Re: [Nek5000-users] Compute the derivatives
Hi Michael, iostep dump works only for the dump of quantities specified as T in your .rea like ***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F Since userchk is called every timestep so you'll need something like if (mod(istep,iostep).eq.0) then ... Best, Aleks ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Paul and Aleks, I have a question regarding this. I have implemented this and it is working nicely, however it is dumping out a .f file every step, rather than every iotime step I have specified in the rea. Do you know how to fix this? - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi JC, To dump the computed derivatives into separate field files you can use in userchk ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ... Best, Aleks On Wed, 2 Jun 2010, [email protected] wrote:
dudxyz is somewhat dated and slow...
I recommend somthing like:
parameter (lt=lx1*ly1*lz1*lelv) common /mygrad/ vxx(lt),vxy(lt),vxz(lt) $ , vyx(lt),vyy(lt),vyz(lt) $ , vzx(lt),vzy(lt),vzz(lt)
call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vyy,vyz,vy) call gradm1(vzx,vzy,vzz,vz)
Note that putting these arrays into a common block, as shown, is a good idea for several reasons, one of which is that it guarantees that the data will be byte-aligned with the cache line. On some machines (e.g., BG/P) this is crucial for proper functionality - for this reason we don't mix variable types in a given common block.
If you subsequently wish to access elements of vxx etc. on an element-by-element basis you can of course do something like
parameter (lt=lx1*ly1*lz1) common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) : :
Paul
On Wed, 2 Jun 2010, [email protected] wrote:
Hi Nek's,
I have a home-made global stability code, but in order to use it I first need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. How could one compute these derivatives using Nek 5k and drop them along with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I assume I have to make use of the subroutine *dudxyz (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs.
Regards, JC
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Thanks! I realized shortly after posting that my userchk is called each step, but still wasn't sure how to check if I was "at an iostep". - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:04:41 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Michael, iostep dump works only for the dump of quantities specified as T in your .rea like ***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F Since userchk is called every timestep so you'll need something like if (mod(istep,iostep).eq.0) then ... Best, Aleks ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Paul and Aleks, I have a question regarding this. I have implemented this and it is working nicely, however it is dumping out a .f file every step, rather than every iotime step I have specified in the rea. Do you know how to fix this? - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi JC, To dump the computed derivatives into separate field files you can use in userchk ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ... Best, Aleks On Wed, 2 Jun 2010, [email protected] wrote:
dudxyz is somewhat dated and slow...
I recommend somthing like:
parameter (lt=lx1*ly1*lz1*lelv) common /mygrad/ vxx(lt),vxy(lt),vxz(lt) $ , vyx(lt),vyy(lt),vyz(lt) $ , vzx(lt),vzy(lt),vzz(lt)
call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vyy,vyz,vy) call gradm1(vzx,vzy,vzz,vz)
Note that putting these arrays into a common block, as shown, is a good idea for several reasons, one of which is that it guarantees that the data will be byte-aligned with the cache line. On some machines (e.g., BG/P) this is crucial for proper functionality - for this reason we don't mix variable types in a given common block.
If you subsequently wish to access elements of vxx etc. on an element-by-element basis you can of course do something like
parameter (lt=lx1*ly1*lz1) common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) : :
Paul
On Wed, 2 Jun 2010, [email protected] wrote:
Hi Nek's,
I have a home-made global stability code, but in order to use it I first need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. How could one compute these derivatives using Nek 5k and drop them along with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I assume I have to make use of the subroutine *dudxyz (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs.
Regards, JC
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Aleks, Do I need to include anything in the header, or common block? I added the condition statement, but the simulation quits on the first time step when it calls userchk. - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:04:41 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Michael, iostep dump works only for the dump of quantities specified as T in your .rea like ***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F Since userchk is called every timestep so you'll need something like if (mod(istep,iostep).eq.0) then ... Best, Aleks ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Paul and Aleks, I have a question regarding this. I have implemented this and it is working nicely, however it is dumping out a .f file every step, rather than every iotime step I have specified in the rea. Do you know how to fix this? - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi JC, To dump the computed derivatives into separate field files you can use in userchk ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ... Best, Aleks On Wed, 2 Jun 2010, [email protected] wrote:
dudxyz is somewhat dated and slow...
