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EDDB_info

EDDB is a program developed by Dariusz W. Szczepanik for computational chemistry, with installation and usage instructions available online. It is recommended to use NBO version >6 for consistent results, and users can perform various analyses using command-line options. Additional functionalities include computing orbital separated indices and visualizing results with tools like Avogadro.

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38 views

EDDB_info

EDDB is a program developed by Dariusz W. Szczepanik for computational chemistry, with installation and usage instructions available online. It is recommended to use NBO version >6 for consistent results, and users can perform various analyses using command-line options. Additional functionalities include computing orbital separated indices and visualizing results with tools like Avogadro.

Uploaded by

luis
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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EDDB

Program developed by Dariusz W. Szczepanik former postdoc of M. Solà.

Information about the program installation and usage is available here:


http://www.eddb.pl/runeddb/
*NOTE: when you install it following the instructions on the webpage you may need to
modify the 1st line of the script (#!/usr/bin/env Rscript --vanilla) according to your machine
requirements.

The recommendation is to use NBO version >6 but I ran simple tests (i.e. benzene, pyridine)
and I was obtaining consistent results with NBO 3 and 6 versions. Note that for running
Gaussian including the NBO6 version in the Beta cluster you should use the g09d01_pgi-
10.1_NBO6 version.

Jobfile (for beta) example:

#!/bin/bash
module unload gaussian
module load g09d01_pgi-10.1_NBO6
cp $SGE_O_WORKDIR/name.com .
g09 name > name.log
formchk name.chk name.fchk
cp *.49 $SGE_O_WORKDIR/.
cp *.log $SGE_O_WORKDIR/.
cp *.chk $SGE_O_WORKDIR/.
cp *.fchk $SGE_O_WORKDIR/.

*********************************************************************************
Other functionalities of EDDB not listed in the manual:

You can compute the orbital separated indices by including the -d (for dissection) flag, like in
the following example:

RunEDDB.R -q -i mol.fchk mol.49 -h -d 1:3 -o eddbH_pi.fchk > eddbH_pi.out

The recommendation is first to check the occupations of spinless NOBD in the output of a
normal eddbH or eddbG calculation (the pi orbitals will have the largest occupations in small
aromatic rings), then visualize the *fchk (Avogadro is recommended, and remember that
EDDB rewrites the fchk with the NOBD orbitals but the labels are not changed. The NOBD
with highest occupation corresponds to orbital 1 in the list of orbitals) obtained from this
eddbG or H calculation to confirm the orbitals one wants to include (corresponding to 1, 2,
and 3 in the example).

Full list of EDDB command-line options:

-a To diagonalize atomic blocks of the EDDB density matrix set it to TRUE


-b To perform the EDDB analysis only for formally bonded atoms set it TRUE
-c To skip the EDDB calculations and perform the NPA analysis set it TRUE
-d [list of NOBD to be considered, e.g. 1:4] to compute the contribution of a particular
orbital(s)
-e [molecular fragment, e.g. 1:4,7,8] select the EDDB_E function
-f [molecular fragment, e.g. 1:4,7,8] select the EDDB_F function
-g select the EDDB_G function
-h select the EDDB_H function
-i [e.g. MOLECULE.FCHK DMNAO.49] select input files
-m To reduce the full basis into the natural minimum basis (NMB) set it TRUE
-o [e.g. EDDB_X.FCHK] export the calculated EDDB_X into a new .FCHK file
-oo To visualize alpha and beta components of the EDDB(r) function set it to TRUE
-p [delocalization pathway, e.g. 1-2-3-4-5-6-1] select the EDDB_P function
-q disable interactive mode
-s To remove the UHF spin contamination and perform the EDDB analysis for paired (closed
subshell) and unpaired electrons (open subshell) set it to TRUE

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