No problem. Sorry I did not think of it sooner.
Matt
On Tue, Jan 28, 2025 at 10:45 AM MIGUEL MOLINOS PEREZ
wrote:
> It works! Thank you again Matt.
>
> Miguel
>
>
> On 24 Jan 2025, at 17:07, MIGUEL MOLINOS PEREZ wrote:
>
> Ohh, I wasn't aware of this function. Thank you Matt, I’ll see if th
It works! Thank you again Matt.
Miguel
On 24 Jan 2025, at 17:07, MIGUEL MOLINOS PEREZ wrote:
Ohh, I wasn't aware of this function. Thank you Matt, I’ll see if that solves
the problem.
Miguel
On 24 Jan 2025, at 17:00, Matthew Knepley wrote:
On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS P
Ohh, I wasn't aware of this function. Thank you Matt, I’ll see if that solves
the problem.
Miguel
On 24 Jan 2025, at 17:00, Matthew Knepley wrote:
On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS PEREZ
mailto:mmoli...@us.es>> wrote:
Sorry I wasn’t clear enough. By “the box is updated” I mean:
On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS PEREZ
wrote:
> Sorry I wasn’t clear enough. By “the box is updated” I mean: I run
> DMGetBoundingBox and the resulting coordinates are updated according to the
> deformation gradient “F".
>
Oh, if you change the periodic extent, which you are, you
Sorry I wasn’t clear enough. By “the box is updated” I mean: I run
DMGetBoundingBox and the resulting coordinates are updated according to the
deformation gradient “F".
Thanks,
Miguel
On 24 Jan 2025, at 16:50, Matthew Knepley wrote:
On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ
mailt
On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ
wrote:
> Thanks Matt, I tried that too, and the problem remains. The box is updated
> only if I set no periodic bcc.
>
What do you mean by "The box is updated"? I am trying to understand how you
test things. Clearly the coordinates are update
Thanks Matt, I tried that too, and the problem remains. The box is updated only
if I set no periodic bcc.
Miguel
On 24 Jan 2025, at 14:20, Matthew Knepley wrote:
On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ
mailto:mmoli...@us.es>> wrote:
Dear Matt, the error was in the implementation
On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ wrote:
> Dear Matt, the error was in the implementation of the volume expansion
> function. I updated it, and it works finte under finite domains. However,
> if I include periodic boundary conditions the volume of the cell does not
> accommodat
Dear Matt, the error was in the implementation of the volume expansion
function. I updated it, and it works finte under finite domains. However, if I
include periodic boundary conditions the volume of the cell does not
accommodate the volume expansion of the particles. The deformation gradient i
You are right!! Thank you again!
Miguel
On Jan 17, 2025, at 5:18 PM, Matthew Knepley wrote:
On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ
mailto:mmoli...@us.es>> wrote:
Now the error is in the call to DMSwarmMigrate
You have almost certainly overwritten memory somewhere. Can you use v
On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ
wrote:
> Now the error is in the call to DMSwarmMigrate
>
You have almost certainly overwritten memory somewhere. Can you use
vlagrind or Address Sanitizer?
Thanks,
Matt
> Miguel
>
> [0]PETSC ERROR:
>
Now the error is in the call to DMSwarmMigrate
Miguel
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger
On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ
wrote:
> Thank you Matt, this the piece of code I use to change the coordinates of
> the DM obtained using:
>
You do not need the call to DMSetCoordinates(). What happens when you
remove it?
Thanks,
Matt
>
> DMSwarmGetCellDM(Simulat
Thank you Matt, this the piece of code I use to change the coordinates of the
DM obtained using:
DMSwarmGetCellDM(Simulation.atomistic_data, &bounding_cell);
DMGetApplicationContext(bounding_cell, &background_mesh);
Thanks,
Miguel
/***
On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ wrote:
> I tried what you suggested, but still I got this error message. Maybe I
> should use main release?
>
No. I suspect something is wrong with the way you are setting coordinates.
Can you share the code?
Thanks,
Matt
> Miguel
>
I tried what you suggested, but still I got this error message. Maybe I should
use main release?
Miguel
[4]PETSC ERROR:
[4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of r
Thank you Matt for the useful info. I’ll try your idea.
Miguel
On 15 Jan 2025, at 16:48, Matthew Knepley wrote:
On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ
mailto:mmoli...@us.es>> wrote:
Thank you Matt.
Yes, I am getting the "CellDM" from the DMSwarm.
1. I have recently overhauled
On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ
wrote:
> Thank you Matt.
>
> Yes, I am getting the "CellDM" from the DMSwarm.
>
> 1. I have recently overhauled this functionality because it was not
> flexible enough for the plasma simulation we do. Thus main and release work
> differently.
Yes, I am getting the "CellDM" from the DMSwarm.
Miguel
On 15 Jan 2025, at 16:08, Mark Adams wrote:
Are you getting the "CellDM" from the DMSwarm?
Mark
On Wed, Jan 15, 2025 at 7:09 AM MIGUEL MOLINOS PEREZ
mailto:mmoli...@us.es>> wrote:
Dear all,
It seems that we can not modify the coordinate
Thank you Matt.
Yes, I am getting the "CellDM" from the DMSwarm.
1. I have recently overhauled this functionality because it was not flexible
enough for the plasma simulation we do. Thus main and release work differently.
Nice to hear that. Should I move to main?
2. I assume you are using rele
On Wed, Jan 15, 2025 at 7:09 AM MIGUEL MOLINOS PEREZ wrote:
> Dear all,
>
> It seems that we can not modify the coordinates of the background mesh
> attached to a DMSwarm simulation. This is a feature?
>
1. I have recently overhauled this functionality because it was not
flexible enough for the
Are you getting the "CellDM" from the DMSwarm?
Mark
On Wed, Jan 15, 2025 at 7:09 AM MIGUEL MOLINOS PEREZ wrote:
> Dear all,
>
> It seems that we can not modify the coordinates of the background mesh
> attached to a DMSwarm simulation. This is a feature?
>
> Best,
> Miguel
>
>
Dear all,
It seems that we can not modify the coordinates of the background mesh attached
to a DMSwarm simulation. This is a feature?
Best,
Miguel
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