Problem with importing from Psi4 .fchk

kazufumi · March 3, 2019, 3:09am

I don’t know whether this is a bug with Avogadro or Psi4 generate a wrong fchk format.
I can’t compare it with Gaussian fchk because I don’t have it.

Environment Information

Avogadro version: 1.2.0
Operating system and version:macOS 10.14（18A391）

Expected Behavior

Rendering Orbitals works well
The fchk file on this site works well in my Environment.
http://www.lct.jussieu.fr/manuels/Gaussian98/show/mogvcm001.htm

Actual Behavior

Avogadro only displays the molecule but doesn’t show orbital nor orbital energy.

Steps to Reproduce

This is the fchk file of CH4 from Psi4

github.com

Mishima-syk/psikit/blob/351b93b635a67c9535cab7cb6a8a00ffed4327b2/examples/fchk/ch4.fchk

Generated by Psi4
     FORCE                           SCF                       6-31G**
Number of atoms                            I                5
Charge                                     I                0
Multiplicity                               I                1
Number of electrons                        I               10
Number of alpha electrons                  I                5
Number of beta electrons                   I                5
Number of basis functions                  I               35
Number of independent functions            I               35
Atomic numbers                             I   N=           5
           6           1           1           1           1
Nuclear charges                            R   N=           5
  6.00000000e+00  1.00000000e+00  1.00000000e+00  1.00000000e+00  1.00000000e+00
Current cartesian coordinates              R   N=          15
 -4.23982907e-09 -1.61349987e-08 -1.37037682e-10 -1.25425320e+00  1.61115075e+00
 -1.57725898e-01 -7.54340811e-01 -1.56154067e+00 -1.08921800e+00  1.58018767e-01
 -5.52220258e-01  1.96568516e+00  1.85057530e+00  5.02610379e-01 -7.18741263e-01
Integer atomic weights                     I   N=           5
          12           1           1           1           1

This file has been truncated. show original

Juanes · September 7, 2025, 12:14am

Apologies for “necrobumping” but this person never got an answer and it may help someone. Seems like for Avogadro to read the orbitals the section in the .fchk file needs to read:

Number of independent functions I 35
Alpha MO coefficients R N= 1225

In the file provided (line 78 and 332) it reads:

MO coefficients (C) R N= 1225

ghutchis · September 7, 2025, 1:51am

I’ll point out that Gaussian documented their format and the Alpha MO coefficients (or Beta) is clear (i.e., it’s a bug with Psi IMHO).

But the appropriate code in Avogadro would be here:

github.com/OpenChemistry/avogadrolibs

avogadro/quantumio/gaussianfchk.cpp

ce0cdb681


      
              m_scftype = Uhf;
              m_alphaOrbitalEnergy = m_orbitalEnergy;
              m_orbitalEnergy = vector<double>();
          
              m_alphaMOcoeffs = m_MOcoeffs;
              m_MOcoeffs = vector<double>();
            }
          
            m_betaOrbitalEnergy =
              readArrayD(in, Core::lexicalCast<int>(list[2]), 16, hartreeToEV);
          } else if (key == "Alpha MO coefficients" && list.size() > 2) {
            if (m_scftype == Rhf) {
              m_MOcoeffs = readArrayD(in, Core::lexicalCast<int>(list[2]), 16);
            } else if (m_scftype == Uhf) {
              m_alphaMOcoeffs = readArrayD(in, Core::lexicalCast<int>(list[2]), 16);
            } else {
              cout << "Error, alpha MO coefficients, n = " << m_MOcoeffs.size() << endl;
            }
          } else if (key == "Beta MO coefficients" && list.size() > 2) {
            m_betaMOcoeffs = readArrayD(in, Core::lexicalCast<int>(list[2]), 16);
          } else if (key == "Total SCF Density" && list.size() > 2) {

Juanes · September 7, 2025, 5:59pm

I’ll see if psi4 still formats the fchk this way and bring it up in their forum if it does

ghutchis · September 7, 2025, 6:31pm

I should be able to patch our code, but I’m sure we’re not the only one who coded like that based on Gaussian’s files and documentation.

Juanes · September 7, 2025, 7:16pm

So maybe its better for them to adjust to everyone else

ghutchis · September 7, 2025, 11:17pm

I think they should definitely match the Gaussian example, since I doubt we’re the only program using those strings.

In the meantime:

github.com/OpenChemistry/avogadrolibs

Tweaks to support field names from Psi4 fchk

master ← ghutchis:read-psi-fchk

opened 11:16PM - 07 Sep 25 UTC

ghutchis

+3 -2

Developer Certificate of Origin Version 1.1 Copyright (C) 2004, 2006 The Lin…ux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.