Author Topic: PTM analysis - orientation of reference templates  (Read 68 times)

Carolina

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PTM analysis - orientation of reference templates
« on: November 10, 2017, 02:27:11 PM »
Dear Mr Stukowsky,
thank You for Your attention. I am using OVITO to analyze an HCP structure where there are zones with different orientation of the c axis.
In other to classify the local crystal structure I used the PTM analysis tool and the CNA tool.
The PTM analysis tool prooved to be more sensible then the CNA tool ( I have strong thermal fluctuations during my simulation ) and also give me informations about the local orientation of the final HCP phase. So I decided to use the PTM tool. If I am right, the information about the local orientation is given with reference to the polyhedron template considered in the PTM analysis. So, my question is: what is the orientation of the polyhedron template of the HCP used for PTM analysis with respect to the x,y,z axis ? I was unable to find this information.
If I perform the PTM analysis on a perfect HCP crystal with the c axis parallel to z axis and with one of the ‘dense’ directions in the basal plane parallel to the x axis I get  some values of the local Orientation in X, Y, Z different than zero so I supposed that the template structure must be oriented differently.

Thank You in advance,
Carolina Baruffi

Alexander Stukowski

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Re: PTM analysis - orientation of reference templates
« Reply #1 on: November 10, 2017, 03:34:36 PM »
Carolina,

That's a good question. I don't know the answer either. I will forward your question to Peter Larsen, the author of the PTM method and the routine in OVITO.

But my first guess is that the answer to your question can be found in this source code file: https://gitlab.com/stuko/ovito/blob/master/src/3rdparty/ptm/deformation_gradient.cpp
I think the penrose_hcp array contains the 12 HCP neighbor vectors expressed in the Cartesian reference coordinate system used by the PTM routine.

I'll let you know if I receive a comment from Peter.

-Alex
« Last Edit: November 10, 2017, 03:36:24 PM by Alexander Stukowski »

Alexander Stukowski

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Re: PTM analysis - orientation of reference templates
« Reply #2 on: November 13, 2017, 08:21:03 AM »
Carolina,

I have received a reply from Peter and need to correct myself:

The template neighbor vectors for the HCP structure are found in line 92 of the source file https://gitlab.com/stuko/ovito/blob/master/src/3rdparty/ptm/index_ptm.h
Orientations computed by the PTM modifier are relative to this (fairly arbitrary) reference orientation.

Carolina

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Re: PTM analysis - orientation of reference templates
« Reply #3 on: November 15, 2017, 12:59:53 PM »
Dear Mr Stukowsky,
thank You for Your quick answer, sorry for the delay in my answer but I didn't get any notification on my email adress of your answer on the forum.
I will take a look at the source code right now and keep You informed !

Best regards,
Carolina Baruffi