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Old   May 8, 2013, 15:39
Default Residual plot for OpenFOAM-ext problem.
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Sangeeta
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Hello everyone,

I am using OpenFOAM-ext for the stressAnalysis problem. I have successfully used Residual script to plot gnuplot in OpenFOAM1.7.1. I have made changes in the Residual script based on OpenFAOM-ext log file but it is showing some error.

Following is the log file in my case:

Time: 1

Time 1, Corrector 0, Solving for U using DICPCG, residual = 1, relative residual = 59362.4

Time 1, Solving for U, Initial residual = 1, Final residual = 1, Relative residual = 59362.4, No outer iterations 1
ExecutionTime = 26.44 s ClockTime = 27 s
ExecutionTime = 26.6 s


Time: 2

Time 2, Corrector 0, Solving for U using DICPCG, residual = 1, relative residual = 1

Time 2, Solving for U, Initial residual = 1, Final residual = 1, Relative residual = 1, No outer iterations 1
ExecutionTime = 37.93 s ClockTime = 38 s
ExecutionTime = 38.12 s


Time: 3

Time 3, Corrector 0, Solving for U using DICPCG, residual = 0.305633, relative residual = 1

Time 3, Solving for U, Initial residual = 0.305633, Final residual = 0.305633, Relative residual = 1, No outer iterations 1
ExecutionTime = 54.7 s ClockTime = 55 s
ExecutionTime = 54.9 s


Time: 4

Time 4, Corrector 0, Solving for U using DICPCG, residual = 0.229696, relative residual = 1

Time 4, Solving for U, Initial residual = 0.229696, Final residual = 0.229696, Relative residual = 1, No outer iterations 1
ExecutionTime = 66.4 s ClockTime = 67 s
ExecutionTime = 66.59 s


Time: 5

Time 5, Corrector 0, Solving for U using DICPCG, residual = 0.155004, relative residual = 1

Time 5, Solving for U, Initial residual = 0.155004, Final residual = 0.155004, Relative residual = 1, No outer iterations 1
ExecutionTime = 83.12 s ClockTime = 83 s
ExecutionTime = 83.3 s


Time: 6

Time 6, Corrector 0, Solving for U using DICPCG, residual = 0.088822, relative residual = 1

Time 6, Solving for U, Initial residual = 0.088822, Final residual = 0.088822, Relative residual = 1, No outer iterations 1
ExecutionTime = 96.02 s ClockTime = 96 s
ExecutionTime = 96.21 s


Time: 7

Time 7, Corrector 0, Solving for U using DICPCG, residual = 0.0763407, relative residual = 1

Time 7, Solving for U, Initial residual = 0.0763407, Final residual = 0.0763407, Relative residual = 1, No outer iterations 1
ExecutionTime = 109.27 s ClockTime = 110 s
ExecutionTime = 109.45 s


Time: 8

Time 8, Corrector 0, Solving for U using DICPCG, residual = 0.0426613, relative residual = 1

Time 8, Solving for U, Initial residual = 0.0426613, Final residual = 0.0426613, Relative residual = 1, No outer iterations 1
ExecutionTime = 121.37 s ClockTime = 122 s
ExecutionTime = 121.57 s


The script I am using to plot gnuplot is:

set terminal png
set output "filename.png"

set logscale y
set title "Residuals"
set ylabel 'Residual'
set xlabel 'Time'
cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
pause 1
reread


It is showing following error:

cat log | grep 'Solving for U' | cut -d' ' -f9
^
"Residuals", line 8: invalid command

sangeeta@sangeeta-laptop:~/Desktop/plateHole0.0001stress$ gnuplot Residuals

cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'Ux' with lines"
^
"Residuals", line 8: invalid command

sangeeta@sangeeta-laptop:~/Desktop/plateHole0.0001stress$ gnuplot Residuals

cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'Ux' with lines"
^
"Residuals", line 8: invalid command


Am I using wrong script? Can anyone explain how I can change the script to plot residual gnuplot based on log file (which I have mentioned above)?

Best regards,
Sangeeta
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Old   May 9, 2013, 04:47
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Quote:
Originally Posted by Sargam05 View Post
Hello everyone,

I am using OpenFOAM-ext for the stressAnalysis problem. I have successfully used Residual script to plot gnuplot in OpenFOAM1.7.1. I have made changes in the Residual script based on OpenFAOM-ext log file but it is showing some error.

