Scripts

Python scripts have been tested on Python 3.

Generate coordinates for hydrocarbons

gen_alkanes.py generates xyz coordinates for alkanes of the form H-(C2H4)n-H given n. An example for n=3 is given in the output file C6H14.xyz. An image of this molecule viewed with Avogadro is given in C6H14.png.

gen_C2H2_n.py generates xyz coordinates for polyacetylenes of the form (C2H2)n given n. An example for n=3 is given in the output file C6H8.xyz. An image of this molecule viewed with Avogadro is given in C6H8.png.

Generate coordinates for graphene sheets

gen_graphene_sheets_circH.py generates xyz coordinates for 'circular' hydrogenated graphene sheets of the form C_{6n^2}H_{6n} given n. For n=1, we just get a single benzene molecule (see file graphene-C6H6.xyz and graphene-C6H6.png). Two examples are given for n=2 and n=5 with images of the sheets viewed with Avogadro in graphene-C24H12.xyz and graphene-C24H12.png (n=2) and graphene-C150H30.xyz and graphene-C150H30.png.

gen_graphene_sheets.py generates xyz coordinates for rectangular graphene sheets (without hydrogen atoms) given n to be the number of carbon atoms. An example for n=5 is given in graphene-C190.xyz. Again, a visualization for the sheet via Avogadro is given in graphene-C190.png. Users will need to manually add hydrogen atoms or modify the script to do so before running any calculations!

Generate coordinates of randomly distributed points in box

gen_points.py generates xyz coordinates for n points randomly distributed in a box of length a in Angstrom. This might be useful in simulation, for example, when the given coordinates are of the centers of mass of molecules such as water molecules. Just for visualization, the points are labeled as Helium atoms in the generated cube.xyz and cube.json file, the latter is used in BAGEL (refer to nubakery.org for more details on this package). An example is given for n=70 and a=50.1 here.

Convert BAGEL input into xyz input

More information on BAGEL can be found here.

BAGEL to xyz

bagel2xyz.py converts BAGEL input file filename.json into xyz format filename.xyz.

BAGEL input file example is in hf.json. This is a very simple calculation for HF molecule using STO-3G basis set and TZVPP-jkfit fitting basis. Note that the coordinates should be in Angstrom.

{ "bagel" : [

{
  "title" : "molecule",
  "symmetry" : "C1",
  "basis" : "sto-3g",
  "df_basis" : "tzvpp-jkfit",
  "angstrom" : "true",
  "geometry" : [
    { "atom" : "H", "xyz" : [     -0.000000000,   -0.000000000,    0.305956000] },
    { "atom" : "F", "xyz" : [     -0.000000000,   -0.000000000,    2.720616000] }
  ]
},

{
  "title" : "hf",
  "thresh" : 1.0e-10
}

]}

Output hf.xyz file:

2
hf.json in xyz format
H    -0.000000000    -0.000000000    0.305956000
F    -0.000000000    -0.000000000    2.720616000

xyz to BAGEL

Now, you can do the reverse, that is, converting xyz file into BAGEL input file using xyz2bagel.sh. You will be asked to provide the name of the xyz file, basis set, as well as fitting basis set, and the method you want to use.

Usage:
./xyz2bagel xyzfile basis df_basis method

For example, to recreate hf.json from hf.xyz, you can do:

./xyz2bagel.sh hf.xyz sto-3g tzvpp-jkfit hf > hf.json

BAGEL to Turbomole inputs

bagel2turbomole.py converts BAGEL input file into a coordinate file coord used by the package Turbomole.

This is an example for coord generated using hf.json.

$coord
-0.000000000    -0.000000000    0.305956000       h
-0.000000000    -0.000000000    2.720616000       f
$user-defined bonds
$end

Well, if you are using Turbomole, you may need to specify the basis and fitting basis, especially if the basis sets you are using are not in the library (or you aren't sure). It's always good to know exactly what basis set you are using.

bagel2turbomole-basis.sh converts basis set in json format to a format used by Turbomole. You will need to specify if you want it to be basis or fitting basis. An example is given for Gd in gd-dz.json to generate a basis file,

./bagel2turbomole-basis.sh gd-dz.json basis > basis

and also gd-dz-jkfit.json to generate an auxbasis file.

./bagel2turbomole-basis.sh gd-dz-jkfit.json jkbas > auxbasis

This files basis and auxbasis follow Turbomole's naming convention, ready to be used.

haianhle/scripts