "udf.hpp"
#include "cfl.hpp"
int my_iostep=100;
/* UDF Functions */
void UDF_LoadKernels(ins_t *ins)
{
}
void UDF_Setup(ins_t *ins)
{
// get IC from nek
if (!ins->readRestartFile) nek_copyTo(ins->startTime);
}
void UDF_ExecuteStep(ins_t *ins, dfloat time, int tstep)
{
dfloat cfl=computeCFL(ins, time, tstep);
if (ins->isOutputStep || cfl>4.0) {
nek_ocopyFrom(time, tstep);
nek_userchk();
}
if (ins->isOutputStep) {
nek_ocopyFrom(time, tstep);
nek_userchk();
}
}
c-----------------------------------------------------------------------
subroutine uservp(i,j,k,eg) ! set variable properties
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer i,j,k,e,eg
c e = gllel(eg)
udiff = 0.0
utrans = 0.0
return
end
c-----------------------------------------------------------------------
subroutine userf(i,j,k,eg) ! set acceleration term
c
c Note: this is an acceleration term, NOT a force!
c Thus, ffx will subsequently be multiplied by rho(x,t).
c
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer i,j,k,e,eg
c e = gllel(eg)
ffx = 0.0
ffy = 0.0
ffz = 0.0
return
end
c-----------------------------------------------------------------------
subroutine userq(i,j,k,eg) ! set source term
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer i,j,k,e,eg
c e = gllel(eg)
qvol = 0.0
return
end
c-----------------------------------------------------------------------
subroutine userbc(i,j,k,f,eg) ! set up boundary conditions
c NOTE ::: This routine MAY NOT be called by every process
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer i,j,k,f,e,eg
e=gllel(eg)
ux = 0.0
uy = 0.0
uz = 1.0
if (cbu.eq.'o ') then
U0 = 1.0 ! characteristic velocity
delta = 0.1 ! small positive constant
pa = dongOutflow(i,j,k,e,f,U0,delta)
endif
flux = 0.0
temp = 0.0
c if (cbc(f,e,1).eq.'W '.AND.cbc(f,e,2).eq.'t ') temp=1.0
if (cbc(f,e,1).eq.'W '.AND.cbc(f,e,2).eq.'f ') flux=1.0
return
end
c-----------------------------------------------------------------------
subroutine useric(i,j,k,eg) ! set up initial conditions
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer i,j,k,e,eg
ux = 0.0
uy = 0.0
uz = 1.0
temp = 0.0
return
end
c-----------------------------------------------------------------------
subroutine userchk
include 'SIZE'
include 'TOTAL'
n=lx1*ly1*lz1*nelt
if (istep.eq.0) then
xxmax = glmax(xm1,n)
yymax = glmax(ym1,n)
zzmax = glmax(zm1,n)
xxmin = glmin(xm1,n)
yymin = glmin(ym1,n)
zzmin = glmin(zm1,n)
if (nio.eq.0) then
write(6,18) xxmin,yymin,zzmin
write(6,19) xxmax,yymax,zzmax
18 format(' xyz min ',5g13.5)
19 format(' xyz max ',5g13.5)
endif
ifxyo=.true.
c call outpost(vx,vy,vz,t,pr,' ')
endif
c if (mod(istep,500).eq.0) then
c umin=glmin(vx,n)
c umax=glmax(vx,n)
c vmin=glmin(vy,n)
c vmax=glmax(vy,n)
c wmin=glmin(vz,n)
c wmax=glmax(vz,n)
c tmin=glmin(t ,n)
c tmax=glmax(t ,n)
c if (nio.eq.0) write(6,1)
c $ istep,time,umin,umax,vmin,vmax,wmin,wmax,tmin,tmax
c 1 format(i9,1p9e11.3,' tmax')
c
c call compute_cfl(cfl,vx,vy,vz,dt)
c call outpost(cflf,vy,vz,pr,t,'cfl')
c endif
c if (istep.gt.0) then
c ifield = 1 ! essential for lambda2 right now
c call lambda2(t(1,1,1,1,2))
c tmin=glmin(t(1,1,1,1,2) ,n)
c tmax=glmax(t(1,1,1,1,2) ,n)
c if (nio.eq.0) write(6,2)istep,time,tmin,tmax
c 2 format(i9,1p3e11.3,' tmax2')
c
c ifxyo = .true.
c ifvo = .true.
c ifpro = .true.
c ifto = .true.
c ifpsco(1) = .true.
cc call outpost(vx,vy,vz,pr,t,' ')
c endif
c call comp_Reynolds
if (mod(istep,500).ne.0) then
call compute_cfl(cfl,vx,vy,vz,1.0)
call outpost(cflf,vy,vz,pr,t,'cfl')
endif
return
end
c-----------------------------------------------------------------------
subroutine usrdat ! This routine to modify element vertices
include 'SIZE'
include 'TOTAL'
return
end
c-----------------------------------------------------------------------
subroutine usrdat3
include 'SIZE'
include 'TOTAL'
return
end
c-----------------------------------------------------------------------
subroutine usrdat2
include 'SIZE'
include 'TOTAL'
integer e,f
ifheat = .false.
