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Nexus: add PySCF examples #1552

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merged 6 commits into from
May 7, 2019
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jtkrogel
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@jtkrogel jtkrogel 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
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Can one of the maintainers verify this patch?

@markdewing
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okay to test

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

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anbenali commented Apr 23, 2019 via email

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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

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@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>

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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...

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anbenali commented May 3, 2019

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

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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
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jtkrogel 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
@ghost ghost removed the in progress label May 7, 2019
@jtkrogel jtkrogel deleted the nx_pyscf_examples branch September 16, 2019 12:10
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5 participants