Nexus: add PySCF examples

[jtkrogel]

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.

[qmc-robot]

Can one of the maintainers verify this patch?

[markdewing]

okay to test

[jtkrogel]

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

[anbenali]

To address point 2, give me 1 or 2 more hours t and finalize the new API for solids as the complex evaluation is almost complete. In the PR in progress your point is addressed I believe but I am still finalizing a few details. For the water energy that is weird.. can you give more details?

…

On Tue, Apr 23, 2019, 13:19 jtkrogel ***@***.***> wrote: @anbenali <https://github.com/anbenali> Any comments on the second point? Is this a reasonable change? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1552 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF4XVQYP23HRZ7ZYYZBBV53PR5HKZANCNFSM4HG4UTVA> .

[jtkrogel]

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]

@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]

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]

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

[anbenali]

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

[jtkrogel]

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