nface = 2*ldim
do e=1,nelv
do f=1,nface
if(cbc(f,e,1).eq.'E '.or.cbc(f,e,1).eq.' ')then
cbc(f,e,1)='E '
cbc(f,e,2)='E '
elseif(cbc(f,e,1).eq.'W ')then ! pebbles
boundaryID(f,e) = 4
cbc(f,e,1)='W '
cbc(f,e,2)='f '
elseif(cbc(f,e,1).eq.'W01')then ! side of cylinder
boundaryID(f,e) = 3
cbc(f,e,1)='W '
cbc(f,e,2)='I '
elseif(cbc(f,e,1).eq.'W02')then ! z_bottom
boundaryID(f,e) = 1
cbc(f,e,1)='v '
cbc(f,e,2)='t '
elseif(cbc(f,e,1).eq.'W03')then ! z_top
boundaryID(f,e) = 2
cbc(f,e,1)='o ' ! Dong's outflow
cbc(f,e,2)='O '
else
write(*,*)'bc incorrect',e,f,cbc(f,e,1)
endif
enddo
enddo
param(18) = 1 ! use algebraic residual norm
return
end
c-----------------------------------------------------------------------
function dongOutflow(ix,iy,iz,iel,iside,u0,delta)
include 'SIZE'
include 'SOLN'
include 'GEOM'
real sn(3)
ux = vx(ix,iy,iz,iel)
uy = vy(ix,iy,iz,iel)
uz = vz(ix,iy,iz,iel)
call getSnormal(sn,ix,iy,iz,iside,iel)
vn = ux*sn(1) + uy*sn(2) + uz*sn(3)
S0 = 0.5*(1.0 - tanh(vn/u0/delta))
dongOutflow = -0.5*(ux*ux+uy*uy+uz*uz)*S0
return
end
c-----------------------------------------------------------------------
subroutine comp_Reynolds
implicit none
include 'SIZE'
include 'TOTAL'
integer i,n,npeb
real Rcyl,Rpeb
real z0,z1,wd,fun_z,wt(lx1*ly1*lz1*lelv)
real zz,dis,glsum,glsc2
real wght_vol,area_peb,area_cyl1,area_cyl2,vz_bar,Dh1,Dh2
npeb = 1568
Rpeb = 1.0
Rcyl = 13.858
! min/max of pebble centers are -1.05733229e+01 1.15912238e+01
! f ------\
! \
! \-----
! o ) .
! P 1 | wd |
wd = 1.5
z0 = -10.573 - 1.0 - wd*0.5
z1 = 11.159 + 1.0 + wd*0.5
n=lx1*ly1*lz1*nelv
do i=1,n
zz=zm1(i,1,1,1)
if (zz>z1) then
dis = -abs(zz-z0)
elseif (zz>z0) then
dis = min(abs(z1-zz),abs(zz-z0))
else
dis = -abs(z0-zz)
endif
fun_z = tanh(dis*wd)
wt(i) = fun_z * bm1(i,1,1,1)
enddo
wght_vol = glsum(wt,n)
area_peb = npeb*4.0*pi*Rpeb*Rpeb
area_cyl1 = 2.0*Rcyl*pi*(z1-z0)
area_cyl2 = 2.0*Rcyl*pi*(z1-z0+wd)
vz_bar=glsc2(wt,vz,n)/wght_vol
Dh1 = 4.0*wght_vol/(area_peb+area_cyl1)
Dh2 = 4.0*wght_vol/(area_peb+area_cyl2)
if(nid.eq.0)then
write(*,1)z0,z1,wd,wght_vol
write(*,2)area_peb,area_cyl1,area_cyl2
write(*,3)time,vz_bar,Dh1,Dh2
endif
1 format('CompRe, domain',1p4e11.3)
2 format('CompRe, s_area',1p3e11.3)
3 format('CompRe, vz/Dh ',1p4e11.3)
return
end
c-----------------------------------------------------------------------
......@@ -13,9 +13,11 @@ Please note that the improvement has not finished.
- Switch to a passive tessellation if the first attempt didn't do well.
- Add local optimization for better performance.
- dump co2 directly
- DEM results from project chrono on nurburg gpu
- Fix some bugs as well
- Geometry and BC:
- Sphere distribution: flat-free
- Sphere radius = 1.0 (Wall)
- Cylinder radius = 26.776 (SYM), (convert SYM to Wall in usr file)
- Zbot of the cylinder = 12.117 (Outflow)
......
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