[aspect-devel] Problem with active tracers & compositional fields

John Naliboff jbnaliboff at ucdavis.edu
Fri May 18 15:12:41 PDT 2018


Hi all,

Apologies, the last few emails I accidentally sent directly to Felipe 
rather than the whole list. See the messages below for a series of replies.

Felipe - yes, if you are using active tracers then they need to be 
everywhere in the domain. If you are modeling a dense layer in the lower 
mantle, then the particle values will determine where that interface is.

Cheers,
John
On 05/18/2018 03:04 PM, FELIPE ORELLANA ROVIROSA wrote:
> John,
>
>          No ! My tracers are purposely located on a subset of the 
> domain, on a layer at the bottom in this particular case.
>
>   is this a problem?
>
> Felipe
>
> On Fri, May 18, 2018 at 3:01 PM, John Naliboff <jbnaliboff at ucdavis.edu 
> <mailto:jbnaliboff at ucdavis.edu>> wrote:
>
>     Hi Felipe,
>
>     I had filled a lower layer of the domain with 10k, 20k..200k, and
>     there were plenty of tracers..
>     But there are still particles throughout the mesh, yes? Not just
>     in the lower layer of the domain?
>
>     So, maybe other ways to generate the tracer particles are more
>     secure with regards to the mesh.
>     Yes, if the ascii file is not working I would try one of the other
>     particle generator options ...
>
>     Cheers,
>     John
>     On 05/18/2018 02:58 PM, FELIPE ORELLANA ROVIROSA wrote:
>>     Hi John,
>>
>>           Thanks a lot for your help.
>>
>>           I added the lines
>>
>>         set Load balancing strategy = remove and add particles
>>         set Minimum tracers per cell = 10
>>         set Maximum tracers per cell = 20
>>
>>      and tried having up to 200k tracers; but it fails by
>>     segmentation fault, again with the same message:
>>     #######################
>>     The name and call sequence of the exception was:
>>         ExcMessage("A cell and all of its neighbors do not contain
>>     any particles. " "The 'cell average' interpolation scheme does
>>     not support this case.")
>>     Additional Information:
>>     A cell and all of its neighbors do not contain any particles. The
>>     'cell average' interpolation scheme does not support this case.
>>     --------------------------------------------------------
>>
>>     Aborting!
>>     ######################
>>         I am pretty sure this is geometrically not tue, as I have
>>     seen the mesh.
>>     For example, when the mesh starts, there are like 10^3 active
>>     cells, thus, ~10 nodes per side. I had filled a lower layer of
>>     the domain with 10k, 20k..200k, and there were plenty of tracers..
>>
>>         So, maybe other ways to generate the tracer particles are
>>     more secure with regards to the mesh.. Certainly, I tried to
>>     implement the uniform box, but I could not make the syntax..I
>>     found no examples. In the end generating my own tracers and using
>>     a file worked perfect for me (I did this for passive tracers).
>>     The thing is, I need my tracers to be located in well-defined
>>     regions of my model box.
>>
>>     cheers,
>>
>>     Felipe
>>
>>
>>
>>     On Fri, May 18, 2018 at 2:26 PM, John Naliboff
>>     <jbnaliboff at ucdavis.edu <mailto:jbnaliboff at ucdavis.edu>> wrote:
>>
>>         Hi Felipe,
>>
>>         You are generating the initial particle positions from an
>>         ASCII file, so hard to know if in fact there is a particle in
>>         each cell. ASPECT seems to think not.
>>
>>         There are particle generator schemes that can ensure you
>>         always have a particle in each cell, but another option is to
>>         enforce a minimum (and maximum) number of particles per cell.
>>         These parameters are defined in particle 'world':
>>         https://github.com/geodynamics/aspect/blob/master/source/particle/world.cc#L748
>>         <https://github.com/geodynamics/aspect/blob/master/source/particle/world.cc#L748>
>>
>>         In the parameter file, enforcing a minimum (ex: 10) and
>>         maximum (ex: 20)number of particles per cell in the particle
>>         subsection would look like:
>>           set Load balancing strategy = remove and add particles
>>           set Minimum number of particles per cell = 10
>>           set Maximum number of particles per cell = 20
>>
>>         I think you may need to do at least one refinement during the
>>         initial time step to have this enforced?
>>
>>         Cheers,
>>         John
>>         On 05/18/2018 02:09 PM, FELIPE ORELLANA ROVIROSA wrote:
>>>
>>>          Hi all,
>>>
>>>                I am implementing a 3D model with one layer of
>>>         compositional fields, I want the convecting system to advect
