How to extract the data of all cells in the domain

openfoamer93 · May 7, 2020, 15:06

Hi

It is a simple question. Suppose that we have a 2D domain
That consists of 9 cells for example (imagine a square of 9 cells)

Then I want to extract the data of the temperature field at each cell and the corresponding data of another field (say mixture fraction Z) in that way I have the full data of each cell in terms of (Tcell,Zcell)

How to do this?

HPE · May 7, 2020, 18:36

I am not sure if I understood your question, so my apologies.

Information within a numerical domain can be interrogated by many means in OpenFOAM: e.g. sample, and probe utilities. Please do search them.

openfoamer93 · May 7, 2020, 20:59

Amazing that really worked. To extract the whole information of the field in a mesh: select > filter > data analysis > probe location > press ok whatever the settings are > then chang the tab "showing" and select your mesh. Finally, save in a csv file.

All the best

zhangyan · May 8, 2020, 04:44

If I correctly understand your demand, there is a utility to deal with such things in my GitHub:
https://github.com/ZhangYanTJU/foam2Columns
It supports any number of fields and transforms them to this format:

Code:

L1: x y z var1 var2 ...
L2: x y z var1 var2 ...
.
.
.
Ln: x y z var1 var2 ...

where n is the cell number, and var1(p), var2(T) are the input variables:

Code:

foam2Columns -fields "(p T)"

openfoamer93 · May 8, 2020, 23:08

Quote:

Originally Posted by zhangyan

If I correctly understand your demand, there is a utility to deal with such things in my GitHub:
https://github.com/ZhangYanTJU/foam2Columns
It supports any number of fields and transforms them to this format:

Code:

L1: x y z var1 var2 ...
L2: x y z var1 var2 ...
.
.
.
Ln: x y z var1 var2 ...

where n is the cell number, and var1(p), var2(T) are the input variables:

Code:

foam2Columns -fields "(p T)"

What an elegant function is this! That exactly what I meant. Also, this function does more than I need which it also specifies the location x y z. The method I mentioned in my comment also works but it is not as easy as this function! So awesome, I will give it a try for sure 👌🏻

openfoamer93 · May 8, 2020, 23:10

That is why I like OpenFOAM. The room for improvement is endless! And collaboration is very effective in the scientific community 🙏

kerim · May 13, 2020, 14:08

Dear zhangyan,
I downloaded foam2Columns into home/run folder. After unzipping and compiling I used it for dambreak case. Using the foam2Columns -fields "(p_rgh)" gives me all info that was proposed. But the execution of the foam2Columns -fields "(alfa.water)" gives nothing.
In another words everything is fine for p_rgh? not for alfa.water. I am using openfoam 7 on ubuntu 16.04 LTS
Any kind of help is highly appreciated.
Kerim

zhangyan · May 14, 2020, 06:17

Quote:

Originally Posted by kerim

Dear zhangyan,
I downloaded foam2Columns into home/run folder. After unzipping and compiling I used it for dambreak case. Using the foam2Columns -fields "(p_rgh)" gives me all info that was proposed. But the execution of the foam2Columns -fields "(alfa.water)" gives nothing.
In another words everything is fine for p_rgh? not for alfa.water. I am using openfoam 7 on ubuntu 16.04 LTS
Any kind of help is highly appreciated.
Kerim

Dear Kerim,
1. Did you type it right? Isn't it alpha.water?
2. Now the foam2Cloumns tool only supports for volScalarField. Is alpha.water a volScalarField?

kerim · May 14, 2020, 11:54

Quote:

Originally Posted by zhangyan

Dear Kerim,
1. Did you type it right? Isn't it alpha.water?
2. Now the foam2Cloumns tool only supports for volScalarField. Is alpha.water a volScalarField?

Dear zhangyan,
1. Yes I did it right.

2. alfa.water is volScalarField.

