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cosymlib

Documentation

https://github.com/grupestructuraelectronicasimetria/cosymlib

Science Score: 59.0%

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Repository

Documentation

Basic Info
  • Host: GitHub
  • Owner: GrupEstructuraElectronicaSimetria
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage: https://cosymlib.readthedocs.io/
  • Size: 49.4 MB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 5
  • Releases: 1
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme License Zenodo

README.md

Build Status Coverage Status PyPI version DOI Open In Colab

CoSymLib

Python library to compute continuous shape and symmetry measures of molecular structures
Online manual: http://cosymlib.readthedocs.io

Main features

  • Continuous Shape and Symmetry measures of molecular geometries
  • Continuous Symmetry measures of electronic structure of molecules
  • Support for common file types including XYZ, coor, pdb & fchk
  • Usage through python API or command line tools

Requirements

  • Python 2.7/3.4 or higher
  • Matplotlib
  • Numpy
  • PyYaml
  • Symgroupy
  • Wfnsympy
  • Huckelpy
  • Blas & Lapack libraries
  • Fortran compiler

Examples using command line tools

Shape measure

````bash $ shape cf4.xyz -c 1 -l

COSYMLIB v0.10.5 Electronic Structure & Symmetry Group Institut de Quimica Teorica i Computacional (IQTC)

Universitat de Barcelona

Available reference structures with 4 Vertices:

Label Sym Info

SP-4 D4h Square T-4 Td Tetrahedron SS-4 C2v Seesaw vTBPY-4 C3v Axially vacant trigonal bipyramid

$ shape cf4.xyz -c 1 -m all

COSYMLIB v0.10.5 Electronic Structure & Symmetry Group Institut de Quimica Teorica i Computacional (IQTC)

Universitat de Barcelona

Structure SP-4 T-4 SS-4 vTBPY-4

cf4, 33.333, 0.000, 9.790, 3.573,

                End of calculation

````

Geometrical symmetry measure

````bash $ gsym cf4.xyz -l

COSYMLIB v0.10.6 Electronic Structure & Symmetry Group Institut de Quimica Teorica i Computacional (IQTC)

Universitat de Barcelona

Available symmetry groups

E Identity Symmetry Ci Inversion Symmetry Group Cs Reflection Symmetry Group Cn Rotational Symmetry Group (n: rotation order) Sn Rotation-Reflection Symmetry Group (n: rotation-reflection order)

$ gsym cf4.xyz -m Ci

COSYMLIB v0.10.6 Electronic Structure & Symmetry Group Institut de Quimica Teorica i Computacional (IQTC)

Universitat de Barcelona

Evaluating symmetry operation : Ci

cf4 16.667

                End of calculation

````

Wave function symmetry analysis

````bash $ mosym NF3.fchk -m C3 -mo

COSYMLIB v0.10.6 Electronic Structure & Symmetry Group Institut de Quimica Teorica i Computacional (IQTC)

Universitat de Barcelona

Symmetry group : C3

Molecule : NF3

Atomic Coordinates (Angstroms)

N -0.000022 0.000014 0.483415 F 1.225707 -0.219543 -0.125324 F -0.802975 -0.951706 -0.125331 F -0.422715 1.171239 -0.125335

WaveFunction: Irred. Rep. Decomposition ------------------ A E
------------------ a-wf 1.000 0.000 b-wf 1.000 0.000 WFN 1.000 0.000

Symmetry axis orientation center: 0.00000036 -0.00000023 0.00244913 axis : 0.00001508 -0.00001685 1.00000000 axis2 : 0.00000000 1.00000000 0.00001685

Molecule : NF3

Atomic Coordinates (Angstroms)

N -0.000022 0.000014 0.483415 F 1.225707 -0.219543 -0.125324 F -0.802975 -0.951706 -0.125331 F -0.422715 1.171239 -0.125335

Alpha MOs: Irred. Rep. Decomposition ------------------------------------ occup E(eV) A E
------------------------------------ 1 1 -708.54 0.994 0.006 2 1 -708.53 0.002 0.998 3 1 -708.53 0.004 0.996 4 1 -424.19 1.000 0.000 5 1 -45.23 1.000 0.000 6 1 -41.57 0.000 1.000 7 1 -41.57 0.000 1.000 8 1 -26.74 1.000 0.000 9 1 -18.48 0.000 1.000 10 1 -18.48 0.000 1.000 11 1 -18.40 1.000 0.000 12 1 -15.18 0.000 1.000 13 1 -15.18 0.000 1.000 14 1 -14.24 1.000 0.000 15 1 -13.54 0.000 1.000 16 1 -13.54 0.000 1.000 17 1 -10.69 1.000 0.000 18 0 12.21 0.000 1.000 19 0 12.21 0.000 1.000 20 0 12.52 1.000 0.000

Beta MOs: Irred. Rep. Decomposition ------------------------------------ occup E(eV) A E
------------------------------------ 1 1 -708.54 0.994 0.006 2 1 -708.53 0.002 0.998 3 1 -708.53 0.004 0.996 4 1 -424.19 1.000 0.000 5 1 -45.23 1.000 0.000 6 1 -41.57 0.000 1.000 7 1 -41.57 0.000 1.000 8 1 -26.74 1.000 0.000 9 1 -18.48 0.000 1.000 10 1 -18.48 0.000 1.000 11 1 -18.40 1.000 0.000 12 1 -15.18 0.000 1.000 13 1 -15.18 0.000 1.000 14 1 -14.24 1.000 0.000 15 1 -13.54 0.000 1.000 16 1 -13.54 0.000 1.000 17 1 -10.69 1.000 0.000 18 0 12.21 0.000 1.000 19 0 12.21 0.000 1.000 20 0 12.52 1.000 0.000

                End of calculation

