[FLASH-USERS] Question about resistivity varying in space

John Zuhone jzuhone at gmail.com
Tue Nov 14 12:12:25 EST 2023 

Ah, you don’t have the blockID, I see now. That’s unfortunate. 

> On Nov 14, 2023, at 12:11 PM, John Zuhone <jzuhone at gmail.com> wrote:
> 
> Adam,
> 
> Sorry, a bit confused—is Grid_getCellCoords not part of the public interface? If so, you can call it from any other module, and get the cell coords that way.  
> 
> John
> 
>> On Nov 14, 2023, at 12:10 PM, Reyes, Adam <adam.reyes at rochester.edu> wrote:
>> 
>> Unfortunately  the MagneticResistivity interface doesn’t pass any information about the grid, blockID or otherwise, only the UNK array at a single cell.
>> 
>> Since the cell coordinates vary linearly I think the AMR prolongation should take care of the case of mesh refinement.
>> *********************************************
>> Adam Reyes
>> 
>> <FLASH.jpg>
>> Code Group Leader, Flash Center for Computational Science  
>> Research Scientist, Dept. of Physics and Astronomy
>> University of Rochester
>> River Campus: Bausch and Lomb Hall, 369  
>> 500 Wilson Blvd. PO Box 270171, Rochester, NY 14627
>> Email adam.reyes at rochester.edu
>> Web https://flash.rochester.edu
>>  (he / him / his)
>> <FLASH-pride-sml.png>
>> 
>> *********************************************
>> 
>> 
>> 
>>> On Nov 14, 2023, at 6:01 PM, John Zuhone <jzuhone at gmail.com> wrote:
>>> 
>>> The solution to put the coordinates in variables is overkill, using up memory, and doesn’t work if you only do it in Simulation_initBlock and then the mesh refines later. 
>>> 
>>> You need to use Grid_getCellCoords, which has a public interface and can be called from the MagneticResistivity unit:
>>> 
>>> use Grid_interface, ONLY: Grid_getCellCoords, Grid_getBlkIndexLimits
>>> 
>>> #include "Flash.h"
>>> 
>>> logical :: gcell = .true. ! True if you need the guardcells, false if not
>>> real :: size(3)
>>> real, dimension(:), allocatable :: xc, yc, zc
>>> integer, dimension(LOW:HIGH,MDIM) :: blkLimits,blkLimitsGC
>>> 
>>> ! for a given blockId: 
>>> 
>>> call Grid_getBlkIndexLimits(blockID,blkLimits,blkLimitsGC)
>>> 
>>> if (gcell) then
>>>   size(1) = blkLimitsGC(HIGH,IAXIS) - blkLimitsGC(LOW,IAXIS) + 1
>>>   size(2) = blkLimitsGC(HIGH,JAXIS) - blkLimitsGC(LOW,JAXIS) + 1
>>>   size(3) = blkLimitsGC(HIGH,KAXIS) - blkLimitsGC(LOW,KAXIS) + 1
>>> else
>>>   size(1) = blkLimits(HIGH,IAXIS) - blkLimits(LOW,IAXIS) + 1
>>>   size(2) = blkLimits(HIGH,JAXIS) - blkLimits(LOW,JAXIS) + 1
>>>   size(3) = blkLimits(HIGH,KAXIS) - blkLimits(LOW,KAXIS) + 1
>>> endif
>>> 
>>> call Grid_getCellCoords(KAXIS, blockId, CENTER, gcell, zc, size(3))
>>> call Grid_getCellCoords(JAXIS, blockId, CENTER, gcell, yc, size(2))
>>> call Grid_getCellCoords(IAXIS, blockId, CENTER, gcell, xc, size(1))
>>> 
>>> The xc, yc, zc now contain the cell coordinates for the block. 
>>> 
>>> 
>>>> On Nov 14, 2023, at 11:29 AM, Leland Ellison <lee at pacificfusion.energy> wrote:
>>>> 
>>>> Hi Ernesto,
>>>> 
>>>> To make a custom magnetic resistivity model that depends on spatial coordinates, I'd do this by customizing the MagneticResitivity_fullState.f90 file in your problem directory. Notice that the fullState version gets passed in the full vector of unknowns and not just the density and temperature. If you look carefully at e.g. diff_advanceMag, it's actually calling the fullState version by passing in the solnVec so this is the one you want to customize. Next, as you noticed, you don't typically have the spatial coordinates available in your solnVec, but it's quite straightforward to add them. For instance, you can add:
>>>> 
>>>> VARIABLE XCTR
>>>> VARIABLE YCTR
>>>> VARIABLE ZCTR 
>>>> 
>>>> in the Config file for your problem, and then in your Simulation_initBlock you can populate these mesh variables with cell centered coordinates, e.g.:
>>>> 
>>>> ! inside your i,j,k mesh loop after you've fetched the spatial coordinates
>>>> #ifdef XCTR_VAR
>>>>         solnData(XCTR_VAR, i,j,k) = xCoord(i)
>>>> #endif
>>>> 
>>>> Then these coordinates will be present in your solnVec for use inside of your customized MagneticResistivity_fullState routine. 
>>>> 
>>>> Hope this helps!
>>>> Lee
>>>> 
>>>> ________________
>>>> Leland Ellison PhD
>>>> 
>>>> 
>>>> On Tue, Nov 14, 2023 at 7:56 AM Ernesto Zurbriggen <ezurbriggen at unc.edu.ar <mailto:ezurbriggen at unc.edu.ar>> wrote:
>>>>> Hi all! 
>>>>> I'm carrying out some single fluid resistive MHD runs with constant resistivity using the /MagneticResistivity/MagneticResistivityMain/Constant unit. 
>>>>> Now I would like to implement a spatially dependent resistivity, but I'm not sure which is the easiest way without modifying different subroutines in different units.  
>>>>> 
>>>>> The optimal implementation would be to create a new unit that keeps the structure of the /MagneticResistivity/MagneticResistivityMain/Constant unit, 
>>>>> so I didn't have to change anything else in other units. But the problem with this idea is that the MagneticResistivity subroutine, 
>>>>> which calculates the resistivity, has no notion of spatial coordinates. And to provide this subroutine with the spatial coordinates doesn't seem obvious. 
>>>>> 
>>>>> Another possibility might be to save the resistivity in a scratchcenter variable, but in this case I couldn't take advantage of the structure of the /MagneticResistivity/MagneticResistivityMain/Constant unit. 
>>>>> 
>>>>> Any ideas or suggestions will be appreciated!
>>>>> 
>>>>> Thanks in advance! 
>>>>> 
>>>>> --
>>>>> PhD Ernesto Zurbriggen,
>>>>> Assistant researcher (CONICET)
>>>>> Email: ezurbriggen@ <mailto:ernesto.zurbriggen at craam.mackenzie.br>unc.edu.ar <http://unc.edu.ar/>
>>>>> IP phone: (+54) 351-535 3776 (int. 75601)
>>>>> 
>>>>> Instituto de Astronomía Teórica y Experimental (IATE-CONICET), 
>>>>> Francisco Laprida sth 922, X5000BGR, Córdoba, Argentina. 
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>>>>> 
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