visualization software

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RickV
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visualization software

Post by RickV » 20 Feb 2014, 15:00

Hello,

Can anyone tell me which is good visualization software for molecules to use with dalton?

Thanks!

Rick

bast
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Re: visualization software

Post by bast » 20 Feb 2014, 15:55

hi Rick, what exactly do you want to do: look at molecules optimized by Dalton (in other words
post-processing)? or construct/visualize molecules that you then want to input into Dalton?
best greetings,
radovan

RickV
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Re: visualization software

Post by RickV » 20 Feb 2014, 16:06

I want to look at the molecules optimized by dalton. Mostly, to check if the right molecule is calculated.
Also, a graphical way to input molecules for dalton calculation would be nice. I don't know if there is a program which does both.

Another requirement is that it should be able to run on Mac OSX.

bast
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Re: visualization software

Post by bast » 20 Feb 2014, 21:14

hi Rick, i like the avogadro program: http://avogadro.cc/wiki/Main_Page
it is cross platform and free. however, i am not aware of any program that reads Dalton output files
directly. in the Dalton output you find the final geometry which is unfortunately
printed in bohr and not in angstrom. in the latter case one could simply copy paste
it and read it as xyz format but that will not work in bohr.
we need to add a xyz format printout to the Dalton output. this is very simple to do and it will
go into the next patch. if you like scripting you can also write a very simple script which
will extract the final structure and convert it to xyz format (angstrom).

taylor
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Re: visualization software

Post by taylor » 20 Feb 2014, 22:31

Molden has the advantage that it runs on everything and Dalton already provides an input file to Molden (it's in the tar.gz file that is by default returned to your working directory when the calculation completes. This provides not only MOs and the final geometry, but also the steps of a geometry optimization, and vibrations and normal modes. The only thing I would say is that the display of the MOs is pretty crude and would not really be considered publication-grade.

Molden is free, and has the additional advantage for old farts like me that virtually everything is written in Fortran except the monster module that interfaces to the X Windows system, which is in C.

Best regards
Pete
P.S. It is available through homebrew and MacPorts (this is not a recommendation, just a statement) but is no trouble to build if you have gcc/gfortran, plus Xquartz (or whatever).

erik
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Re: visualization software

Post by erik » 21 Feb 2014, 08:47

I can recommend molden if all you need is to have a look at the molecule where, as Pete correctly states, everything is already ready as DALTON outputs the molden.inp file.
For xyz coordinates I really like the program chimera, http://www.cgl.ucsf.edu/chimera/ (I think this program also works on both Mac, windows and linux). It can also make MOs (cube files) and densitites etc. quite nice

Really a nice thing if the xyz coordinates where printed. This is probaby the wrong place to suggest things for further development, but since we are already on the topic, the xyz file might as well be packed along the other things in the tar.gz file. In case of a geometry optimization, it should then only be the optimized geometry that was dumbed.

bast
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Re: visualization software

Post by bast » 21 Feb 2014, 08:53

i agree with you Erik - i will put it in.

RickV
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Re: visualization software

Post by RickV » 21 Feb 2014, 10:24

I can see the need for an xyz output file. I myself lack the skills to write a script for it.
I just tried molden but I don't like the program very much. It doesn't show the bonds.
I just can't seem to find any visualization software that works with dalton ouput (in bohr).

bast
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Re: visualization software

Post by bast » 21 Feb 2014, 17:33

hi Rick. i just implemented this as part of the very soon (hopefully next week) to be released 2013.2 patch.

RickV
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Re: visualization software

Post by RickV » 28 Feb 2014, 10:27

Awesome!

saisudhakar
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Re: visualization software

Post by saisudhakar » 02 Dec 2015, 10:37

Molden will work only on Linux ? or on Windows also?

arnfinn
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Re: visualization software

Post by arnfinn » 02 Dec 2015, 12:25

saisudhakar wrote:Molden will work only on Linux ? or on Windows also?
This is the Dalton forum; not a Molden forum. Maybe you can find something on this page: http://www.cmbi.ru.nl/molden/

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