[Nek5000-users] Stream function
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Jul 13 07:13:37 CDT 2018
Hi,
I guess the errors under point 2 are related to the fact that you try to
include the same common block multiple times, i.e. you probably have
TOTAL and INPUT, SOLN and MASS. Just make sure that you have the
relevant variables included via common blocks.
Regarding point 1: In the end, you would need to decide what your
boundary conditions for the Poisson/Helmholtz equation really are. For
the example, we consider an all Dirichlet boundary, which can then be
achieved with v2mask (or in fact v1mask as well i guess); this because
all solid boundaries are connected and have thus the same value for the
streamfunction. For your case, I guess you have periodicity in the
streamwise direction, and solid wall at y=0. Not sure what one really
needs to impose on the upper boundary... but in the end, this is why we
use vmask2 in the example.
Hope this helps,
Philipp
On 2018-07-12 20:47, nek5000-users at lists.mcs.anl.gov wrote:
> Hi Philipp,
>
> Thanks very much for the userchk routine.
>
> I have been testing this with the Blasius example in Nek. I am hoping to implement this with my geometry (a 2-D backward facing step with the Blasius profile at the inlet upstream from the step).
>
> For the Blasius example in Nek, I used VisIt and checked rhs and psi from the stfc0.f* file, but psi does not look physical.
>
> 1. What is the purpose of using v2mask? I wonder whether I should specify a different mask...
>
> 2. Including declarations from 'INPUT', 'SOLN', and 'MASS' produced a long list of errors (please see below). To run the code, I commented three lines related to including 'INPUT', 'SOLN', and 'MASS'so that these are not included, but I wonder whether that would create problems?
>
> Any advice would be appreciated.
>
> Thanks very much.
>
> Hannah
>
>
> INPUT:14:16: Error: Symbol ‘param’ at (1) already has basic type of REAL
> INPUT:22:27: Error: Symbol ‘param’ at (1) is already in a COMMON block
> INPUT:25:20: Error: Symbol ‘matype’ at (1) already has basic type of INTEGER
> INPUT:30:28: Error: Symbol ‘matype’ at (1) is already in a COMMON block
> INPUT:34:26: Error: Symbol ‘if3d’ at (1) already has basic type of LOGICAL
> INPUT:50:26: Error: Symbol ‘if3d’ at (1) is already in a COMMON block
> INPUT:66:27: Error: Symbol ‘ifnav’ at (1) already has basic type of LOGICAL
> INPUT:69:27: Error: Symbol ‘hcode’ at (1) already has basic type of CHARACTER
> INPUT:70:27: Error: Symbol ‘ocode’ at (1) already has basic type of CHARACTER
> INPUT:71:27: Error: Symbol ‘drivc’ at (1) already has basic type of CHARACTER
> INPUT:72:26: Error: Symbol ‘rstv’ at (1) already has basic type of CHARACTER
> INPUT:73:28: Error: Symbol ‘textsw’ at (1) already has basic type of CHARACTER
> INPUT:74:27: Error: Symbol ‘initc’ at (1) already has basic type of CHARACTER
> INPUT:75:27: Error: Symbol ‘hcode’ at (1) is already in a COMMON block
> INPUT:77:29: Error: Symbol ‘turbmod’ at (1) already has basic type of CHARACTER
> INPUT:80:28: Error: Symbol ‘reafle’ at (1) already has basic type of CHARACTER
> INPUT:81:28: Error: Symbol ‘reafle’ at (1) is already in a COMMON block
> INPUT:83:29: Error: Symbol ‘session’ at (1) already has basic type of CHARACTER
> INPUT:84:29: Error: Symbol ‘session’ at (1) is already in a COMMON block
> INPUT:86:20: Error: Symbol ‘cr_re2’ at (1) already has basic type of INTEGER
> INPUT:87:33: Error: Symbol ‘cr_re2’ at (1) is already in a COMMON block
