I know how to use the Gaussview's user interface to add a new atom & create a covalent bond between it and an atom that already exists in a gaussian input file. But is there a way to do this by command line? Please help. I have a huge number of files & I want an atom at a specific location to all of them but it will be exceedingly difficult to open each such file in gauss view individually & add atoms to them.
If your geometry files are somewhat symmetrized, you can add a line with the atom coordinates to each of them using a linux shell script (or python, if you prefer that). A covalent bond is a "resulting" property, so in a simple geometry input file that does not need to be specified.
Adding a single atom of any element (except the noble gases) shall definitely alter the spin multiplicity/charge of the system. So, in addition to appending a new line with element name and coordinates (assuming the geometry is written in cartesian), you shall also need to modify the charge/multiplicity line in the input file.
A bond is a resulting property in DFT as mentioned by Jürgen Weippert, but if your input is written in z-matrix format, you need to include distance, angle and dihedral parameters. In such a case, several lines needs to be inserted in the input file as shown in the following example with ">>"
0 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1 0
H 1 B4 3 A3 2 D2 0
>> He 1 B5 2 A4 3 D3 0
B1 1.07000000
B2 1.07000000
B3 1.07000000
B4 1.07000000
>> B5 5.00000000
A1 109.47120255
A2 109.47125080
A3 109.47121829
>> A4 54.00000000
D1 -119.99998525
D2 120.00000060
>> D3 30.00000000
If the input coordinates are written in cartesian, you just need to append one line with the element name and the x y z coordinates as follows:
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.07000000
H 1.00880579 0.00000000 -0.35666635
H -0.50440312 -0.87365131 -0.35666635
H -0.50440269 0.87365135 -0.35666686
>> He 3.50314635 -2.02254249 2.93892626
If the element is not a noble gas, correction to the charge and multiplicity line is also required.
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