Z-matrix reader / editor

General Discussion Suggestions
1

Greetings,

I see some old posts (circa 2010) about Z-matrix editors in Avogadro. I cannot find any in the current version though. Is there an option for these?

~ Juan

2

No, it was a development feature for Avogadro 1, but it never “shipped”

What in particular features would you want? For example, building up a new molecule by z-matrix? Or would you want some way of creating a z-matrix from an existing structure, pasting in a z-matrix, etc?

3

Well I was just taking a look at some geometries I optimized with CFOUR (which preferably operates in Z-matrix format) and thought it would be nice to be able to just copy-paste the structure in my ZMAT file as opposed to go hunt for the Cartesian structure in the output file.

Also, building Z-matrix is somewhat of an art so it would be nice to have an editor to do that and be able to see in real time if the Z-matrix you are producing makes sense or not. At the moment what I have to do is build the Z-matrix, send a calculation to see if it crashes, and try to figure out what I am doing wrong.

4

Since z-matrix formats differ, can you give me a rough idea what CFOUR expects? That might be a first step. I have some code for internal → Cartesian and Cartesian → internal.

5

Hmm I can give you an example, if that’s what you mean? Here’s a Z-matrix that works in both CFOUR and QChem:

Fe
C 1 rFeCAx
C 1 rFeCEq 2 a90
C 1 rFeCEq 3 a120 2 dn90
C 1 rFeCEq 3 a120 2 d90
C 1 rFeCAx 3 a90 4 dn90
O 1 rFeOAx 3 a90 4 d90
O 1 rFeOAx 3 a90 4 dn90
O 1 rFeOEq 2 a90 3 d0
O 1 rFeOEq 2 a90 4 d0
O 1 rFeOEq 2 a90 5 d0

rFeCAx =    1.829565855794663
rFeCEq =    1.830427937707052
rFeOAx =    2.983800083699976
rFeOEq =    2.987529988574558
a90    =   90.00000
a120   =  120.00000
dn90   =  -90.00000
d0     =    0.00000
d90    =   90.00000

This is the info they have about it: CFOUR | Main / Molecular Geometry Input

6

Yeah, the variable substitution thing is going to be a bit of a pain, but I’ll see what I can do. One caveat is that it’s going to be a busy next month or two with teaching and grant writing. (But let me know if there are collaboration / funding ideas.)

Presumably an ideal z-matrix editor for Avo2 would check for symmetric bonds / angles based on the perceived point group symmetry

7

Why would it?

And no worries - good luck with that! If you’re referring to funding ideas from my end - I avoid having to deal with money and grant writing like the plague :grin: I just find people who need other people to do cool science.

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