> INPUT:89:24: Error: Symbol ‘re2off_b’ at (1) already has basic type of INTEGER
> INPUT:90:31: Error: Symbol ‘re2off_b’ at (1) is already in a COMMON block
> INPUT:94:13: Error: Symbol ‘xc’ at (1) already has basic type of REAL
> INPUT:98:24: Error: Symbol ‘xc’ at (1) is already in a COMMON block
> INPUT:100:20: Error: Symbol ‘igroup’ at (1) already has basic type of INTEGER
> INPUT:101:28: Error: Symbol ‘igroup’ at (1) is already in a COMMON block
> INPUT:103:28: Error: Symbol ‘ccurve’ at (1) already has basic type of CHARACTER
> INPUT:104:25: Error: Symbol ‘cbc’ at (1) already has basic type of CHARACTER
> INPUT:105:25: Error: Symbol ‘cbc’ at (1) is already in a COMMON block
> INPUT:107:19: Error: Symbol ‘ieact’ at (1) already has basic type of INTEGER
> INPUT:108:27: Error: Symbol ‘ieact’ at (1) is already in a COMMON block
> INPUT:112:20: Error: Symbol ‘numsts’ at (1) already has basic type of INTEGER
> INPUT:113:26: Error: PARAMETER attribute of ‘numsts’ conflicts with PARAMETER attribute at (1)
> INPUT:115:20: Error: Symbol ‘numflu’ at (1) already has basic type of INTEGER
> INPUT:118:29: Error: Symbol ‘numflu’ at (1) is already in a COMMON block
> INPUT:121:17: Error: Symbol ‘bcf’ at (1) already has basic type of INTEGER
> INPUT:122:26: Error: Symbol ‘bcf’ at (1) is already in a COMMON block
> INPUT:124:24: Error: Symbol ‘bctyps’ at (1) already has basic type of CHARACTER
> INPUT:125:29: Error: Symbol ‘bctyps’ at (1) is already in a COMMON block
> SOLN:4:18: Error: Symbol ‘lvt1’ at (1) already has basic type of INTEGER
> SOLN:5:41: Error: PARAMETER attribute of ‘lvt1’ conflicts with PARAMETER attribute at (1)
> SOLN:6:41: Error: PARAMETER attribute of ‘lvt2’ conflicts with PARAMETER attribute at (1)
> SOLN:7:45: Error: PARAMETER attribute of ‘lbt1’ conflicts with PARAMETER attribute at (1)
> SOLN:8:45: Error: PARAMETER attribute of ‘lbt2’ conflicts with PARAMETER attribute at (1)
> SOLN:10:42: Error: PARAMETER attribute of ‘lorder2’ conflicts with PARAMETER attribute at (1)
> SOLN:14:13: Error: Symbol ‘bq’ at (1) already has basic type of REAL
> SOLN:15:22: Error: Symbol ‘bq’ at (1) is already in a COMMON block
> SOLN:18:16: Error: Symbol ‘vxlag’ at (1) already has basic type of REAL
> SOLN:33:13: Error: Symbol ‘vx’ at (1) already has basic type of REAL
> SOLN:52:27: Error: Symbol ‘vxlag’ at (1) is already in a COMMON block
> SOLN:59:13: Error: Symbol ‘bx’ at (1) already has basic type of REAL
> SOLN:78:13: Error: Symbol ‘bx’ at (1) is already in a COMMON block
> SOLN:82:18: Error: Symbol ‘nu_star’ at (1) already has basic type of REAL
> SOLN:83:29: Error: Symbol ‘nu_star’ at (1) is already in a COMMON block
> SOLN:85:13: Error: Symbol ‘pr’ at (1) already has basic type of REAL
> SOLN:86:22: Error: Symbol ‘pr’ at (1) is already in a COMMON block
> SOLN:88:14: Error: Symbol ‘qtl’ at (1) already has basic type of REAL
> SOLN:89:25: Error: Symbol ‘qtl’ at (1) is already in a COMMON block
> SOLN:91:15: Error: Symbol ‘p0th’ at (1) already has basic type of REAL
> SOLN:92:27: Error: Symbol ‘p0th’ at (1) is already in a COMMON block
> SOLN:94:18: Error: Symbol ‘v1mask’ at (1) already has basic type of REAL
> SOLN:106:28: Error: Symbol ‘v1mask’ at (1) is already in a COMMON block
> SOLN:111:15: Error: Symbol ‘vxp’ at (1) already has basic type of REAL
> SOLN:133:25: Error: Symbol ‘vxp’ at (1) is already in a COMMON block
> SOLN:138:16: Error: Symbol ‘jp’ at (1) already has basic type of INTEGER
