Running "Lymberopoulos_with_argon_metastables".

[Abdelhak MISSAOUI]

When i run "Lymberopoulos_with_argon_metastables.i". i get this error:

*** ERROR ***
Lymberopoulos_with_argon_metastables.i:13: section 'MeshModifiers' does not have an associated "Action".
Did you misspell it?
Lymberopoulos_with_argon_metastables.i:14: section 'MeshModifiers/left' does not have an associated "Action".
Did you misspell it?
Lymberopoulos_with_argon_metastables.i:19: section 'MeshModifiers/right' does not have an associated "Action".
Did you misspell it?
 

[csde...@ncsu.edu]

Good afternoon,

MeshModifiers is an old function in MOOSE that was somewhat recently removed altogether and those files "slipped through the cracks" during the updates. To fix this, just replace lines 8-24 of "Lymberopoulos_with_argon_metastables.i" with:

[Mesh]

  [./geo]

    type = FileMeshGenerator

    file = 'Lymberopoulos.msh'

  [../]

  [./left]

    type = SideSetsFromNormalsGenerator

    normals = '-1 0 0'

    new_boundary = 'left'

    input = geo

  [../]

  [./right]

    type = SideSetsFromNormalsGenerator

    normals = '1 0 0'

    new_boundary = 'right'

    input = left

  [../]

[]

Also, the input file "RF_Plasma.i" is a shorten and more updated version of "Lymberopoulos_with_argon_metastables.i" (they only main difference is that "RF_Plasma.i" uses Actions to shorten input files and "Lymberopoulos_with_argon_metastables.i" does not). Thank you for catching the error for that input file.

Thank you,

Corey DeChant

[Alexander Lindsay]

Let's open an issue for this and make sure we add at least Syntax Checks for these inputs

--
You received this message because you are subscribed to the Google Groups "zapdos-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to zapdos-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/28da24c5-4ad6-40dd-b398-448e0c1cf699n%40googlegroups.com.

[csde...@ncsu.edu]

Ok, no problem. I just opened an issue for this.

[Abdelhak MISSAOUI]

 

hello,

i want to replace "Lymberopoulos.msh" by " Lymberopoulos_paper.msh  " in mech file.

when i run with " cd projects/zapdos/problems; ../zapdos-opt -i Lymberopoulos_with_argon_metastables.i --color off 2>&1 | tee log.txt
"i also changed the time step and i get this:  (is there a problem in time step and how to choose the time step knowing taht i want only test rapidly.

Framework Information:
MOOSE Version:           git commit 10a8305684 on 2020-11-04
LibMesh Version:         a62cd9cef65556bd080c8fbed00a43016a2d5bff
PETSc Version:           3.13.3
SLEPc Version:           3.13.3
Current Time:            Thu Nov 12 21:10:17 2020
Executable Timestamp:    Wed Nov  4 20:54:20 2020

Parallelism:
  Num Processors:          1
  Num Threads:             1

Mesh:
  Parallel Type:           replicated
  Mesh Dimension:          1
  Spatial Dimension:       1
  Nodes:                  
    Total:                 19
    Local:                 19
  Elems:                  
    Total:                 18
    Local:                 18
  Num Subdomains:          1
  Num Partitions:          1

Nonlinear System:
  Num DOFs:                95
  Num Local DOFs:          95
  Variables:               { "em" "Ar+" "Ar*" "mean_en" "potential" }
  Finite Element Types:    "LAGRANGE"
  Approximation Orders:    "FIRST"

Auxiliary System:
  Num DOFs:                402
  Num Local DOFs:          402
  Variables:               { "emDeBug" "Ar+_DeBug" "Ar*_DeBug" "mean_enDeBug" } { "Te" "x" } "x_node"
                             { "em_lin" "Ar+_lin" "Ar*_lin" } "Ar" "Efield" { "Current_em" "Current_Ar"
                             "emRate" "exRate" "swRate" "deexRate" "quRate" "poolRate" "TwoBRate" "ThreeBRate"
                             }
  Finite Element Types:    "LAGRANGE" "MONOMIAL" "LAGRANGE" "MONOMIAL" "LAGRANGE" "MONOMIAL" "MONOMIAL"
                             
  Approximation Orders:    "FIRST" "CONSTANT" "FIRST" "CONSTANT" "FIRST" "CONSTANT" "CONSTANT"

Execution Information:
  Executioner:             Transient
  TimeStepper:             PostprocessorDT
  Solver Mode:             NEWTON
  MOOSE Preconditioner:    SMP

LEGACY MODES ENABLED:
 This application uses the legacy material output option: material properties are output only on TIMESTEP_END, not INITIAL. To remove this message, set 'use_legacy_material_output' to false in this application. If there are gold output files that contain material property output for which output occurs on INITIAL, then these will generate diffs due to zero values being stored, and these tests should be re-golded.