````

Example using Python API

````python from cosymlib import Molecule, Geometry

Define geometry

geometry = Geometry(positions=[[ 0.0000, 0.0000, 0.0000], [ 0.5288, 0.1610, 0.9359], [ 0.2051, 0.8240, -0.6786], [ 0.3345, -0.9314, -0.4496], [-1.0685, -0.0537, 0.1921]], symbols=['C', 'H', 'H', 'H', 'H'])

Shape measure

shpmeasure = geometry.getshapemeasure('T-4', centralatom=1)

Geometrical symmetry measure

symgeommeasure = geometry.getsymmetrymeasure('C3', central_atom=1)

Create molecule from geometry (generate electronic structure with Extended Hukel method)

molecule = Molecule(geometry)

Wave function symmetry measure

wfsymmeasure = molecule.getwfsymmetry('Td')

Electronic density measure

denssymmeasure = molecule.getdenssymmetry('Td') ````

Contact info

Abel Carreras
abelcarreras83@gmail.com
Donostia International Physics Center (DIPC)

Pere Alemany
p.alemany@ub.edu
Electronic Structure & Symmetry group
Department of Materials Science and Physical Chemistry
Institut de Química Teòrica i Computacional (IQTC-UB)
University of Barcelona

GitHub Events

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  • Watch event: 1
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  • Push event: 9
Last Year
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 9

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 427
  • Total Committers: 7
  • Avg Commits per committer: 61.0
  • Development Distribution Score (DDS): 0.585
Top Committers
Name Email Commits
efrem k****n@g****m 177
abel a****3@g****m 173
efrem e****z@g****m 30
efrembernuz e****z@u****u 27
Ferran Jimenez f****c@g****m 13
perealemany p****y@u****u 6
Miquel l****l@u****u 1
Committer Domains (Top 20 + Academic)
ub.edu: 3

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 12
  • Total pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 2 hours
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.08
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
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Top Authors
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  • abelcarreras (6)
  • MiquelLlunell (4)
  • perealemany (1)
  • andrewtarzia (1)
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  • dependabot[bot] (2)
Top Labels
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bug (4) enhancement (3)
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 250 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 35
  • Total maintainers: 1
pypi.org: cosymlib

Continuous measures of shape and symmetry

  • Versions: 35
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 250 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 13.5%
Average: 19.9%
Dependent repos count: 21.6%
Forks count: 22.7%
Stargazers count: 31.9%
Maintainers (1)
abelcarreras83
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • PyYAML >=5.1
  • huckelpy >=0.2
  • matplotlib *
  • numpy >=1.16.6
  • symgroupy *
  • wfnsympy *
setup.py pypi
  • PyYAML *
  • huckelpy *
  • matplotlib *
  • numpy *
  • symgroupy *
  • wfnsympy *
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • pypa/cibuildwheel v2.4.0 composite
  • pypa/gh-action-pypi-publish v1.4.2 composite
docs/requirements.readthedocs.txt pypi
  • PyYAML *
  • matplotlib *
  • numpy >=1.8.2,<1.21.5
  • pointgroup *
  • wheel *