Following is the log file in my case:

Time: 1

Time 1, Corrector 0, Solving for U using DICPCG, residual = 1, relative residual = 59362.4

Time 1, Solving for U, Initial residual = 1, Final residual = 1, Relative residual = 59362.4, No outer iterations 1
ExecutionTime = 26.44 s ClockTime = 27 s
ExecutionTime = 26.6 s


Time: 2

Time 2, Corrector 0, Solving for U using DICPCG, residual = 1, relative residual = 1

Time 2, Solving for U, Initial residual = 1, Final residual = 1, Relative residual = 1, No outer iterations 1
ExecutionTime = 37.93 s ClockTime = 38 s
ExecutionTime = 38.12 s


Time: 3

Time 3, Corrector 0, Solving for U using DICPCG, residual = 0.305633, relative residual = 1

Time 3, Solving for U, Initial residual = 0.305633, Final residual = 0.305633, Relative residual = 1, No outer iterations 1
ExecutionTime = 54.7 s ClockTime = 55 s
ExecutionTime = 54.9 s


Time: 4

Time 4, Corrector 0, Solving for U using DICPCG, residual = 0.229696, relative residual = 1

Time 4, Solving for U, Initial residual = 0.229696, Final residual = 0.229696, Relative residual = 1, No outer iterations 1
ExecutionTime = 66.4 s ClockTime = 67 s
ExecutionTime = 66.59 s


Time: 5

Time 5, Corrector 0, Solving for U using DICPCG, residual = 0.155004, relative residual = 1

Time 5, Solving for U, Initial residual = 0.155004, Final residual = 0.155004, Relative residual = 1, No outer iterations 1
ExecutionTime = 83.12 s ClockTime = 83 s
ExecutionTime = 83.3 s


Time: 6

Time 6, Corrector 0, Solving for U using DICPCG, residual = 0.088822, relative residual = 1

Time 6, Solving for U, Initial residual = 0.088822, Final residual = 0.088822, Relative residual = 1, No outer iterations 1
ExecutionTime = 96.02 s ClockTime = 96 s
ExecutionTime = 96.21 s


Time: 7

Time 7, Corrector 0, Solving for U using DICPCG, residual = 0.0763407, relative residual = 1

Time 7, Solving for U, Initial residual = 0.0763407, Final residual = 0.0763407, Relative residual = 1, No outer iterations 1
ExecutionTime = 109.27 s ClockTime = 110 s
ExecutionTime = 109.45 s


Time: 8

Time 8, Corrector 0, Solving for U using DICPCG, residual = 0.0426613, relative residual = 1

Time 8, Solving for U, Initial residual = 0.0426613, Final residual = 0.0426613, Relative residual = 1, No outer iterations 1
ExecutionTime = 121.37 s ClockTime = 122 s
ExecutionTime = 121.57 s


The script I am using to plot gnuplot is:

set terminal png
set output "filename.png"

set logscale y
set title "Residuals"
set ylabel 'Residual'
set xlabel 'Time'
cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
pause 1
reread


It is showing following error:

cat log | grep 'Solving for U' | cut -d' ' -f9
^
"Residuals", line 8: invalid command

sangeeta@sangeeta-laptop:~/Desktop/plateHole0.0001stress$ gnuplot Residuals

cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'Ux' with lines"
^
"Residuals", line 8: invalid command

sangeeta@sangeeta-laptop:~/Desktop/plateHole0.0001stress$ gnuplot Residuals

cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'Ux' with lines"
^
"Residuals", line 8: invalid command


Am I using wrong script? Can anyone explain how I can change the script to plot residual gnuplot based on log file (which I have mentioned above)?

Best regards,
Sangeeta
You missed to use the keywords: plot "< before your command.
plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines

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Old   May 9, 2013, 04:55
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Also, refer the following page:

Tutorial of how to plot residuals !
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Old   May 9, 2013, 14:53
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Hi Tushar,

Thank so much for the inputs. I have used "plot" as you suggested:

set terminal png
set output "filename.png"
set logscale y
set title "Residuals"
set ylabel 'Residual'
set xlabel 'Iteration'
plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
pause 1
reread

but still it is showing following error:

plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
"Residuals", line 8: Bad data on line 1

I did go through some posts for plotting gnuplot for residuals and I have tried to do this as mentioned in the posts but still it is showing some error. Do you have any idea way it is coming?

Thanks,
Sangeeta
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Old   May 10, 2013, 01:48
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Quote:
Originally Posted by Sargam05 View Post
Hi Tushar,

Thank so much for the inputs. I have used "plot" as you suggested:

set terminal png
set output "filename.png"
set logscale y
set title "Residuals"
set ylabel 'Residual'
set xlabel 'Iteration'
plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
pause 1
reread

but still it is showing following error:

plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
"Residuals", line 8: Bad data on line 1

I did go through some posts for plotting gnuplot for residuals and I have tried to do this as mentioned in the posts but still it is showing some error. Do you have any idea way it is coming?

Thanks,
Sangeeta

Try these steps.. I always follow these for plotting residuals.


