Citation links not displaying correctly.

I have been trying the AVAS example, but before being able to do anything about it, there is an issue with a self-consistent calculation. Line:
https://github.com/pyscf/pyscf-doc/blob/93f34be682adf516a692e28787c19f10cbb4b969/examples/mcscf/43-avas.py#L49
is not able to finish execution.
I have tried it both in my personal laptop for larger times than an hour, and in google colab for more than half an hour and it never finishes. I am inclined to think there might be an issue.
(Installation was done in both cases via pip install pyscf)

Hello every body,
I do some jobs using Pyscf and I want to trace some spectrums, how can i do?
or is there any soft or programs to extract them from log or chk files ?

thanks

A friend of mine contacted me saying that the instructions at https://pyscf.org/code-rule.html is incorrect since psutil.virtual_memory() returns 11 values, not 10.

Sure enough, running the example code

import psutil
total, available, percent, used, free, active, inactive, buffers, cached, shared = psutil.virtual_memory()

gives me the error

>>> total, available, percent, used, free, active, inactive, buffers, cached, shared = psutil.virtual_memory()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ValueError: too many values to unpack (expected 10)

This is with Python 3.9.4.

A perennial question is how to use get_bands with HF. One should either
(i) shift the BZ mesh or
(ii) use exxdiv="vcut_sph" (or "ws?")
This should be documented since this comes up from time to time.

We should have a way to expose what is in the examples without people having to read each example. Could be pushed to the website, e.g. like matplotlib gallery of examples.

I believe sphinx_rtd_theme is also needed as a prerequisite unless I have been doing things wrong?

discussion of default integral precision and screening thresholds for molecules should be placed somewhere

Should it be 10 steps in comment?

Hello!

This page: https://pyscf.org/user/scf.html#property-calculations

says: see the examples in examples/prop/17-stability.py

which links to: https://github.com/pyscf/pyscf/tree/master/examples/prop/17-stability.py

that does not exist any more at that link. Should it be pointing to something here: https://github.com/pyscf/pyscf.github.io/blob/master/examples/prop/01-freq.py ?

MP2 documentation (re-)write with the user documentation as the highest priority.

Hello everyone.
I am new in PySCF, I have already worked with gaussian and orca..
gaussian generates a log and chk file that we use to visualize the orbitals and energy properties, but with PySCF it's not the same thing, I saw that you have to generate a Cubegen or molden file, I tried but its didn't go well.
possible a hand to understand this procedure?
Thanks.

Can anyone assist me with writing for loops in pyscf?

We need to document for every method whether it has R, U, G and complex orbital support.

The current install instruction of linking BLAS library was written for Intel CPU. For AMD CPU (and other CPUs), it would be helpful to add an instruction for the possible choices of BLAS library and their settings in cmake command. See relevant discussions in pyscf/pyscf#980

Problem

Currently source/user/gto.rst doesn't have any examples showing how to initialize a molecule using an XYZ file.

Solution

Add another example, something along the lines of:

mol = gto.M(atom="coronene.xyz", basis="ccpvtz", verbose=5)

Hello!

I hope you are doing well!

We are a security research team. Our tool automatically detected a vulnerability in this repository. We want to disclose it responsibly. GitHub has a feature called Private vulnerability reporting, which enables security research to privately disclose a vulnerability. Unfortunately, it is not enabled for this repository.

Can you enable it, so that we can report it?

Thanks in advance!

PS: you can read about how to enable private vulnerability reporting here: https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/configuring-private-vulnerability-reporting-for-a-repository

The manual has several examples hard-coded in its source. This is suboptimal, since running the examples then requires copypasting the code to a Python terminal. A better solution would be to replace the hard-coded examples by include statements; that way users can run the examples without copy-paste.

The current API documentation puts all the functions in the same web page, which seems not clear. It would be better to use the same style as numpy documentation where each page contains only one function.