By the way, after execution of the command

foam2Columns -fields "(alfa.water)" in the terminal I got a file alphaPhi0.water. But it is not that file I am looking for. Frakly speaking I don't understand what kind of file I got.

Please see attachments for more information.
Kerim

alfa.water.jpg

alfa.water1.jpg

alfa.water2.jpg

alphaPhi0.water.jpg

p_rgh.jpg

kerim · May 14, 2020, 12:23

Dear zhangyan,

I just used foam2Cloumns tool for bouyantCavity case which uses buoyantSimpleFoam solver. Direct application of foam2Cloumns tool gives an error
keyword PIMPLE is undefined in dictionary "/home/kerim/run/buoyantCavity/system/fvSolution".

As you know buoyantSimpleFoam solver use only SIMPLE, not PIMPLE.

After changing SIMPLE to PIMPLE I got foam2Columns_p_T file. That is what I was looking for.
Could you explain me why do I have above mentioned error?
Kerim
bouyantCavity-1.jpg

bouyanCavity-2.jpg

zhangyan · May 14, 2020, 18:53

Quote:

Originally Posted by kerim

Dear zhangyan,
1. Yes I did it right.

2. alfa.water is volScalarField.

By the way, after execution of the command

foam2Columns -fields "(alfa.water)" in the terminal I got a file alphaPhi0.water. But it is not that file I am looking for. Frakly speaking I don't understand what kind of file I got.

Please see attachments for more information.
Kerim

Attachment 77624

Attachment 77625

Attachment 77626

Attachment 77627

Attachment 77628

In the first picture, you inout alfa.water
But I found it from the last picture, at 0.5 s, you only got alpha.water.
I don't know why you want to try alfa.water.

zhangyan · May 14, 2020, 18:54

Quote:

Originally Posted by kerim

Dear zhangyan,

I just used foam2Cloumns tool for bouyantCavity case which uses buoyantSimpleFoam solver. Direct application of foam2Cloumns tool gives an error
keyword PIMPLE is undefined in dictionary "/home/kerim/run/buoyantCavity/system/fvSolution".

As you know buoyantSimpleFoam solver use only SIMPLE, not PIMPLE.

After changing SIMPLE to PIMPLE I got foam2Columns_p_T file. That is what I was looking for.
Could you explain me why do I have above mentioned error?
Kerim
Attachment 77629

Attachment 77630

Thank you for pointing this out.
It will give me a chance to improve this tool.
I'll check it soon.

olesen · May 14, 2020, 19:57

Quote:

Originally Posted by zhangyan

If I correctly understand your demand, there is a utility to deal with such things in my GitHub:
https://github.com/ZhangYanTJU/foam2Columns
It supports any number of fields and transforms them to this format:
[CODE]
L1: x y z var1 var2 ...
L2: x y z var1 var2 ...

Looks nice. Dealing with the proper sorting (in parallel) tends to be a bit of a memory hog. If you are interested, you might take a look at the cellCentreSet. It should do something similar with run-time selectable output format.

https://www.openfoam.com/documentati...t.html#details

kerim · May 15, 2020, 01:25

Quote:

Originally Posted by zhangyan

In the first picture, you inout alfa.water
But I found it from the last picture, at 0.5 s, you only got alpha.water.
I don't know why you want to try alfa.water.

Dear Zhangyan,

Alfa.water helps to determine the position of free surface between two fluids - water and air. The value of alfa.water=.05 represents free surface and that is why I need to extract from OpenFOAM alfa.water by using foam2Columns tool.
Kerim

kerim · May 15, 2020, 01:28

Quote:

Originally Posted by zhangyan

Thank you for pointing this out.
It will give me a chance to improve this tool.
I'll check it soon.