Open the case folder in your console window (terminal).

execute the $application (for eg. icoFoam or any $Foam which you are using) and simultaneously write a log file using the following command in the terminal:

$application >log


Then open gnuplot in the same console window, and execute the following command:

set logscale y
set title "Residuals"
set ylabel 'Residual'
set xlabel 'Iteration'
plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
pause 1
reread

I wish this will solve your problem.
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Old   May 10, 2013, 02:02
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Try to edit your output log file like the following and then follow the procedure as mentioned in my earlier post....


// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Reading transportProperties

Reading field p

Reading field U

Reading/calculating face flux field phi


Starting time loop

Time: 1

Solving for U using DICPCG, Initial residual = 1, Final residual = 1, Relative residual = 59362.4, No outer iterations 1
ExecutionTime = 26.44 s ClockTime = 27 s
ExecutionTime = 26.6 s


Time: 2

Solving for U using DICPCG, Initial residual = 1, Final residual = 1, Relative residual = 1, No outer iterations 1
ExecutionTime = 37.93 s ClockTime = 38 s
ExecutionTime = 38.12 s


Time: 3

Solving for U using DICPCG, Initial residual = 0.305633, Final residual = 0.305633, Relative residual = 1, No outer iterations 1
ExecutionTime = 54.7 s ClockTime = 55 s
ExecutionTime = 54.9 s


Time: 4

Solving for U using DICPCG, Initial residual = 0.229696, Final residual = 0.229696, Relative residual = 1, No outer iterations 1
ExecutionTime = 66.4 s ClockTime = 67 s
ExecutionTime = 66.59 s


Time: 5

Solving for U using DICPCG, Initial residual = 0.155004, Final residual = 0.155004, Relative residual = 1, No outer iterations 1
ExecutionTime = 83.12 s ClockTime = 83 s
ExecutionTime = 83.3 s

Time: 6

Solving for U using DICPCG, Initial residual = 0.088822, Final residual = 0.088822, Relative residual = 1, No outer iterations 1
ExecutionTime = 96.02 s ClockTime = 96 s
ExecutionTime = 96.21 s


Time: 7

Solving for U using DICPCG, Initial residual = 0.0763407, Final residual = 0.0763407, Relative residual = 1, No outer iterations 1
ExecutionTime = 109.27 s ClockTime = 110 s
ExecutionTime = 109.45 s


Time: 8

Solving for U using DICPCG, Initial residual = 0.0426613, Final residual = 0.0426613, Relative residual = 1, No outer iterations 1
ExecutionTime = 121.37 s ClockTime = 122 s
ExecutionTime = 121.57 s

#########

I think that was the problem with your case, I hope now you are able to plot.
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Old   May 10, 2013, 12:35
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Hi Tushar,

Thank you so much for the suggestions! I have edited some of the initial part of the log file and used the command you mentioned in gnuplot but it is still showing following error:

Terminal type set to 'wxt'
gnuplot> set logscale y
gnuplot> set title "Residuals"
gnuplot> set ylabel 'Residual'
gnuplot> set xlabel 'Iteration'
gnuplot> plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
Bad data on line 1

gnuplot> pause 1
gnuplot> reread

I do not know if something is wrong in logs file. I am also attaching the log and logs folders as attachment. Please let me know if something is wrong in these folders.

Best regards,
Sangeeta
Attached Files
File Type: zip log.zip (11.7 KB, 9 views)
File Type: zip logs.zip (3.5 KB, 4 views)
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Old   May 11, 2013, 02:00
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Quote:
Originally Posted by Sargam05 View Post
Hi Tushar,

Thank you so much for the suggestions! I have edited some of the initial part of the log file and used the command you mentioned in gnuplot but it is still showing following error:

Terminal type set to 'wxt'
gnuplot> set logscale y
gnuplot> set title "Residuals"
gnuplot> set ylabel 'Residual'
gnuplot> set xlabel 'Iteration'
gnuplot> plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
Bad data on line 1

gnuplot> pause 1
gnuplot> reread

I do not know if something is wrong in logs file. I am also attaching the log and logs folders as attachment. Please let me know if something is wrong in these folders.

Best regards,
Sangeeta
Can you please upload the controlDict file?
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Old   May 11, 2013, 05:24
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Quote:
Originally Posted by Sargam05 View Post
Time: 8

Time 8, Corrector 0, Solving for U using DICPCG, residual = 0.0426613, relative residual = 1

Time 8, Solving for U, Initial residual = 0.0426613, Final residual = 0.0426613, Relative residual = 1, No outer iterations 1
ExecutionTime = 121.37 s ClockTime = 122 s
ExecutionTime = 121.57 s
Quote:
Originally Posted by Sargam05 View Post
gnuplot> plot "< cat log | grep 'Solving for U' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
Bad data on line 1
You grep for 'Solving for U' split by space and use the 9th field but as you can see there are different lines in your log file containing the grep string. The problem is for the line with the corrector the 9th field is "DICPCG" and gnuplot only works with numbers. You have restrict your grep string so it only matches the line with your residual.
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Old   May 11, 2013, 14:13
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Hi Tushar and Daniel,

Thank you for the reply. Tushar please find controlDict file as attachment.