*** Warning ***
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:523: unused parameter 'AuxKernels/em_lin/convert_moles'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:529: unused parameter 'AuxKernels/Ar+_lin/convert_moles'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:535: unused parameter 'AuxKernels/Ar*_lin/convert_moles'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:717: unused parameter 'Materials/GasBasics/position_units'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:745: unused parameter 'Materials/reaction_0/position_units'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:754: unused parameter 'Materials/reaction_1/position_units'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:763: unused parameter 'Materials/reaction_2/position_units'
/home/abdo2/projects/zapdos/problems/Lymberopoulos_with_argon_metastables.i:772: unused parameter 'Materials/reaction_3/position_units'


Time Step 0, time = 0

Postprocessor Values:
+----------------+-------------------+
| time           | InversePlasmaFreq |
+----------------+-------------------+
|   0.000000e+00 |      2.086484e-09 |
+----------------+-------------------+


Time Step 1, time = 1e-08, dt = 1e-08
 0 Nonlinear |R| = 1.414214e+13
      0 Linear |R| = 1.414214e+13
      1 Linear |R| = 2.220446e-03
  Linear solve converged due to CONVERGED_RTOL iterations 1
      Line search: Using full step: fnorm 1.414213562373e+13 gnorm 5.202600950229e+12
 1 Nonlinear |R| = 5.202601e+12
      0 Linear |R| = 5.202601e+12
      1 Linear |R| = 8.168565e-04
  Linear solve converged due to CONVERGED_RTOL iterations 1
      Line search: gnorm after quadratic fit 4.707508010877e+12
      Line search: Quadratically determined step, lambda=1.0000000000000001e-01
 2 Nonlinear |R| = 4.707508e+12
      0 Linear |R| = 4.707508e+12
      1 Linear |R| = 7.391223e-04
  Linear solve converged due to CONVERGED_RTOL iterations 1
      Line search: Using full step: fnorm 4.707508010877e+12 gnorm 1.731795416351e+12
 3 Nonlinear |R| = 1.731795e+12
      0 Linear |R| = 1.731795e+12
      1 Linear |R| = 1.014376e-03
  Linear solve converged due to CONVERGED_RTOL iterations 1
      Line search: objective function at lambdas = 1. is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.5 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.25 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.125 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.0625 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.03125 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.015625 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.0078125 is Inf or Nan, cutting lambda
      Line search: Using full step: fnorm 1.731795416351e+12 gnorm 1.725043785870e+12
 4 Nonlinear |R| = 1.725044e+12
      0 Linear |R| = 1.725044e+12
      1 Linear |R| = 6.870600e-04
  Linear solve converged due to CONVERGED_RTOL iterations 1
      Line search: objective function at lambdas = 1. is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.5 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.25 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.125 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.0625 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.03125 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.015625 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.0078125 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.00390625 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.00195312 is Inf or Nan, cutting lambda
      Line search: objective function at lambdas = 0.000976562 is Inf or Nan, cutting lambda
Nonlinear solve did not converge due to DIVERGED_FNORM_NAN iterations 4
 Solve Did NOT Converge!
Aborting as solve did not converge


*** ERROR ***
Solve failed and timestep already at or below dtmin, cannot continue!

Stack frames: 12
0: libMesh::print_trace(std::ostream&)
1: moose::internal::mooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
2: callMooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, MooseApp*)
3: /home/abdo2/projects/moose/framework/libmoose-opt.so.0(+0x5f085d) [0x7f7e6c2fe85d]
4: /home/abdo2/projects/moose/framework/libmoose-opt.so.0(+0xd13473) [0x7f7e6ca21473]
5: TimeStepper::computeStep()
6: Transient::execute()
7: MooseApp::executeExecutioner()
8: MooseApp::run()
9: ../zapdos-opt(+0x41d1) [0x55ce914701d1]
10: __libc_start_main
11: ../zapdos-opt(+0x44af) [0x55ce914704af]
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

Le jeu. 12 nov. 2020 à 21:47, csde...@ncsu.edu <csde...@ncsu.edu> a écrit :

Ok, no problem. I just opened an issue for this.