Dear Zangyan,

Thank you very much for your post.
I look forward to hear from you.
Kerim

zhangyan · May 15, 2020, 05:09

Quote:

Originally Posted by kerim

Dear Zhangyan,

Alfa.water helps to determine the position of free surface between two fluids - water and air. The value of alfa.water=.05 represents free surface and that is why I need to extract from OpenFOAM alfa.water by using foam2Columns tool.
Kerim

Maybe you can try:

Code:

foam2Columns -fields "(alpha.water)

alpha instead of alfa

kerim · May 15, 2020, 06:47

Quote:

Originally Posted by zhangyan

Maybe you can try:

Code:

foam2Columns -fields "(alpha.water)

alpha instead of alfa

Dear Zhangyan,

Right now I have reinstalled ubuntu 16.04.6 LTS 64 bit, OpenFoam 7 and foam2Columns. Than I copied alpha.water from 0 folder and pasted in terminal. After execution of the command foam2Columns -fields "(alpha.water)" I got foam2Columns_alpha.water file I was looking for.

Frankly speaking I don't understand of the reason of my previous mistakes.

Now everything is OK with foam2Columns tool. Please see the attached figures.

Thanks a lot to you. Your help is highly appreciated.
It will be great to expand foam2Columns for volVectorField quantity like velocity.
Kerim

alpha.water-1.jpg

alpha.water-2.jpg

alpha.water-3.jpg

alpha.water-4.jpg

picture-wmake.jpg

zhangyan · September 8, 2020, 13:47

Hi,
Now it supports for volVectorField!
https://github.com/ZhangYanTJU/foam2Columns

Quote:

Originally Posted by kerim

Dear Zhangyan,

Right now I have reinstalled ubuntu 16.04.6 LTS 64 bit, OpenFoam 7 and foam2Columns. Than I copied alpha.water from 0 folder and pasted in terminal. After execution of the command foam2Columns -fields "(alpha.water)" I got foam2Columns_alpha.water file I was looking for.

Frankly speaking I don't understand of the reason of my previous mistakes.

Now everything is OK with foam2Columns tool. Please see the attached figures.

Thanks a lot to you. Your help is highly appreciated.
It will be great to expand foam2Columns for volVectorField quantity like velocity.
Kerim

Attachment 77658

Attachment 77659

Attachment 77660

Attachment 77661

Attachment 77662

kerim · September 9, 2020, 02:23

Quote:

Originally Posted by zhangyan

Hi,
Now it supports for volVectorField!
https://github.com/ZhangYanTJU/foam2Columns

Dear zhangyan

Thanks a lot to you. Your help will be highly appreciated bythe OpenFOAM community.

Bodo1993 · November 19, 2020, 23:21

Quote:

Originally Posted by zhangyan

Hi,
Now it supports for volVectorField!
https://github.com/ZhangYanTJU/foam2Columns

Hi zhangyan,
I am wondering if foam2Columns works for OpenFOAM v6. I tried to compile the code with wmake but I got the below error.

Code:

Making dependency list for source file foam2Columns.C
g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam6/src/finiteVolume/lnInclude -I/opt/openfoam6/src/meshTools/lnInclude -I/opt/openfoam6/src/sampling/lnInclude -I/opt/openfoam6/src/lagrangian/basic/lnInclude -IlnInclude -I. -I/opt/openfoam6/src/OpenFOAM/lnInclude -I/opt/openfoam6/src/OSspecific/POSIX/lnInclude   -fPIC -c foam2Columns.C -o Make/linux64GccDPInt32Opt/foam2Columns.o
foam2Columns.C: In function ‘int main(int, char**)’:
foam2Columns.C:109:21: error: ‘fileType’ has not been declared
                     fileType::directory
                     ^~~~~~~~
/opt/openfoam6/wmake/rules/General/transform:25: recipe for target 'Make/linux64GccDPInt32Opt/foam2Columns.o' failed
make: *** [Make/linux64GccDPInt32Opt/foam2Columns.o] Error 1

May 7, 2020, 15:06	How to extract the data of all cells in the domain	#1
openfoamer93 New Member Bssam Join Date: Nov 2019 Posts: 14 Rep Power: 3	Hi It is a simple question. Suppose that we have a 2D domain That consists of 9 cells for example (imagine a square of 9 cells) Then I want to extract the data of the temperature field at each cell and the corresponding data of another field (say mixture fraction Z) in that way I have the full data of each cell in terms of (Tcell,Zcell) How to do this?