Daniel even after changing the script based on log file following error is comping:

plot "< cat log | grep 'Solving for U using DICPCG' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
"Residuals", line 8: Bad data on line 1
Attached Files
File Type: zip controlDict.zip (597 Bytes, 9 views)
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Old   May 11, 2013, 14:42
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Quote:
Originally Posted by Sargam05 View Post
Hi Tushar and Daniel,

Thank you for the reply. Tushar please find controlDict file as attachment.

Daniel even after changing the script based on log file following error is comping:

plot "< cat log | grep 'Solving for U using DICPCG' | cut -d' ' -f9 | tr -d ','" title 'U' with lines
^
"Residuals", line 8: Bad data on line 1
It is always a good idea to test this first in a console.

Check the output of:

Code:
cat log | grep 'Solving for U using DICPCG' | cut -d' ' -f9 | tr -d ','
It should give you a series of "DICPCG". This is because the line you are grepping for the residual is in field 12 and not in field 9. So you can either use
Code:
cat log | grep 'Solving for U using DICPCG' | cut -d' ' -f12 | tr -d ','
or
Code:
cat log | grep 'Solving for U,' | cut -d' ' -f9 | tr -d ','
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Old   May 11, 2013, 21:37
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Hi Daniel,

Thank you so much for the suggestions. Now it plotting residuals. I appreciate your help!

I also like to thank Tushar for his inputs.

Best regards,
Sangeeta
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Old   May 13, 2013, 06:50
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Quote:
Originally Posted by Sargam05 View Post
Hi Daniel,

Thank you so much for the suggestions. Now it plotting residuals. I appreciate your help!

I also like to thank Tushar for his inputs.

Best regards,
Sangeeta
It's good to see, you are getting your residual plots.
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Old   May 30, 2013, 01:04
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Hello everyone
for plotting residuals by gnuplot, I want to plot p-residuals for a special row of p-solver not every row. for example, in icoFoam, I want to plot initial residual for p for every time step not for evey pisoLoop.
Best Regards
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Old   May 30, 2013, 05:22
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Quote:
Originally Posted by EmadTandis View Post
Hello everyone
for plotting residuals by gnuplot, I want to plot p-residuals for a special row of p-solver not every row. for example, in icoFoam, I want to plot initial residual for p for every time step not for evey pisoLoop.
Best Regards
That is what pyFoamPlotWatcher.py from the PyFoam-utilities does out of the box (plot only the first residual of a timestep).
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Old   May 30, 2013, 16:57
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Thanks
but can you tell me about use of this utility?
for plotting residuals, I type " gnuplot plotInstruction" on terminal. that plotInstruction is a text file based on this forum.
can I do this by writing new thing in this file?

Best Regards
Emad Tandis
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Old   May 30, 2013, 19:48
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Quote:
Originally Posted by EmadTandis View Post
Thanks
but can you tell me about use of this utility?
for plotting residuals, I type " gnuplot plotInstruction" on terminal. that plotInstruction is a text file based on this forum.
can I do this by writing new thing in this file?

Best Regards
Emad Tandis
This utility analyzes the logfile and plots the residuals
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Old   July 1, 2014, 07:51
Default pyFoam error on OpenFOAM Extend
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Originally Posted by gschaider View Post
That is what pyFoamPlotWatcher.py from the PyFoam-utilities does out of the box (plot only the first residual of a timestep).
Dear Bernhard,

This thread is related to OpenFOAM Extend in particular and I was getting an error running pyFoamPlotWatcher.py on Extend. I guess I need to make changes to extract data from log file correctly. Can you please point me in the right direction? The error is here: Support thread for "Solid Mechanics Solvers added to OpenFOAM Extend"

Thanks in advance!

Jibran
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Old   July 2, 2014, 18:29
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Originally Posted by Jibran View Post
Dear Bernhard,

This thread is related to OpenFOAM Extend in particular and I was getting an error running pyFoamPlotWatcher.py on Extend. I guess I need to make changes to extract data from log file correctly. Can you please point me in the right direction? The error is here: Support thread for "Solid Mechanics Solvers added to OpenFOAM Extend"

Thanks in advance!

Jibran
That is a long thread and the permalink took me to an unrelated posting. Which post number?
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Old   July 3, 2014, 06:59
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Quote:
Originally Posted by gschaider View Post
That is a long thread and the permalink took me to an unrelated posting. Which post number?
Hmm, that is quite strange because it takes me directly to my post (#238 on last page of the thread)
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