[CIG-SHORT] Direction of traction-normal for Neumann BC

Francisco Delgado fjd49 at cornell.edu
Thu Jun 19 12:58:16 PDT 2014 

Ok, I'll give that a try.

Thanks


On Thu, Jun 19, 2014 at 3:43 PM, Brad Aagaard <baagaard at usgs.gov> wrote:

> Francisco,
>
> The current journal files work for me with CUBIT 14.1 and 14.0. When I go
> back to CUBIT 13.2, I reproduce your problem. My guess is that Trelis
> 14.0.4 is based on CUBIT 13.2. Do you have access to the current version of
> Trelis? I would like to avoid revising the script to work with older
> versions of Trelis and CUBIT.
>
> Brad
>
>
>
> On 06/19/2014 12:25 PM, Francisco Delgado wrote:
>
>> Version 14.0.4, I've run the code line by line several times but I only
>> get
>> to Surface 33, Surfaces 35 and 36 just do not appear.
>>
>>
>> On Thu, Jun 19, 2014 at 3:15 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>
>>  On 06/19/2014 12:13 PM, Francisco Delgado wrote:
>>>
>>>  Brad, I updated to Trelis but I still get the same error
>>>>
>>>>
>>> What version of Trelis are you using?
>>>
>>> Brad
>>>
>>>
>>>   On Thu, Jun 19, 2014 at 3:10 PM, Brad Aagaard <baagaard at usgs.gov>
>>> wrote:
>>>
>>>>
>>>>   Francisco,
>>>>
>>>>>
>>>>> CUBIT 12.0 is several years old. There have been some significant
>>>>> improvements, so it would be good to move to the current version. We
>>>>> try
>>>>> to
>>>>> keep our CUBIT/Trelis examples up to date for the current versions. As
>>>>> in
>>>>> this case, some small tweaks are sometimes necessary.
>>>>>
>>>>> CUBIT is no longer available to non-US gov't institutions, so you would
>>>>> have to get Trelis from csimsoft.com. There is a 30-day free trial
>>>>> available.
>>>>>
>>>>> Brad
>>>>>
>>>>>
>>>>>
>>>>> On 06/19/2014 12:03 PM, Francisco Delgado wrote:
>>>>>
>>>>>   Brad, I'm using Cubit 12.0. Should I get a newer one??
>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Jun 19, 2014 at 2:54 PM, Brad Aagaard <baagaard at usgs.gov>
>>>>>> wrote:
>>>>>>
>>>>>>    Francisco,
>>>>>>
>>>>>>
>>>>>>> Which version of CUBIT or Trelis are you using? I am using CUBIT
>>>>>>> 14.1.
>>>>>>> I
>>>>>>> did have to update the surface ids from when I originally used the
>>>>>>> script 3
>>>>>>> years ago (I don't recall which version of CUBIT I was using at the
>>>>>>> time).
>>>>>>>
>>>>>>> Brad
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 06/19/2014 11:49 AM, Francisco Delgado wrote:
>>>>>>>
>>>>>>>    Hello, I've been following the magma chamber example and I get
>>>>>>> some
>>>>>>>
>>>>>>>  errors
>>>>>>>> in Cubit when creating the geometry. In the geometry.jou file when I
>>>>>>>> get
>>>>>>>> to
>>>>>>>> lines 44 and 45, Cubit tells that those surfaces do not exist. What
>>>>>>>> faces
>>>>>>>> are 35 and 36?? The two pieces of the upper surface??
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Jun 19, 2014 at 10:56 AM, Brad Aagaard <baagaard at usgs.gov>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>     Satoshi,
>>>>>>>>
>>>>>>>>
>>>>>>>>  The Neumann BC is intended to be applied to an external boundary.
>>>>>>>>> For a
>>>>>>>>> spherical pressure source, the domain should not include the
>>>>>>>>> material
>>>>>>>>> inside the sphere (it needs to be a cavity). This will result in a
>>>>>>>>> consistent normal direction for the boundary.
>>>>>>>>>
>>>>>>>>> If the spherical boundary is all one surface, then you can still
>>>>>>>>> run
>>>>>>>>> into
>>>>>>>>> problems when PyLith initializes the boundary. It may find
>>>>>>>>> horizontal
>>>>>>>>> normal directions. This means the default way it uniquely defines
>>>>>>>>> the
>>>>>>>>> two
>>>>>>>>> tangential directions breaks down. The workaround is to subdivide
>>>>>>>>> the
>>>>>>>>> surface into quadrants so that you can use a user-defined
>>>>>>>>> up-direction
>>>>>>>>> to
>>>>>>>>> get consistent directions tangential and normal directions for the
>>>>>>>>> Neumann
>>>>>>>>> BC. Attached is a small magma chamber example that illustrates
>>>>>>>>> this.
>>>>>>>>>
>>>>>>>>> We are working on a more detailed magma chamber and dike example
>>>>>>>>> for
>>>>>>>>> a
>>>>>>>>> workshop next week and we will create an examples section under
