From owner-chemistry |-at-| ccl.net Thu Dec 30 09:00:00 2021 From: "Geoffrey Hutchison geoff.hutchison\a/gmail.com" To: CCL Subject: CCL:G: Quantum chemistry interoperability library? Message-Id: <-54553-211230085109-341-NdopeChUVFi4TjkXX+YN4w],[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_8591CB49-82F9-40CC-BCFC-3DA0A69BD523" Date: Thu, 30 Dec 2021 08:51:01 -0500 Mime-Version: 1.0 (Mac OS X Mail 15.0 \(3693.40.0.1.81\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison###gmail.com] --Apple-Mail=_8591CB49-82F9-40CC-BCFC-3DA0A69BD523 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii This was at least part of the point of the QC JSON schema. MolSSI sponsored at least one workshop where this was discussed and a = draft was written. At that workshop several years ago, in which many developers, including = quantum programs (NWChem, Q-Chem, Psi4, Molpro, GAMESS .. I know pretty = much the entire community was invited), analysis programs (Horton), = community programs (cclib, Open Babel, Avogadro, Jmol, etc.) were there. = It was a big enough meeting that I'm sure I missed some people. Issues of normalization, metadata, input files (e.g. keywords), = program-specific features, etc were all discussed. The idea was to first get out a "better Molden" interchange. So if you (personally) and/or MolSSI want to push this again, it would = be great. Perhaps either a virtual meeting or discussion forum can get things = moving again? Cheers, -Geoff P.S. The work and some discussion is here: = https://github.com/MolSSI/QCSchema --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh[*]pitt.edu twitter: [*]ghutchis web: https://hutchison.chem.pitt.edu/ > On Dec 29, 2021, at 8:01 PM, Susi Lehtola = susi.lehtola[A]alumni.helsinki.fi wrote: >=20 >=20 > Sent to CCL by: Susi Lehtola [susi.lehtola{=3D}alumni.helsinki.fi] > Hello, >=20 >=20 >=20 > I am again hitting my head against the wall, since I am having trouble > passing data from one quantum chemistry code to another. >=20 > What we are missing as a community is a standard interoperability > library for passing basis set and wave function data from one program = to > another. The de facto standard is GAUSSIAN's formatted checkpoint > library, but it also has some deficiencies; for instance, it's not > machine precision. >=20 > Because the library should store all the necessary data for at least = SCF > wave functions, that is, the Gaussian basis set and the molecular > orbitals (MOs) and their occupation numbers, an interface to this > library could also serve as a tool for checkpointing calculations that > have not converged. >=20 > Some pieces of the necessary functionality are certainly around. Many > quantum chemistry programs have implemented their own formatted > checkpoint i/o functions. Quantum chemistry analysis programs have > needed to implement their own parsers for the .fchk / MOLDEN / etc = formats. >=20 > I do not think that writing such a common interface library should be > too difficult. All that is needed is >=20 > 1. a data structure that is able to express the data in a common = format and >=20 > 2. input and output functions to translate the data from/to specific > quantum chemistry code formats. >=20 > In addition to the .fchk and molden formats, the common interface > library should also be able to read various programs' native data = files >> from disk, like DENS and XDENS in TURBOMOLE. >=20 > Since many pieces of the puzzle are already around, and the problem > affects the whole community, I would like to get everyone's feedback = on > this idea. >=20 > If there was, say, a portable open-source C++ library with C, Fortran > and Python frontends for handling molecular wave function data, would > you be willing to use it in your own program package? What kinds of > features would you need in it? Does such a library already exist? >=20 > Susi >=20 > PS. I work as a Software Scientist at the Molecular Sciences Software > Institute at Virginia Tech (http://molssi.org), but I am sending this > message from my Helsinki address since it's what I've used here for > close to a decade. > --=20 > ------------------------------------------------------------------ > Mr. Susi Lehtola, PhD Adjunct Professor > susi.lehtola##alumni.helsinki.fi University of Helsinki > http://susilehtola.github.io/ Finland > ------------------------------------------------------------------ > Susi Lehtola, FT dosentti > susi.lehtola##alumni.helsinki.fi Helsingin yliopisto > http://susilehtola.github.io/ > ------------------------------------------------------------------ >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_8591CB49-82F9-40CC-BCFC-3DA0A69BD523 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
This was at least part of the point of the QC JSON = schema.