I recommend somthing like:
parameter (lt=lx1*ly1*lz1*lelv) common /mygrad/ vxx(lt),vxy(lt),vxz(lt) $ , vyx(lt),vyy(lt),vyz(lt) $ , vzx(lt),vzy(lt),vzz(lt)
call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vyy,vyz,vy) call gradm1(vzx,vzy,vzz,vz)
Note that putting these arrays into a common block, as shown, is a good idea for several reasons, one of which is that it guarantees that the data will be byte-aligned with the cache line. On some machines (e.g., BG/P) this is crucial for proper functionality - for this reason we don't mix variable types in a given common block.
If you subsequently wish to access elements of vxx etc. on an element-by-element basis you can of course do something like
parameter (lt=lx1*ly1*lz1) common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) : :
Paul
On Wed, 2 Jun 2010, [email protected] wrote:
Hi Nek's,
I have a home-made global stability code, but in order to use it I first need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. How could one compute these derivatives using Nek 5k and drop them along with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I assume I have to make use of the subroutine *dudxyz (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs.
Regards, JC
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I think I see the issue, my iostep is set to zero because my iotime is 0.01. Is there a way to check the time directly, and compare it to the iotime, rather than comparing the steps to iostep? ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:25:35 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Aleks, Do I need to include anything in the header, or common block? I added the condition statement, but the simulation quits on the first time step when it calls userchk. - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:04:41 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Michael, iostep dump works only for the dump of quantities specified as T in your .rea like ***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F Since userchk is called every timestep so you'll need something like if (mod(istep,iostep).eq.0) then ... Best, Aleks ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Paul and Aleks, I have a question regarding this. I have implemented this and it is working nicely, however it is dumping out a .f file every step, rather than every iotime step I have specified in the rea. Do you know how to fix this? - Michael ----- Original Message ----- From: [email protected] To: [email protected] Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi JC, To dump the computed derivatives into separate field files you can use in userchk ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ... Best, Aleks On Wed, 2 Jun 2010, [email protected] wrote:
dudxyz is somewhat dated and slow...
I recommend somthing like:
parameter (lt=lx1*ly1*lz1*lelv) common /mygrad/ vxx(lt),vxy(lt),vxz(lt) $ , vyx(lt),vyy(lt),vyz(lt) $ , vzx(lt),vzy(lt),vzz(lt)
call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vyy,vyz,vy) call gradm1(vzx,vzy,vzz,vz)
Note that putting these arrays into a common block, as shown, is a good idea for several reasons, one of which is that it guarantees that the data will be byte-aligned with the cache line. On some machines (e.g., BG/P) this is crucial for proper functionality - for this reason we don't mix variable types in a given common block.
If you subsequently wish to access elements of vxx etc. on an element-by-element basis you can of course do something like
parameter (lt=lx1*ly1*lz1) common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) : :
Paul
On Wed, 2 Jun 2010, [email protected] wrote:
Hi Nek's,
I have a home-made global stability code, but in order to use it I first need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. How could one compute these derivatives using Nek 5k and drop them along with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I assume I have to make use of the subroutine *dudxyz (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs.
Regards, JC
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Michael, time is "time" --- so you can trigger that way if you prefer it to iostep/istep. Paul On Thu, 1 Jul 2010, [email protected] wrote:
I think I see the issue, my iostep is set to zero because my iotime is 0.01. Is there a way to check the time directly, and compare it to the iotime, rather than comparing the steps to iostep?
----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:25:35 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives
Aleks,
Do I need to include anything in the header, or common block? I added the condition statement, but the simulation quits on the first time step when it calls userchk.
- Michael
----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 8:04:41 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives
Hi Michael,
iostep dump works only for the dump of quantities specified as T in your .rea like
***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F
Since userchk is called every timestep so you'll need something like
if (mod(istep,iostep).eq.0) then ...
Best, Aleks
----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives
Hi Paul and Aleks,
I have a question regarding this. I have implemented this and it is working nicely, however it is dumping
out a .f file every step, rather than every iotime step I have specified in the rea.