>>>         active tracers (they have a density differential).
>>>
>>>                The model seems to have correct syntax, as it starts
>>>         to run. But it fails, it fails by segmentation fault: The
>>>         last liens of the log file state that there some cells and
>>>         all of their neighbors do not contain any particles, and
>>>         that makes the interpolation to crash.
>>>
>>>               But, I have been increasing the number of tracer
>>>         particles, all the way up to 10^5. I have plotted them, and
>>>         they would be waaay more than enough to fill all the cells
>>>         of the model, at least in its early stages.
>>>
>>>           what is going on here?
>>>
>>>           I am pasting the pertinent lines of my prm file:
>>>
>>>         subsection Postprocess
>>>           set List of postprocessors = visualization, temperature
>>>         statistics, velocity statistics, composition statistics,
>>>         tracers #,particle count statistics, dynamic topography
>>>
>>>         #  subsection Dynamic Topography
>>>         #    set Density above = 1000
>>>         #  end
>>>
>>>           subsection Visualization
>>>          #   set List of output variables = dynamic topography
>>>             set List of output variables = density
>>>             set Time between graphical output = 3.1558e14 # 10 Ma
>>>             set Output format = vtu
>>>             set Number of grouped files = 1
>>>
>>>         #   subsection Dynamic Topography
>>>         #      set Density above = 1000
>>>         #   end
>>>
>>>           end #end Visualization
>>>
>>>           subsection Tracers
>>>             set Number of tracers = 10000
>>>             set List of tracer properties = initial position,
>>>         initial composition, velocity, pT path
>>>             set Interpolation scheme = cell average
>>>             set Update ghost particles = true
>>>             set Time between data output = 3.1558e14
>>>             set Data output format = vtu
>>>             set Particle generator name = ascii file
>>>         #    set Number of grouped files = 1
>>>          #
>>>             subsection Generator
>>>               subsection Ascii file
>>>                 set Data directory = ./
>>>                 set Data file name = MyTracers_100k_lower.txt
>>>               end
>>>             end
>>>
>>>           end
>>>
>>>         end #end Postprocess
>>>
>>>         subsection Compositional fields
>>>           set Number of fields = 1
>>>           set Names of fields = lower  #, upper
>>>           set Compositional field methods = particles #, particles
>>>           set Mapped particle properties = lower:initial lower #,
>>>         upper:initial upper
>>>         end
>>>
>>>         This is a fraction of the output log:
>>>
>>>         Number of active cells: 4,096 (on 5 levels)
>>>         Number of degrees of freedom: 184,598
>>>         (107,811+4,913+35,937+35,937)
>>>
>>>         *** Timestep 0:  t=0 seconds
>>>            Solving temperature system... 0 iterations.
>>>         [compute-0-3:29728] *** Process received signal ***
>>>         [compute-0-3:29728] Signal: Segmentation fault (11)
>>>         [compute-0-3:29728] Signal code: Address not mapped (1)
>>>         [compute-0-3:29728] Failing at address: 0xffffffff000186a0
>>>         [compute-0-4:28813] *** Process received signal ***
>>>         [compute-0-25:06630] *** Process received signal ***
>>>         [compute-0-25:06630] Signal: Segmentation fault (11)
>>>         ...
>>>
>>>         ...
>>>         The violated condition was:
>>>             non_empty_neighbors != 0
>>>         The name and call sequence of the exception was:
>>>             ExcMessage("A cell and all of its neighbors do not
>>>         contain any particles. " "The 'cell average' interpolation
>>>         scheme does not support this case.")
>>>         Additional Information:
>>>         A cell and all of its neighbors do not contain any
>>>         particles. The 'cell average' interpolation scheme does not
>>>         support this case.
>>>         --------------------------------------------------------
>>>
>>>         Aborting!
>>>         ##################
>>>         cheers,
>>>         Felipe
>>>
>>>
>>>         _______________________________________________
>>>         Aspect-devel mailing list
>>>         Aspect-devel at geodynamics.org
>>>         <mailto:Aspect-devel at geodynamics.org>
>>>         http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>>         <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
>>
>>
>
>

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