MolSSI = sponsored at least one workshop where this was discussed and a draft was = written.

At = that workshop several years ago, in which many developers, including = quantum programs (NWChem, Q-Chem, Psi4, Molpro, GAMESS .. I know pretty = much the entire community was invited), analysis programs (Horton), = community programs (cclib, Open Babel, Avogadro, Jmol, etc.) were there. = It was a big enough meeting that I'm sure I missed some = people.

Issues = of normalization, metadata, input files (e.g. keywords), = program-specific features, etc were all discussed.

The idea was to first = get out a "better Molden" interchange.

So if you (personally) and/or MolSSI = want to push this again, it would be great.

Perhaps either a virtual meeting or = discussion forum can get things moving again?

Cheers,
-Geoff

P.S. The work and some discussion is here: https://github.com/MolSSI/QCSchema

---
Prof. Geoffrey = Hutchison
Department of Chemistry
University = of Pittsburgh
tel: (412) 648-0492
email: geoffh[*]pitt.edu
twitter: [*]ghutchis
web: https://hutchison.chem.pitt.edu/

On Dec 29, 2021, at 8:01 PM, Susi Lehtola susi.lehtola[A]alumni.helsinki.fi = <owner-chemistry[*]ccl.net> wrote:


Sent to CCL by: Susi Lehtola [susi.lehtola{=3D}alumni.helsinki.fi]
Hello,



I am again hitting my head against the wall, since I am = having trouble
passing data from one quantum chemistry = code to another.

What we are missing as a = community is a standard interoperability
library for = passing basis set and wave function data from one program to
another. The de facto standard is GAUSSIAN's formatted = checkpoint
library, but it also has some deficiencies; for = instance, it's not
machine precision.

Because the library should store all the necessary data for = at least SCF
wave functions, that is, the Gaussian basis = set and the molecular
orbitals (MOs) and their occupation = numbers, an interface to this
library could also serve as = a tool for checkpointing calculations that
have not = converged.

Some pieces of the necessary = functionality are certainly around. Many
quantum chemistry = programs have implemented their own formatted
checkpoint = i/o functions. Quantum chemistry analysis programs have
needed to implement their own parsers for the .fchk / MOLDEN = / etc formats.

I do not think that writing = such a common interface library should be
too difficult. = All that is needed is

1. a data structure = that is able to express the data in a common format and

2. input and output functions to translate the data from/to = specific
quantum chemistry code formats.

In addition to the .fchk and molden formats, the common = interface
library should also be able to read various = programs' native data files
from disk, like DENS and XDENS in TURBOMOLE.

Since many pieces of the puzzle = are already around, and the problem
affects the whole = community, I would like to get everyone's feedback on
this = idea.

If there was, say, a portable = open-source C++ library with C, Fortran
and Python = frontends for handling molecular wave function data, would
you be willing to use it in your own program package? What = kinds of
features would you need in it? Does such a = library already exist?

Susi
PS. I work as a Software Scientist at the Molecular Sciences = Software
Institute at Virginia Tech (http://molssi.org), but I am = sending this
message from my Helsinki address since it's = what I've used here for
close to a decade.
-- =
---------------------------------------------------------------= ---
Mr. Susi Lehtola, PhD =             Ad= junct Professor
susi.lehtola##alumni.helsinki.fi =   University of Helsinki
http://susilehtola.github.io/ =     Finland
---------------------------------------------------------------= ---
Susi Lehtola, FT =             &n= bsp;    dosentti
susi.lehtola##alumni.helsinki.fi =   Helsingin yliopisto
http://susilehtola.github.io/
---------------------------------------------------------------= ---



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