> SOLN:139:25: Error: Symbol ‘jp’ at (1) is already in a COMMON block
> MASS:4:14: Error: Symbol ‘bm1’ at (1) already has basic type of REAL
> MASS:11:23: Error: Symbol ‘bm1’ at (1) is already in a COMMON block
> /home/Hannah/NekExamples/blasius/c3.f:360:25:
>
> call compute_f (f1,w ,t )
> 1
> Warning: Actual argument contains too few elements for dummy argument ‘w’ (1/4) at (1)
> makefile:119: recipe for target 'nek5000' failed
> make: *** [nek5000] Error 1
> ________________________________________
> From: Nek5000-users [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> Sent: Thursday, July 12, 2018 3:37 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Stream function
>
> Ok, so can you please just try the attached code in userchck? It should
> work (at least does for us) in 2D. Essentially, the steps are:
> 1. copmute z-vorticity in a new array vorticity
> 2. construct the rhs by multiplying with -bm1
> 3. setup the Helmholtz problem and tolerances
> 4. solve the Helmholtz problem and storing the results in a new array phi
> 5. write out everything in two files.
>
> In this code you do not use the temperature at all, which I guess is
> fine for a 2D case (which I guess is what you look at).
>
> best regards,
> Philipp
>
> On 2018-07-10 22:33, Philipp Schlatter wrote:
>> Dear Hannah,
>> sorry that I only see the post now. Are you still having problems with
>> the stream function, or does it work now?
>> Best regards,
>> Philipp
>>
>> On 2018-07-02 16:40, nek5000-users at lists.mcs.anl.gov wrote:
>>> Hi JC,
>>>
>>> Yes, the mv_wall example computes the streamfunction, but it applies
>>> tmask, tmult that I could not find where they are defined in the
>>> file. I was experimenting with different masks.
>>>
>>> Do you know how postnek compute the streamfunction?
>>>
>>> I think it is computed in the subroutine strfct(psi) in postnek2.f,
>>> but I am not sure what happens in the routine?
>>>
>>> Thanks,
>>>
>>> Hannah
>>> ________________________________________
>>> From: Nek5000-users [nek5000-users-bounces at lists.mcs.anl.gov] on
>>> behalf of nek5000-users at lists.mcs.anl.gov
>>> [nek5000-users at lists.mcs.anl.gov]
>>> Sent: Friday, June 29, 2018 3:47 AM
>>> To: nek5000-users at lists.mcs.anl.gov
>>> Subject: Re: [Nek5000-users] Stream function
>>>
>>> Hi Hannah,
>>>
>>> I tried to implement the streamfunction as well (for a 2D cylinder flow)
>>> and it would appear that, doing naïvely, the tmask is set to zero
>>> everywhere. Hence, when rhs * tmask is computed in the hmholtz
>>> subroutine, rhs is set to zero everywhere and it then makes sense that
>>> the returned streamfunction is zero everywhere as well.
>>>
>>> Not sure how to do fix this properly though. Any help would be
>>> appreciated indeed :)
>>>
>>>
>>> ++
>>> JC
>>>
>>>
>>> On 06/28/2018 09:41 PM, nek5000-users at lists.mcs.anl.gov wrote:
>>>> Hi Philipp,
>>>>
>>>> Thanks very much for your comments. Yes, the delta* works only for
>>>> the parallel plate.
>>>>
>>>> The streamfunction computation with the Blasius example is still not
>>>> working. I suspect I am not using the correct mask (vmult /tmult,
>>>> imsh as well).
>>>>
>>>> Using the Blasius example, v1mask, vmult (imsh = 1), I dumped the
>>>> streamfuntion to the temperature field. However, it only contains
>>>> negative values and does not look physical (I pasted userchk below).
>>>>
>>>> Another Nek Example, “mv_wall”, computes the streamfunction from the
>>>> Possison equation using vorticity. It uses tmask, tmult, and imsh = 2.
