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shankar1729 / jdftx

JDFTx: software for joint density functional theory
http://jdftx.org
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Issue with solvation calculation #134

Closed mchen88 closed 3 years ago

mchen88 commented 3 years ago

Hi Shankar,

I'm using JDFTx to calculate the solvation energy of 2 layer and 3 layer graphene surface, but encountered some issues. It reminds me that "the coulumb truncation embedding center is not invariant under symmetries." I've already double checked the coulumb truncation embedding position, which looked right to me.

Here is a screenshot: " Folded 1 k-points by 6x6x1 to 36 k-points. Coulomb truncation embedding center is not invariant under symmetry matrix: [ -1 0 0 ] [ 0 -1 0 ] [ 0 0 -1 ] [ 3.5725e-07 0.250001 0.338527 ] Coulomb truncation embedding center is not invariant under symmetries. End date and time: Thu Aug 20 10:21:48 2020 (Duration: 0-0:00:01.20) Failed. " Input files and output files are attached in this ticket. Your help would be much appreciated!

Best, Mingpeng solvation.zip

shankar1729 commented 3 years ago

Set the embedding center halfway between the two layers. The overall system has a space group symmetry that maps one layer to the other, and the error you are getting is making sure that you don't break that symmetry by the coulomb truncation.

Best, Shankar

mchen88 commented 3 years ago

Dear Shankar,

Thank you so much for your quick response. Actually setting the embedding center halfway between the two layers was the very beginning setting I had for the calculation, but it failed. Later on I tested the embedding center at some other positions including the first layer graphene (0 0 0.0846) and second layer graphene (0 0 0.2539, which is the one attached in the original ticket), always giving me the same error, saying that: " Folded 1 k-points by 6x6x1 to 36 k-points. Coulomb truncation embedding center is not invariant under symmetry matrix: [ -1 0 0 ] [ 0 -1 0 ] [ 0 0 -1 ] [ 3.5725e-07 0.250001 0.338527 ] Coulomb truncation embedding center is not invariant under symmetries. End date and time: Fri Aug 21 09:04:43 2020 (Duration: 0-0:00:01.24) Failed. " Please let me know what else I can try. Thank you!

Best, Mingpeng

On Fri, Aug 21, 2020 at 7:11 AM Ravishankar Sundararaman < notifications@github.com> wrote:

Set the embedding center halfway between the two layers. The overall system has a space group symmetry that maps one layer to the other, and the error you are getting is making sure that you don't break that symmetry by the coulomb truncation.

Best, Shankar

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/shankar1729/jdftx/issues/134#issuecomment-678311032, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANHPP5K2IBMC3QVRXL5UUOLSBZ573ANCNFSM4QGWQEVQ .

-- Mingpeng Chen PhD candidate Department of Chemistry and Biochemistry University of California 1156 High St, Santa Cruz, CA 95064 mchen88@ucsc.edu

shankar1729 commented 3 years ago

Seems to work if you set:

coulomb-truncation-embed 0 0 0.1692635565

Must have just been a matter of not enough precision for the symmetry check.

Best, Shankar