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A collection of interpretive chemical tools for analyzing outputs of the quantum chemistry calculations.

Home Page: https://chemtools.org/

License: GNU General Public License v3.0

Python 100.00%

conceptual-dft atoms-in-molecules population-analysis molecular-orbital-theory density-matrices kinetic-energy-density

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[QUESTION] Will this repository be updated?

I would love to use this tool, but I am completely unable to install it. When trying to install the master branch, I run into issues installing Horton and Libint (#error LibInt must be compiled with an angular momentum limit of at least MAX_SHELL_TYPE, which I was not able to fix. I also tried installing the GSoC fork (#46), but then it tries to import something from denspart which doesn't seem to have ever existed? (ImportError: cannot import name 'partition' from 'denspart.mbis'). I tried using Conda too, but with no luck.

Will there be updates to the codebase and/or documentation to allow people to use it?

For completeness

OS: Debian 12
Python version: Python 3.11.2, Miniconda with Python 3.9.16
NumPy version: numpy 1.24.2
SciPy version: scipy 1.10.1

[BUG] Pull Request Template

Describe the bug
When I was making the PR #31, the pullrequest template was not used.

To Reproduce
Hopefully, make another PR and see?

Expected behavior
The PR template in https://github.com/theochem/chemtools/blob/master/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md
should appear when we make the pull request

[BUG] Using ORCA output files

Describe the bug
I am trying to use chemtools with ORCA output files. Looking at the code, I've seen that both .wfn and .mkl files are parsed.

After using orca_2aim to generate the .wfn file, I try to load it using CondensedConceptualDFT.from_file(file_path, model="quadratic"), but get this error:

Traceback (most recent call last):
  File "cdft.py", line 11, in <module>
    tool = CondensedConceptualDFT.from_file(file_path, model="quadratic")
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 452, in from_file
    molecules = cls.load_file(fname)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 142, in load_file
    molecule = Molecule.from_file(fnames)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/wrappers/molecule.py", line 111, in from_file
    iodata = IOData.from_file(os.path.join(os.getcwd(), str(fname)))
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/iodata.py", line 308, in from_file
    result.update(load_wfn(filename))
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 206, in load_wfn
    mo_count, mo_occ, mo_energy, coefficients, energy = load_wfn_low(filename)
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 94, in load_wfn_low
    num_mo, num_primitives, num_atoms = helper_num(f)
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 47, in helper_num
    assert line.startswith('GAUSSIAN')
AssertionError

The line begins with GTO instead of GAUSSIAN. If I remove this assertion, I get this error instead:

Traceback (most recent call last):
  File "cdft.py", line 11, in <module>
    tool = CondensedConceptualDFT.from_file(file_path, model="quadratic")
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 452, in from_file
    molecules = cls.load_file(fname)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 142, in load_file
    molecule = Molecule.from_file(fnames)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/wrappers/molecule.py", line 111, in from_file
    iodata = IOData.from_file(os.path.join(os.getcwd(), str(fname)))
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/iodata.py", line 308, in from_file
    result.update(load_wfn(filename))
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 208, in load_wfn
    permutation = get_permutation_basis(type_assignment)
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 163, in get_permutation_basis
    permutation = get_permutation_orbital(type_assignment)
  File "/home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib/python3.7/site-packages/horton/io/wfn.py", line 121, in get_permutation_orbital
    length = degeneracy[value]
KeyError: 4

If I use the .mkl file generated by orca_2mkl instead, I get this output instead:

User:           raphael
Machine info:   Linux Hydre 6.1.0-9-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) x86_64
Time:           2023-06-08T08:54:15.508964
Python version: 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0]
HORTON version: 2.1.0
Current Dir:    /home/raphael/tmp/orca
Command line:   cdft.py
HORTON module:  /home/raphael/1XX_General/109_Software/109.05_Python/mambaforce/envs/chemtools37/lib
                /python3.7/site-packages/horton/log.py

Initialized: <horton.gbasis.cext.GOBasis object at 0x14b38ee92910>
  Number of basis functions         : 138
  Number of normalization constants : 183
  Maximum shell type                : 3
  Center     0 :  S8 S8 S1 S1 S1 P3 P1 P1 P1 Dp1 Dp1 Dp1 Fp1 Fp1
  Center     1 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     2 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     3 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     4 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1

Detected incorrect normalization of orbitals loaded from a file.
Trying to fix it as if it was a file generated by ORCA.
Initialized: <horton.gbasis.cext.GOBasis object at 0x14b38ee92280>
  Number of basis functions         : 138
  Number of normalization constants : 183
  Maximum shell type                : 3
  Center     0 :  S8 S8 S1 S1 S1 P3 P1 P1 P1 Dp1 Dp1 Dp1 Fp1 Fp1
  Center     1 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     2 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     3 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1
  Center     4 :  S3 S1 S1 S1 P1 P1 P1 Dp1 Dp1

Detected typical ORCA errors in file. Fixing them...
Traceback (most recent call last):
  File "cdft.py", line 11, in <module>
    tool = CondensedConceptualDFT.from_file(file_path, model="quadratic")
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 453, in from_file
    return cls.from_molecule(molecules, model, approach, scheme, **kwargs)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 481, in from_molecule
    gcdft = GlobalConceptualDFT.from_molecule(molecule, model)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/conceptual.py", line 249, in from_molecule
    dict_energy = get_dict_energy(molecule)
  File "/home/raphael/1XX_General/109_Software/109.02_Chemistry/chemtools/chemtools/toolbox/utils.py", line 190, in get_dict_energy
    nelec + 1: molecule.energy + lumo_e,
TypeError: unsupported operand type(s) for +: 'NoneType' and 'float'

To Reproduce

from chemtools import CondensedConceptualDFT

file_path = "sp.mkl" # or "sp.wfn"
tool = CondensedConceptualDFT.from_file(file_path, model="quadratic")

.wfn and .mkl files

Expected behavior
I would expect chemtools to parse the files correctly like it does for .fchk files and calculate the relevant properties.

System Information:

OS: Debian 11, Linux 6.1.0-9-amd64
Python version: 3.7.12 (conda)
Numpy version: 1.21.6
Scipy version: 1.7.3

Docker update

Hello, are you by any chance planning to update the Docker image that was published by tczorro on Dockerhub 3 years ago ?
Thank you for the info !

Matplotlib backend configuration

In some scenario's (not sure which), usage of matplotlib on macos with the default backend leads to non-obvious errors. See for example:

https://travis-ci.com/theochem/tinydft/jobs/200737929#L297
theochem/tinydft#1

This is solved in chemtools with the following line:

chemtools/chemtools/outputs/plot.py

Line 27 in b899469

matplotlib.use('agg')

The problem with this solution is that it makes it impossible to use plt.show to pop up a windows with a plot.

The ideal solution would be to figure out how to install matplotlib on macos, such that the default backend works.

This is the corresponding matplotlib issue: matplotlib/matplotlib#13096 (It is closed??)

This is the corresponding conda issue: ContinuumIO/anaconda-issues#10554

How to plot NCI plot from outputs of VASP?

Dear developers,

Please help me with how we can plot NCI plots from POSCAR?

from chemtools import NCI nci = NCI.from_file('POSCAR') nci.generate_plot('poscar') nci.generate_scripts('poscar')

Error: AttributeError: Atomic Orbitals information is needed!

Thanks,

failing test test_plane_mesh

I think there are a few errors in the function plane_mesh: np.linspace needs scalars as the 2 first arguments, whereas arrays are supplied.
can you please take a look?
thank you in advance.

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