>>>>
>>>> I tried implementing what was done in the “mv_wall” example in the
>>>> Blasius example, but the computed streamfunction is zero everywhere.
>>>>
>>>> Any ideas what I might be doing wrong?
>>>>
>>>> Any advice would be appreciated!
>>>>
>>>> Thanks again,
>>>>
>>>> Hannah
>>>>
>>>> c-----------------------------------------------------------------------
>>>> subroutine userchk
>>>> include 'SIZE'
>>>> include 'TOTAL'
>>>>
>>>> common /myblas/ ub(lx1,ly1,lz1,lelt),vb(lx1,ly1,lz1,lelt)
>>>>
>>>> common /blasiusr/ u(lx1,ly1,lz1,lelv),v(lx1,ly1,lz1,lelv)
>>>> common /blasiusg/ bin(lx1,ly1,lz1,lelv)
>>>> common /scrns/ dum(lx1*ly1*lz1*lelv)
>>>>
>>>> common /xtream/ psi(lx1*ly1*lz1*lelt)
>>>> $ , rhs(lx1*ly1*lz1*lelt)
>>>> $ , h1 (lx1*ly1*lz1*lelt)
>>>> $ , h2 (lx1*ly1*lz1*lelt)
>>>>
>>>> parameter (lt=lx1*ly1*lz1*lelt)
>>>> common /scrns/ vort(lt,3),w1(lt),w2(lt)
>>>>
>>>> integer bin
>>>> real normu(50),normv(50)
>>>>
>>>> real xmax,xmin,dx
>>>> save xmax,xmin,dx
>>>>
>>>> n = nx1*ny1*nz1*nelv
>>>> ifheat=.false.
>>>> call comp_vort3(vort , w1, w2, vx, vy, vz)
>>>> call copy (t,vort,n) ! Vorticity --> T
>>>> ifto = .true. ! Dump vorticity as T
>>>> c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>>> c Compute streamfunction from vorticity
>>>> call col3 (rhs,t,bm1,n) ! B*omega
>>>> call rone (h1,n)
>>>> call rzero(h2,n)
>>>>
>>>> ifield = 1
>>>> tol = param(22)
>>>> imsh = 1
>>>> call hmholtz('psi ',psi,rhs,h1,h2,v1mask,vmult,imsh,
>>>> $ tol,200,1)
>>>> call copy (t,psi,n) ! Psi --> T (for output)
>>>> c. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>>>
>>>> nfldt = 1 + npscal
>>>>
>>>> if (istep.eq.0) call outpost2(vx,vy,vz,pr,t,nfldt,' ')
>>>>
>>>> do i=1,n
>>>> dum(i) = 1.-vx(i,1,1,1)
>>>> enddo
>>>> tot_deficit = glsc2(dum,bm1,n)
>>>> xmin = glmin(xm1,n)
>>>> xmax = glmax(xm1,n)
>>>> delta_star = tot_deficit/(xmax-xmin)
>>>> tmin = glmin(t,n)
>>>> tmax = glmax(t,n)
>>>> vortmin = glmin(vort,n)
>>>> vortmax = glmax(vort,n)
>>>> if (nid.eq.0) write(6,1) istep,time,delta_star,vortmin,vortmax
>>>> if (nid.eq.0) write(6,1) istep,tmin,tmax
>>>> 1 format(i8,1p4e13.5,' blasius: delta*')
>>>>
>>>> return
>>>> end
>>>> c-----------------------------------------------------------------------
>>>>
>>>>
>>>> ________________________________________
>>>> From: Nek5000-users [nek5000-users-bounces at lists.mcs.anl.gov] on
>>>> behalf of nek5000-users at lists.mcs.anl.gov
>>>> [nek5000-users at lists.mcs.anl.gov]
>>>> Sent: Tuesday, June 26, 2018 1:22 PM
>>>> To: nek5000-users at lists.mcs.anl.gov
>>>> Subject: Re: [Nek5000-users] Stream function
>>>>
>>>> Hi,
>>>> To correctly compute the stream function, the rhs of the Poisson
>>>> equation needs to be the (negative) vorticity. Therefore, the line
>>>>
>>>> call col2(rhs,bm1,n)
>>>>
>>>> is wrong, and should be something like
>>>>
>>>> call col3(rhs, vorticity, bm1, n)
>>>>
>>>> where vorticity should be the computed vorticity using comp_vort.