Do you know how to fix this?
- Michael
----- Original Message ----- From: [email protected] To: [email protected] Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives
Hi JC,
To dump the computed derivatives into separate field files you can use in userchk
ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ...
Best, Aleks
On Wed, 2 Jun 2010, [email protected] wrote:
dudxyz is somewhat dated and slow...
I recommend somthing like:
parameter (lt=lx1*ly1*lz1*lelv) common /mygrad/ vxx(lt),vxy(lt),vxz(lt) $ , vyx(lt),vyy(lt),vyz(lt) $ , vzx(lt),vzy(lt),vzz(lt)
call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vyy,vyz,vy) call gradm1(vzx,vzy,vzz,vz)
Note that putting these arrays into a common block, as shown, is a good idea for several reasons, one of which is that it guarantees that the data will be byte-aligned with the cache line. On some machines (e.g., BG/P) this is crucial for proper functionality - for this reason we don't mix variable types in a given common block.
If you subsequently wish to access elements of vxx etc. on an element-by-element basis you can of course do something like
parameter (lt=lx1*ly1*lz1) common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) : :
Paul
On Wed, 2 Jun 2010, [email protected] wrote:
Hi Nek's,
I have a home-made global stability code, but in order to use it I first need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. How could one compute these derivatives using Nek 5k and drop them along with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I assume I have to make use of the subroutine *dudxyz (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs.
Regards, JC
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Hi all, Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ? thank you all francesco
Franceso, we just store the velocity, temperature and pressure and not the gradients. Also, we construct the time derivates based on field of interest and do not store them. hth, Stefan ----- Original Message ----- From: [email protected] To: [email protected] Sent: Thursday, November 25, 2010 7:36:10 PM Subject: [Nek5000-users] T and P derivatives Hi all, Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ? thank you all francesco _______________________________________________ Nek5000-users mailing list [email protected] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
Hi Francesco, Don't waste too much time looking - we're happy to answer! As Stefan commented, we don't store the gradients, we just compute them. Typical usage would be subroutine userchk include 'SIZE' include 'TOTAL' common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) $ , px(lx1*ly1,lz1*lelt) $ , py(lx1*ly1,lz1*lelt) $ , pz(lx1*ly1,lz1*lelt) call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz) if (lx2.ne.lx1) then ! use something different for mesh 2 call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pr) else call gradm1(px,py,pz,pr) endif --- Paul On Thu, 25 Nov 2010, [email protected] wrote:
Hi all,
Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ?
thank you all
francesco
PS ... slight bug in what I sent... Should read:
call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pm1)
On Fri, 26 Nov 2010, [email protected] wrote:
Hi Francesco,
Don't waste too much time looking - we're happy to answer!
As Stefan commented, we don't store the gradients, we just compute them. Typical usage would be
subroutine userchk include 'SIZE' include 'TOTAL' common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) $ , px(lx1*ly1,lz1*lelt) $ , py(lx1*ly1,lz1*lelt) $ , pz(lx1*ly1,lz1*lelt)
call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz)
if (lx2.ne.lx1) then ! use something different for mesh 2 call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pr) else call gradm1(px,py,pz,pr) endif
--- Paul
On Thu, 25 Nov 2010, [email protected] wrote:
Hi all,
Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ?
thank you all
francesco
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thank you, i was just hoping to save same operations. francesco On 11/26/2010 03:48 PM, [email protected] wrote:
PS ... slight bug in what I sent... Should read:
call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pm1)
On Fri, 26 Nov 2010, [email protected] wrote:
Hi Francesco,
Don't waste too much time looking - we're happy to answer!
As Stefan commented, we don't store the gradients, we just compute them. Typical usage would be
subroutine userchk include 'SIZE' include 'TOTAL' common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) $ , px(lx1*ly1,lz1*lelt) $ , py(lx1*ly1,lz1*lelt) $ , pz(lx1*ly1,lz1*lelt)
call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz)
if (lx2.ne.lx1) then ! use something different for mesh 2 call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pr) else call gradm1(px,py,pz,pr) endif
--- Paul
On Thu, 25 Nov 2010, [email protected] wrote:
Hi all,
Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ?
thank you all
francesco
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