Continuous measures of shape and symmetry
Project description
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
$ 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
$ 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
$ 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
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
shp_measure = geometry.get_shape_measure('T-4', central_atom=1)
# Geometrical symmetry measure
sym_geom_measure = geometry.get_symmetry_measure('C3', central_atom=1)
#Create molecule from geometry (generate electronic structure with Extended Hukel method)
molecule = Molecule(geometry)
# Wave function symmetry measure
wf_sym_measure = molecule.get_wf_symmetry('Td')
# Electronic density measure
dens_sym_measure = molecule.get_dens_symmetry('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
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