>>>>>>>>> PyLith
>>>>>>>>> User
>>>>>>>>> Resources (http://wiki.geodynamics.org/software:pylith:start) in
>>>>>>>>> the
>>>>>>>>> next
>>>>>>>>> week and post it there.
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>> Brad
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 06/19/2014 02:09 AM, Satoshi Okuyama wrote:
>>>>>>>>>
>>>>>>>>>     Hello,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>  Recently I started using pylith and I already love it. However, I
>>>>>>>>>> have
>>>>>>>>>> an question about Neumann boundary condition;
>>>>>>>>>>
>>>>>>>>>> What determines the direction of positive traction-normal?
>>>>>>>>>>
>>>>>>>>>> or
>>>>>>>>>>
>>>>>>>>>> What determines the order of the vertices when pylith construct
>>>>>>>>>> faces
>>>>>>>>>> from a group of vertices for boundary condition?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Here is my story,
>>>>>>>>>>
>>>>>>>>>> I am trying to simulate the deformation caused by a pressure
>>>>>>>>>> source. I
>>>>>>>>>> created a mesh with spherical source and put all the vertices on
>>>>>>>>>> source
>>>>>>>>>> surface into a group, then applied Neumann BC with just
>>>>>>>>>> traction-normal.
>>>>>>>>>>
>>>>>>>>>> However, the deformation of the source was far from isotropic. I
>>>>>>>>>> checked
>>>>>>>>>> the initial traction and found that deflation (traction toward
>>>>>>>>>> source
>>>>>>>>>> center) is applied to some faces, while inflation is applied to
>>>>>>>>>> the
>>>>>>>>>> others.
>>>>>>>>>>
>>>>>>>>>> Following is an example of initial-traction output. I placed 5
>>>>>>>>>> vertices
>>>>>>>>>> on a plane of z=0 and formed 4 triangle face. Then I applied +1Pa
>>>>>>>>>> of
>>>>>>>>>> traction-normal to this group.
>>>>>>>>>>
>>>>>>>>>> ############################################################
>>>>>>>>>> ###########
>>>>>>>>>> # vtk DataFile Version 2.0
>>>>>>>>>> Simplicial Mesh Example
>>>>>>>>>> ASCII
>>>>>>>>>> DATASET UNSTRUCTURED_GRID
>>>>>>>>>> POINTS 5 double
>>>>>>>>>> -1.000000e+00 -1.000000e+00 0.000000e+00
>>>>>>>>>> 1.000000e+00 -1.000000e+00 0.000000e+00
>>>>>>>>>> 1.000000e+00 1.000000e+00 0.000000e+00
>>>>>>>>>> -1.000000e+00 1.000000e+00 0.000000e+00
>>>>>>>>>> 0.000000e+00 0.000000e+00 0.000000e+00
>>>>>>>>>> CELLS 4 16
>>>>>>>>>> 3  2 1 4
>>>>>>>>>> 3  3 0 4
>>>>>>>>>> 3  3 2 4
>>>>>>>>>> 3  4 1 0
>>>>>>>>>> CELL_TYPES 4
>>>>>>>>>> 5
>>>>>>>>>> 5
>>>>>>>>>> 5
>>>>>>>>>> 5
>>>>>>>>>> CELL_DATA 4
>>>>>>>>>> VECTORS initial_traction double
>>>>>>>>>> 0.000000e+00 0.000000e+00 -1.000000e+00
>>>>>>>>>> 0.000000e+00 0.000000e+00 1.000000e+00
>>>>>>>>>> 0.000000e+00 0.000000e+00 -1.000000e+00
>>>>>>>>>> 0.000000e+00 0.000000e+00 -1.000000e+00
>>>>>>>>>> ############################################################
>>>>>>>>>> ###########
>>>>>>>>>>
>>>>>>>>>> As you see, 2nd cell (or face) receives traction of (0,0,1) while
>>>>>>>>>> other
>>>>>>>>>> cells receives (0,0,-1). I noticed that if I consider 2 vectors -
>>>>>>>>>> 1st
>>>>>>>>>> vertex to 2nd, and 1st to 3rd - the direction of the traction
>>>>>>>>>> vector
>>>>>>>>>> is
>>>>>>>>>> equal to the cross product of them.
>>>>>>>>>>
>>>>>>>>>> cell #1:
>>>>>>>>>>        v1: #2 -> #1 = ( 0,-2,0)
>>>>>>>>>>        v2: #2 -> #4 = (-1,-1,0)
>>>>>>>>>>        v1 x v2 = (0,0,-2)
>>>>>>>>>>
>>>>>>>>>> cell #2:
>>>>>>>>>>        v1: #3 -> #0 = ( 0,-2,0)
>>>>>>>>>>        v2: #3 -> #4 = ( 1,-1,0)
>>>>>>>>>>        v1 x v2 = (0,0,2)
>>>>>>>>>>
>>>>>>>>>> One step closer to the answer, I believe. But I have no idea how
>>>>>>>>>> this
>>>>>>>>>> order is determined. The order of the vertices for 2nd cell is
>>>>>>>>>> 3-0-4,
>>>>>>>>>> not 3-4-0. But why?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>> ----
>>>>>>>>>> Satoshi Okuyama
>>>>>>>>>> _______________________________________________
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>
>>>>>>
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-- 
--------------------------------------------------------
Francisco Delgado
PhD student in Geophysics
Cornell University
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