gimic

Gauge-including magnetically induced currents.

https://github.com/qmcurrents/gimic

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 3 DOI reference(s) in README
  • Academic publication links
    Links to: zenodo.org
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary

Keywords

currents quantum-chemistry
Last synced: 6 months ago · JSON representation ·

Repository

Gauge-including magnetically induced currents.

Basic Info
  • Host: GitHub
  • Owner: qmcurrents
  • License: gpl-2.0
  • Language: Python
  • Default Branch: master
  • Homepage: https://gimic.readthedocs.io
  • Size: 22.6 MB
Statistics
  • Stars: 28
  • Watchers: 4
  • Forks: 19
  • Open Issues: 23
  • Releases: 2
Topics
currents quantum-chemistry
Created about 9 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation Zenodo

README.md

DOI test status

GIMIC: gauge-including magnetically induced currents

Documentation: https://gimic.readthedocs.io

About GIMIC

The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format.

Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices.

Example

There is an annotated example input in the examples directory.

Citation

For a recommended code citation, please check the at the bottom-right of https://zenodo.org/record/8180434 (on that page, search for "Cite as"). Also the DOI badge on top of the README links to that page.

When using GIMIC please cite:

  • J. Juselius, D. Sundholm, J. Gauss, Calculation of Current Densities Using Gauge- Including Atomic Orbitals. J. Chem. Phys. 2004, 121, 3952-3963

  • H. Fliegl, S. Taubert, O. Lehtonen, D. Sundholm, The Gauge Including Magnetically Induced Current Method. Phys. Chem. Chem. Phys. 2011, 13, 20500-20518

Review:

  • D. Sundholm, H. Fliegl, R. J. Berger, Calculations of Magnetically Induced Current Densities: Theory and Applications. WIREs Comput. Mol. Sci. 2016, 6, 639-678

Open-shell calculations:

  • S. Taubert, D. Sundholm, J Juselius, Calculation of Spin-Current Densities Using Gauge-Including Atomic Orbitals. J. Chem. Phys. 2011, 134, 054123:1-12

ACID:

  • H. Fliegl, J. Jusélius, D. Sundholm, Gauge-Origin Independent Calculations of the Anisotropy of the Magnetically Induced Current Densities, J. Phys. Chem. A, 120, 2016, 5658-5664

When using the G09 interface:

  • M. Rauhalahti, S. Taubert, D. Sundholm, V. Liegeois, Calculations of current densities for neutral and doubly charged persubstituted benzenes using ective core potentials. Phys. Chem. Chem. Phys. 2017, 19, 7124-7131

When using the NumGrid libary:

  • https://github.com/dftlibs/numgrid#citation

NMR shielding constants based on the current density:

  • RK Jinger, H Fliegl, R Bast, M Dimitrova, S Lehtola, D Sundholm, Spatial contributions to nuclear magnetic shieldings, J. Phys. Chem. A, 125, 1778-1786

Magnetizability based on the current density:

  • S Lehtola, M Dimitrova, H Fliegl, D Sundholm, Benchmarking magnetizabilities with recent density functionals, J. Chem. Theo. Comp., 17, 1457-1468

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  The gauge including magnetically induced current density
  method (GIMIC)
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Jonas
    family-names: Juselius
    email: jonas.juselius@gmail.com
    affiliation: Tromsø
    orcid: 'https://orcid.org/0000-0003-4498-3806'
  - given-names: Radovan
    family-names: Bast
    email: radovan.bast@uit.no
    affiliation: Tromsø
    orcid: 'https://orcid.org/0000-0003-4498-3806'
  - given-names: Heike
    family-names: Fliegl
    email: heike.fliegl@gmail.com
    affiliation: Karlsruhe
    orcid: 'https://orcid.org/0000-0002-7541-115X'
  - given-names: Dage
    family-names: Sundholm
    email: Dage.Sundholm@chem.helsinki.fi
    affiliation: Helsinki
    orcid: 'https://orcid.org/0000-0002-2367-9277'
  - given-names: Maria
    family-names: Dimitrova
    email: Maria.Dimitrova@gmail.com
    affiliation: Helsinki
    orcid: 'https://orcid.org/0000-0002-0711-3484'
  - given-names: Lukas
    family-names: Wirz
    affiliation: Helsinki
    orcid: 'https://orcid.org/0000-0002-6577-7166'
  - given-names: Vincent
    family-names: Liegeois
    affiliation: Namur
    orcid: 'https://orcid.org/0000-0003-2919-8025'
  - given-names: Chandan
    family-names: Kumar
    affiliation: Munich
  - given-names: Thomas
    family-names: Kjærgaard
    affiliation: Copenhagen
    orcid: 'https://orcid.org/0000-0001-5986-5840'
  - given-names: Jörg
    family-names: Kussmann
    email: jkupc@cup.uni-muenchen.de
    affiliation: Munich
    orcid: 'https://orcid.org/0000-0002-4724-8551'
  - given-names: Jaakko
    family-names: Pyykkö
    affiliation: Helsinki
  - given-names: Teemu
    family-names: Järvinen
    affiliation: Helsinki
    orcid: 'https://orcid.org/0000-0001-9234-9071'
  - given-names: Jürgen
    family-names: Gauss
    affiliation: Mainz
    orcid: 'https://orcid.org/0000-0002-6432-9345'
repository-code: 'https://github.com/qmcurrents/gimic'
url: 'https://gimic.readthedocs.io/en/latest/'
abstract: >-
  The gauge including magnetically induced current method
  (GIMIC) is used to obtain magnetically induced current
  densities in molecules. It provides detailed information
  about electron delocalization, aromatic character, and
  current pathways in molecules. GIMIC needs molecular
  coordinates, basis set and the atomic orbital density as
  well as the first order perturbed density matrices as
  input information. It is freely available and interfaced
  to several well known quantum chemistry software packages
  like for example Turbomole. Based on Gimic output
  information it is possible to visualize the current
  density with the ParaView software package. Beside the
  current density it is possible to obtain nuclear magnetic
  shieldings as well as magnetizability information with
  GIMIC. For this purpose the program has been interfaced to
  the NumGrid library, which provides optimized atomic grids
  for accurate numerical calculations.
keywords:
  - magnetically induced current density
  - aromaticity
  - integration
  - numerical methods
  - London orbitals
license: GPL-2.0
version: '2.2.1'
date-released: '2023-07-25'

GitHub Events

Total
  • Issues event: 1
  • Pull request event: 1
  • Fork event: 2
Last Year
  • Issues event: 1
  • Pull request event: 1
  • Fork event: 2

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
proxy.golang.org: github.com/qmcurrents/gimic
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • cython *
  • numpy *
  • pyparsing ==2.4.7
  • pyyaml *
  • runtest ==2.3.2
  • sphinx *
  • sphinx_rtd_theme *
.github/workflows/test-debug.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/validate-cff.yml actions
  • actions/checkout v3 composite
  • dieghernan/cff-validator main composite