May 7, 2020, 18:36		#2
HPE Senior Member Herpes Free Engineer Join Date: Sep 2019 Location: The Home Under The Ground with the Lost Boys Posts: 688 Rep Power: 8	I am not sure if I understood your question, so my apologies. Information within a numerical domain can be interrogated by many means in OpenFOAM: e.g. sample, and probe utilities. Please do search them. __________________ The OpenFOAM community is the biggest contributor to OpenFOAM: User guide/Wiki-1/Wiki-2/Code guide/Code Wiki Nilsson/Guerrero/Holzinger/Holzmann/Nagy/Santos/Nozaki/Jasak-FSB OpenFOAM Governance and Technical Committees Report bugs/Request features: OpenFOAM (ESI-OpenCFD-Trademark) Report bugs/Request features: FOAM-Extend (Wikki-FSB) Report bugs: OpenFOAM.org How to create a MWE. OF Journal OFv2012

May 8, 2020, 04:44		#4
zhangyan Senior Member Yan Zhang Join Date: May 2014 Posts: 116 Rep Power: 8	If I correctly understand your demand, there is a utility to deal with such things in my GitHub: https://github.com/ZhangYanTJU/foam2Columns It supports any number of fields and transforms them to this format: Code: L1: x y z var1 var2 ... L2: x y z var1 var2 ... . . . Ln: x y z var1 var2 ... where n is the cell number, and var1(p), var2(T) are the input variables: Code: foam2Columns -fields "(p T)" HPE, openfoamer93 and Tobermory like this. __________________ https://openfoam.top

May 13, 2020, 14:08	How to extract the data of all cells in the domain	#7
kerim Member abdikerim kurbanaliev Join Date: Jun 2010 Location: Kyrgyzstan, Osh Posts: 75 Rep Power: 12	Dear zhangyan, I downloaded foam2Columns into home/run folder. After unzipping and compiling I used it for dambreak case. Using the foam2Columns -fields "(p_rgh)" gives me all info that was proposed. But the execution of the foam2Columns -fields "(alfa.water)" gives nothing. In another words everything is fine for p_rgh? not for alfa.water. I am using openfoam 7 on ubuntu 16.04 LTS Any kind of help is highly appreciated. Kerim

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May 7, 2020, 20:59		#3
openfoamer93 New Member Bssam Join Date: Nov 2019 Posts: 14 Rep Power: 3	Amazing that really worked. To extract the whole information of the field in a mesh: select > filter > data analysis > probe location > press ok whatever the settings are > then chang the tab "showing" and select your mesh. Finally, save in a csv file. All the best

May 8, 2020, 23:10		#6
openfoamer93 New Member Bssam Join Date: Nov 2019 Posts: 14 Rep Power: 3	That is why I like OpenFOAM. The room for improvement is endless! And collaboration is very effective in the scientific community 🙏

May 14, 2020, 12:23		#10
kerim Member abdikerim kurbanaliev Join Date: Jun 2010 Location: Kyrgyzstan, Osh Posts: 75 Rep Power: 12	Dear zhangyan, I just used foam2Cloumns tool for bouyantCavity case which uses buoyantSimpleFoam solver. Direct application of foam2Cloumns tool gives an error keyword PIMPLE is undefined in dictionary "/home/kerim/run/buoyantCavity/system/fvSolution". As you know buoyantSimpleFoam solver use only SIMPLE, not PIMPLE. After changing SIMPLE to PIMPLE I got foam2Columns_p_T file. That is what I was looking for. Could you explain me why do I have above mentioned error? Kerim bouyantCavity-1.jpg bouyanCavity-2.jpg

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