On Thursday, November 12, 2020 at 3:28:31 PM UTC-5 alexlin...@gmail.com wrote:

Let's open an issue for this and make sure we add at least Syntax Checks for these inputs

On Thu, Nov 12, 2020 at 12:22 PM csde...@ncsu.edu <csde...@ncsu.edu> wrote:

--

You received this message because you are subscribed to the Google Groups "zapdos-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to zapdos-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/28da24c5-4ad6-40dd-b398-448e0c1cf699n%40googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "zapdos-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to zapdos-users...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/994a2428-c151-44c5-966b-6411712bef99n%40googlegroups.com.

--
You received this message because you are subscribed to a topic in the Google Groups "zapdos-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/zapdos-users/drMKqU1xQqI/unsubscribe.
To unsubscribe from this group and all its topics, send an email to zapdos-users...@googlegroups.com.

[csde...@ncsu.edu]

Good morning,

To change the mesh file, edited the input file (replace "file = 'Lymberopoulos.msh'" with file = 'Lymberopoulos_paper.msh'). Just note that "Lymberopoulos_paper.msh" is a less refine mesh, but it better matches with the mesh used in the Lymberopoulos paper. (Quick question: did you editing "Lymberopouls.msh"? Because your number of nodes seems very low.)

For the time step, that is a physical problem. This input file is of an argon RF discharge at 13.56MHz, so a time step of 1e-8 is just too big to capture all the correct physicals (namely the response time of the electrons).  If you are looking for rapid testing, that is what the "tests" directory is for. For example, the "/tests/Lymberopoulos_rf_discharge/" tests using an argon RF discharge but only for about 4 RF cycles.

Thank you,

Corey DeChant

[Abdelhak MISSAOUI]

thank you Corey

yes,  edited the mesh, can you please tell me how to specify the number of RF cycles.?

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/482e969a-f845-4cc1-9466-b6f8a1444c40n%40googlegroups.com.

[csde...@ncsu.edu]

No problem.  Currently, you can't directly specify the number of RF cycles, you can only specify the end time. To did this, in the "Executioner" block you can edit the "end_time = " option. Since this is a discharge at 13.56 MHz, the period is about 74 ns. So if we want to run for about 4 RF cycles,  we input "end_time = 3e-7". 

[Abdelhak MISSAOUI]

 Hello

thank you for your reply, now i want to refine the mesh  i think by increasing the number of nodes in mesh, i think by gmsh Lymberopoulos_paper.geo but in this interface where can i change the number of nodes? knowing this gemetry is 1D.

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/a98eb85f-9496-4e00-8470-063c06805c2an%40googlegroups.com.

[csde...@ncsu.edu]

Good afternoon,

The "Lymberopoulos_paper.geo" was written with the help of a third party software (I believe I used Matlab), since the node positions are base on a formulation in the Lymberopoulos paper (link here: https://aip.scitation.org/doi/abs/10.1063/1.352926?casa_token=aCh7Tns0n_sAAAAA:Di16akVNExV1IVMa82Vpm_3MbWzeqcJHPbBq2qRG4iFiDFUC01dckVnHjCgjWjfY_Uni8DOKyg). In case you do not have access, the formulation is:

where x is a node location, L is the spacing between electrodes, and N_p is the total number of nodes. So in summary, I just had Matlab print out a Gmsh text file based on the formulation above. Also as a reference, here is a link to the Gmsh reference manual, since it is not a MOOSE code, but we do use it a lot for mesh designs (https://gmsh.info/doc/texinfo/gmsh.html).

Thank you,

Corey DeChant

[csde...@ncsu.edu]

It seems the formula is not showing up after I hit send, so it is in this attachment.

[Abdelhak MISSAOUI]

So, where can i change the Np from the interface.?
 

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/941807b5-ff6a-4f05-bf06-6fdf70409c8cn%40googlegroups.com.

[csde...@ncsu.edu]

Good afternoon,

There is no interface to change Np within Zapdos/MOOSE, since I used Matlab to help write the Gmsh. Zapdos/MOOSE can only read Gmsh files but not create them (MOOSE does have its own mesh building system but it is not Gmsh). To create a Gmsh file, you need to write it by hand or use the help of a third part software (like Matlab or Python). Attached is the Matlab code I used to help write the Gmsh file.

Thank you,

Corey DeChant

[Abdelhak MISSAOUI]

Now i understatnd, Thank you very much.

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/d23e12d6-6470-4391-8ef5-46eb96f08cfan%40googlegroups.com.

[Alexander Lindsay]

You can always uniformly refine the mesh by specifying in your input file:

[Mesh]

  file = blah-blah-blah

  uniform_refine = 1

[]

That would uniformly refine the mesh once. You can change the number provided to `uniform_refine` if you want it refine more, e.g. uniform_refine = 2 will uniformly refine the mesh twice.

