SOAP to compute the descriptor for one atom only

[qzhu2017]

@David-Zagaceta

Support we have a structure with 4 atoms, the default descriptor calculation returns the descriptor for all atoms in the unit cell. Can you enable the option to compute the descriptors for the selected center atoms only.

For instance calculate(structure, ids=[0,1]) This means that we want to compute the descriptors for only atom 0 and 1.

[qzhu2017]

@yanxon The above will be also applied to ACSF and EAMD.

[qzhu2017]

@David-Zagaceta @yanxon
calculate(structure, ids=[0,1]) By default, ids=None which means to compute the descriptor for all atoms. Otherwise, ids should be a list of integers, which allows one to compute the descriptors for the selected atoms only.

[David-Zagaceta]

id's corresponds to indices not types right?

On Fri, Sep 11, 2020 at 10:20 AM Qiang Zhu notifications@github.com wrote:

calculate(structure, ids=[0,1]) By default, ids=None which means to compute the descriptor for all atoms. Otherwise, ids should be a list of integers, which allows one to compute the descriptors for the selected atoms only.

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[qzhu2017]

Yes. That’s right

On Fri, Sep 11, 2020 at 2:21 PM David Zagaceta notifications@github.com wrote:

id's corresponds to indices not types right?

On Fri, Sep 11, 2020 at 10:20 AM Qiang Zhu notifications@github.com wrote:

calculate(structure, ids=[0,1])

By default, ids=None which means to compute the descriptor for all atoms.

Otherwise, ids should be a list of integers, which allows one to compute

the descriptors for the selected atoms only.

—

You are receiving this because you were mentioned.

Reply to this email directly, view it on GitHub

<https://github.com/qzhu2017/PyXtal_FF/issues/23#issuecomment-691217250 ,

or unsubscribe

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-- [image: Photograph] http://www.skarif2.io/ Qiang Zhu Assistant Professor University of Nevada Las Vegas • Physics and Astronomy Phone ⋅ +1 702 895 1710 Email ⋅ qiang.zhu@unlv.edu Address ⋅ BPB 232, 4505 S. Maryland Parkway https://www.google.com/maps/place/Robert+L.+Bigelow+Physics,+Las+Vegas,+NV+89119/@36.1092077,-115.1454793,17z/data=!3m1!4b1!4m5!3m4!1s0x80c8c5aacc5bd7bf:0x57992e2f948155c0!8m2!3d36.1092077!4d-115.1432906 [image: github] https://github.com/qzhu2017[image: linkedin] https://qzhu2017.github.io/

[qzhu2017]

@David-Zagaceta @yanxon

I have solved this issue.

[qzhu2017]

Currently, it can only compute the descriptor for the 1st atom. But this should be fine.