[CIG-SHORT] Direction of traction-normal for Neumann BC
Brad Aagaard
baagaard at usgs.gov
Thu Jun 19 12:43:57 PDT 2014
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
>>>>>>>>> _______________________________________________
>>>>>>>>> CIG-SHORT mailing list
>>>>>>>>> CIG-SHORT at geodynamics.org
>>>>>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>>
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