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/CAJD%3DfEAu2MUaoMXHwvYa84vsvP8LTaVFGst3qJwiMWKSDNkNJg%40mail.gmail.com.

[Abdelhak MISSAOUI]

hello evryone, when i run my file i get this error:

*** ERROR ***

Solve failed and timestep already at or below dtmin, cannot continue!

knowing i want to run this file for 200 rf cyles (with f =13.56MHz), and i only changed the time step :

[Executioner]
  type = Transient
  #end_time = 0.00737463126
  end_time = 1.5e-5
  petsc_options = '-snes_converged_reason -snes_linesearch_monitor'
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_factor_shift_type -pc_factor_shift_amount -ksp_type -snes_linesearch_minlambda'
  petsc_options_value = 'lu NONZERO 1.e-10 fgmres 1e-3'
  nl_rel_tol = 1e-08
  #nl_abs_tol = 7.6e-5 #Commit out do to test falure on Mac
  dtmin = 1e-14
  l_max_its = 20

  #Time steps based on the inverse of the plasma frequency
  [./TimeStepper]
    type = PostprocessorDT
    postprocessor = InversePlasmaFreq
  [../]
[]

[Outputs]
  perf_graph = true
  [./out]
    type = Exodus
  [../]
[]

thanks

[csde...@ncsu.edu]

Good morning,

I am currently going through and updating all the files in the "Problems" directory. The problems for this file are two main syntax/option errors (first, some of the metastable reactions are missing the "_target_eq_u = true", and secondly, the potential BCs are missing the "preset = false" option). In the meantime, I was going to attached the corrected input file, but I am getting an error while attaching the file to this message. So, I will send you a direct email with the input file.

Also, it might be a good "debug" exercise to compare the failing input file with the test file, find the differences, and see why does differences matter (this is because the test files have to be updated and must pass before Zapdos is updated, while the "Problems" directory has example files that are currently not directly tested).

Thank you,

Corey DeChant 

[Abdelhak MISSAOUI]

so, after running the corrected file i get some problems:

1- ion density Ar+ has a negative values

2- the electric field and electron temperature are always zero.

--
You received this message because you are subscribed to the Google Groups "zapdos-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to zapdos-users...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/4d441103-1de9-45ae-8dbe-4eff05540656n%40googlegroups.com.

[csde...@ncsu.edu]

Good afternoon,

What data visualization tool are you using? Also, if possible, can you please show us the graphs that have those results with a legend using the Zapdos variable names. My first guess is that visualization software is showing the wrong data. For the densities, you need to look at the variables named "species_lin" (e.g. for ions that would be Ar+_lin). Zapdos solves densities in the logarithmic form to avoid negative densities (so a solution value of Ar+ = -20 converts to Ar+_lin = 1.24e15 m^-3).

Thank you,

Corey DeChant

[Abdelhak MISSAOUI]

im using Paraveiw, i tried to visualize Ar and Ar+_lin i get this figures please see the attached files

________________________________________________________________________

To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/6eb19412-59c0-4e1c-80c9-2cb590d781b9n%40googlegroups.com.

[csde...@ncsu.edu]

You current have the time set to zero, so you are showing the initial conditions. Aux-variables (such as "Ar+_lin", "Efield", and "Te") are initial set to zero and are calculated during the linear steps and at the end of the time step, by default. Changing the time, or pressing the green play button, should change the density. Also as a side note: you should set "X Array Name" to either "arc_length", "x", or "x_node" (arc_length normalizes the distance between the boundaries, x shows the numerical distance between boundaries while smoothing out Aux-variables, and x_node does the same thing as x but for primary variable, such as "potential"). 

[Abdelhak MISSAOUI]

Thank you, now i want to get the cycle-averaged density or cycle-averaged electric field for the last rf cycle.. should i add a script for that?

________________________________________________________________________

Abdelhak MISSAOUI

Ph.D student

Laboratory of Physic of Matter and Radiation  (LPMR)

Mohammed first university - Faculty of Sciences

Phone : +212611782643 

ORCID ID: https://orcid.org/0000-0002-5849-562X

_________________________________________________________________________

You received this message because you are subscribed to a topic in the Google Groups "zapdos-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/zapdos-users/drMKqU1xQqI/unsubscribe.
To unsubscribe from this group and all its topics, send an email to zapdos-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/zapdos-users/4f14b112-c193-4c66-b8ab-e64a00142844n%40googlegroups.com.

[csde...@ncsu.edu]

You could, if you are familiar with writing script for Paraview (I believe Paraview uses Python for its scripting). You could also use Paraview temporal filters to extract the last RF cycle and then uses the temporal statistic filter to compute the average of the extract cycle. Either way should work fine.