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Add examples at README.md
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@abelcarreras
abelcarreras committed Apr 15, 2022
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Expand Up @@ -28,6 +28,189 @@ Requirements
- Huckelpy
- Blas & Lapack libraries
- Fortran compiler

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
----------------------------------------------------------------------
````


Python API example
------------------
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