Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Nexus: add PySCF examples #1552

Merged
merged 6 commits into from May 7, 2019

Conversation

@jtkrogel
Copy link
Contributor

commented Apr 18, 2019

In this PR, examples are added for PySCF and PySCF to QMCPACK workflows for both molecular and solid state cases (water molecule and diamond).

There are two issues that remain before this PR can be merged.

  • In the PySCF to QMCPACK workflow for all electron water, the QMCPACK total energy does not agree with PySCF Hartree-Fock (deferred until later)
  • In the PySCF to QMCPACK workflow for diamond, convert4qmc changes its output format relative to the molecular case (it appends "Twist0" to all file names). This should not happen unless requested (moving target for both users and Nexus). The existing -prefix mechanism might be preferred here.

Once confirmed by @anbenali, separate GitHub issues + resolution can be made for these points.

@ghost ghost assigned jtkrogel Apr 18, 2019

@ghost ghost added the in progress label Apr 18, 2019

@qmc-robot

This comment has been minimized.

Copy link
Collaborator

commented Apr 18, 2019

Can one of the maintainers verify this patch?

@markdewing

This comment has been minimized.

Copy link
Contributor

commented Apr 18, 2019

okay to test

@jtkrogel

This comment has been minimized.

Copy link
Contributor Author

commented Apr 23, 2019

@anbenali Any comments on the second point? Is this a reasonable change?

@anbenali

This comment has been minimized.

Copy link
Contributor

commented Apr 23, 2019

@jtkrogel

This comment has been minimized.

Copy link
Contributor Author

commented Apr 23, 2019

For point 2, all that is needed is that the files made by convert4qmc have the same names whether you are running a molecule or a solid.

For the water case (point 1), this is what I get with PySCF:

converged SCF energy = -76.0302783714398

And this is what I get with QMCPACK:

viribus>qmca -e 200 -q e *scalar*
vmc  series 0  LocalEnergy           =  -74.856150 +/- 0.058227 

The files are attached. See scf.py, c4q.in, and vmc.in.xml. Hopefully it is a novice mistake on my part.
for_anouar.zip

@jtkrogel

This comment has been minimized.

Copy link
Contributor Author

commented Apr 23, 2019

@anbenali I see it now. Pyscf is changing the atomic coordinates (presumably because symmetries are on?)

This is the input structure (angstrom):

 H    0.00000000   0.75716000   0.58626000
 H    0.00000000   0.75716000  -0.58626000
 O    0.00000000   0.00000000   0.00000000

This is what comes out of convert4qmc:

    <attrib name="position" datatype="posArray">
  0.0000000000e+00  0.0000000000e+00 -2.8616500650e-01
  0.0000000000e+00  1.1078708378e+00  1.1446600260e+00
  0.0000000000e+00 -1.1078708378e+00  1.1446600260e+00
</attrib>
    <attrib name="ionid" datatype="stringArray">
 O H H 
</attrib>
@anbenali

This comment has been minimized.

Copy link
Contributor

commented Apr 23, 2019

Point 2 has been address in PR #1560. Point 1 is strange... Let me look at it.. yes symmetries are on but this is strange to move the Oxygen atom coordinates...

@anbenali

This comment has been minimized.

Copy link
Contributor

commented May 3, 2019

@jtkrogel : changes that will enable this PR are now awaiting in PR #1578

@anbenali
Copy link
Contributor

left a comment

Waiting for #1578 to me merged to accept this merge.

@jtkrogel jtkrogel changed the title [WIP] Nexus: add PySCF examples Nexus: add PySCF examples May 6, 2019

@jtkrogel

This comment has been minimized.

Copy link
Contributor Author

commented May 6, 2019

Please go ahead and merge this one in. I can check for compatibility and post a brief update if needed.

@ghost ghost assigned markdewing May 6, 2019

@ghost ghost assigned ye-luo May 6, 2019

@markdewing markdewing merged commit 5ddd6b3 into QMCPACK:develop May 7, 2019

3 checks passed

rhea-cpu
Details
rhea-cuda-experimental
Details
rhea-gpu
Details

@ghost ghost removed the in progress label May 7, 2019

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
5 participants
You can’t perform that action at this time.