Hello
I have some errors after run dft calcul on creating cube and molden files
here is the code
from pyscf import gto
from pyscf import dft
from pyscf.tools import cubegen
from pyscf.tools import molden
import os
os.OMP_NUM_THREADS=6

strfile='C6Ge6H6'
strpath= '/home/dev/Documents/New Job 5-5-22/Cation/' + strfile +'/B3lyp/'
strpath_xyz= '/home/dev/Documents/My Jobs/' + strfile + '/'
Mol_C= gto.Mole()

Mol_C.atom ="""H 0.000000000000 0.000000000000 0.000000000000
C 0.000000000000 0.000000000000 1.087900000000
H 1.025681956337 0.000000000000 1.450533333333
H -0.512840978169 0.888266630391 1.450533333333
H -0.512840978169 -0.888266630391 1.450533333333"""

Mol_C.basis = 'def2-qzvp'
Mol_C.verbose = 5
Mol_C.charge = 1
Mol_C.spin = 1
Mol_C.max_memory=12000
Mol_C.output = strpath + strfile + '_B3lyp.log'
Mol_C.build()

mf = dft.UKS(Mol_C)
mf.xc = 'B3LYP'
mf.chkfile = strpath + strfile + '_B3lyp.chk'
mf.run()
energy = mf.kernel(mf.make_rdm1())
cubegen.orbital(Mol_C, strpath + strfile + '_B3lyp_mo1_orb.cube', mf.mo_coeff[:,0])
cubegen.density(Mol_C, strpath + strfile + '_B3lyp_dens.cube', mf.make_rdm1())
cubegen.mep(Mol_C, strpath + strfile + '_B3lyp_pot_mep.cube', mf.make_rdm1())

with open(strpath + strfile + 'mo' + '.molden', 'w') as f1:
molden.header(Mol_C, f1)
molden.orbital_coeff(Mol_C, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)

print({strfile: energy})

error for cube
shapes (8000,177) and (2,177) not aligned: 177 (dim 1) != 2 (dim 0)
error for molden
IndexError: index 2 is out of bounds for axis 0 with size 2

can some body helps please?

There should be an Authors section in the manual detailing the authorship of the various sections. The pinned post on Slack is a good initial guess.

I think it would be nice to have a fifth subsection in pbc, explaining how k point sampled post HF methods are done.

Documentation tends to be always the last thing developers pay attention to, and often what happens is that once a feature is complete and merged, one moves onto the next thing so documentation is never kept up to date. (A good way to avoid this is to force people to document their code by not allowing undocumented code to be merged in in the first place!)

A major issue in PySCF is that it is quite distinctively a developer code. Setting up calculations requires programming, and the user has to explicitly take care of things that happen automatically in other codes, such as the removal of linear dependencies. (I actually still look at the examples distributed as part of PySCF to set up my calculations!) This special characteristic means that documentation is hugely important.

In the old documentation, the tutorial(!) had a lot of specialized code and customizations, like

• a function that printed out the occupations by symmetry in section 5.5.1, Hartree-Fock; this happens automatically in other codes, or
• a hand-written implementation of unrestricted MP2 in section 5.5.2

While these examples underline the flexibility of PySCF, I'm not sure their proper place is in the tutorial chapter; a much better place would be in the developer documentation. The tutorial section should just consist of straightforward examples for professional quantum chemists, that is, people who already know what they want to do, and just want to see how to run that calculation with PySCF.

Of course, not all bases can be covered in the tutorial, so also the user documentation will have several examples on how to run a bit more complicated calculations with PySCF. As in the manuals for other programs, the user documentation should contain at least a minimal level of theory of what is done in the code and how the equations are solved along with any relevant citations.

Another issue with the current version of the documentation is that molecular and crystalline calculations are discussed together, which makes the documentation extremely hard to follow. The discussion should be started out with molecules - which are easier - and then continue in a new section to crystals, where the differences to molecular calculations can be discussed.

The user documentation should also not go too deep into the code. The code design belongs in the developer documentation section. The developer documentation is the "hard-core" version, with the class structures, coding styles, etc. The section builds on top of the user documentation, so the theory already presented in the user section does not need to be repeated; however, algorithmic details should be discussed at a deeper level in the developer section.

Hi, could you please add a link to our pyscf-AC0 extension? https://github.com/CQCL/pyscf-ac0
It is an unofficial port of Pernal group's GAMMCOR https://github.com/pernalk/GAMMCOR and implements the CAS-AC0 method described by them in https://doi.org/10.1021/acs.jctc.8b00213

For what reason the version of sphinxcontrib-bibtex is fixed to 1.0.0 in requirements.txt ?
I find that 1.0.0 does not work with python 3.10 and when I switch it to 2.4.2, there's no problem for compilation.