>>>>
>>>> I guess your calculation of delta* only works for parallel boundary
>>>> layers.
>>>>
>>>> Philipp
>>>>
>>>>
>>>>
>>>> On 2018-06-26 18:35, nek5000-users at lists.mcs.anl.gov wrote:
>>>>> Hi Phillip,
>>>>>
>>>>> I am using the “Blasius” example test outputting the streamfunction
>>>>> as a
>>>>> scalar.
>>>>>
>>>>> I included my code below. I am not sure what I am doing wrong.
>>>>>
>>>>> In userchk, I added “compute streamfunction from vorticity” from the
>>>>> psi_omega example, but it does not compute the psi properly… (max_psi =
>>>>> min_psi = 0 in every step)
>>>>>
>>>>> c-----------------------------------------------------------------------
>>>>>
>>>>>
>>>>> subroutine userchk
>>>>>
>>>>> include 'SIZE'
>>>>>
>>>>> include 'TOTAL'
>>>>>
>>>>> common /myblas/ ub(lx1,ly1,lz1,lelt),vb(lx1,ly1,lz1,lelt)
>>>>>
>>>>> common /blasiusr/ u(lx1,ly1,lz1,lelv),v(lx1,ly1,lz1,lelv)
>>>>>
>>>>> common /blasiusg/ bin(lx1,ly1,lz1,lelv)
>>>>>
>>>>> common /scrns/ dum(lx1*ly1*lz1*lelv)
>>>>>
>>>>> common /xtream/ psi(lx1*ly1*lz1*lelt)
>>>>>
>>>>> $ , rhs(lx1*ly1*lz1*lelt)
>>>>>
>>>>> $ , h1 (lx1*ly1*lz1*lelt)
>>>>>
>>>>> $ , h2 (lx1*ly1*lz1*lelt)
>>>>>
>>>>> integer bin
>>>>>
>>>>> real normu(50),normv(50)
>>>>>
>>>>> real xmax,xmin,dx
>>>>>
>>>>> save xmax,xmin,dx
>>>>>
>>>>> n = nx1*ny1*nz1*nelv
>>>>>
>>>>> c. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>>>>
>>>>> c Compute streamfunction from vorticity
>>>>>
>>>>> call col2(rhs,bm1,n)
>>>>>
>>>>> call rone (h1 ,n)
>>>>>
>>>>> call rzero(h2 ,n)
>>>>>
>>>>> tol = param(22)
>>>>>
>>>>> imsh = 1
>>>>>
>>>>> call hmholtz('psi ',psi,rhs,h1,h2,v1mask,vmult,imsh,tol,200,1)
>>>>>
>>>>> c. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>>>>
>>>>> if (istep.eq.0) call outpost(vx,vy,vz,pr,psi,' ')
>>>>>
>>>>> c Compute delta*
>>>>>
>>>>> do i=1,n
>>>>>
>>>>> dum(i) = 1.-vx(i,1,1,1)
>>>>>
>>>>> enddo
>>>>>
>>>>> tot_deficit = glsc2(dum,bm1,n)
>>>>>
>>>>> xmin = glmin(xm1,n)
>>>>>
>>>>> xmax = glmax(xm1,n)
>>>>>
>>>>> delta_star = tot_deficit/(xmax-xmin)
>>>>>
>>>>> psimin = glmin(psi,n)
>>>>>
>>>>> psimax = glmax(psi,n)
>>>>>
>>>>> if (nid.eq.0) write(6,1) istep,time,delta_star,psimin,psimax
>>>>>
>>>>> 1 format(i8,1p4e13.5,' blasius: delta*')
>>>>>
>>>>> return
>>>>>
>>>>> end
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Nek5000-users mailing list
>>>>> Nek5000-users at lists.mcs.anl.gov
>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>>>
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>>>
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