Bader analysis

Development
1

I was wondering if it would be possible and useful to implement Bader analysis in Avogadro. There is several minimization algorithms implemented already which makes Avogadro evolve beyond simple visualization program, why not implement Bader analysis? It needs charge density Gaussian like cube file. There is standalone program for it, of course, but integration into Avogadro GUI would be useful, too

http://theory.cm.utexas.edu/bader/

References:

*  G. Henkelman, A. Arnaldsson, and H. Jónsson,  A fast and robust algorithm for Bader decomposition of charge density, Comput. Mater. Sci. 36, 254-360 (2006).

* E. Sanville, S. D. Kenny, R. Smith, and G. Henkelman An improved grid-based algorithm for Bader charge allocation, J. Comp. Chem. 28, 899-908 (2007).

* W. Tang, E. Sanville, and G. Henkelman A grid-based Bader analysis algorithm without lattice bias, J. Phys.: Condens. Matter 21, 084204 (2009).
2

Great idea! Please, submit it to feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” jasius_1@yahoo.com:

I was wondering if it would be possible and useful to implement Bader analysis in Avogadro. There is several minimization algorithms implemented already which makes Avogadro evolve beyond simple visualization program, why not implement Bader analysis? It needs charge density Gaussian like cube file. There is standalone program for it, of course, but integration into Avogadro GUI would be useful, too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A. Arnaldsson, and H. Jónsson,  A fast and robust algorithm for Bader decomposition of charge density, Comput. Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny, R. Smith, and G. Henkelman An improved grid-based algorithm for Bader charge allocation, J. Comp. Chem. 28, 899-908 (2007).

 * W. Tang, E. Sanville, and G. Henkelman A grid-based Bader analysis algorithm without lattice bias, J. Phys.: Condens. Matter 21, 084204 (2009).

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev

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–
Regards,
Konstantin

3

Will do. I just got a positive response from the software developers below, they are also sharing they source code on their website. see below:

That would be great. As long as you keep the author list and the references that describe the algorithm (which are listed in the source), it can be incorporated into another code. It would also be nice if improvements to the algorithm could be updated in a derived code, but this is not a requirement. We’re all for a community improvement of these tools. - Graeme

— On Thu, 4/1/10, Konstantin Tokarev annulen@yandex.ru wrote:

From: Konstantin Tokarev annulen@yandex.ru
Subject: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Thursday, April 1, 2010, 3:53 AM
Great idea! Please, submit it to
feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” jasius_1@yahoo.com:

I was wondering if it would be possible and useful to
implement Bader analysis in Avogadro. There is several
minimization algorithms implemented already which makes
Avogadro evolve beyond simple visualization program, why not
implement Bader analysis? It needs charge density Gaussian
like cube file. There is standalone program for it, of
course, but integration into Avogadro GUI would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A.

Arnaldsson, and H. Jónsson, A fast and robust
algorithm for Bader decomposition of charge density, Comput.
Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny, R.

Smith, and G. Henkelman An improved grid-based algorithm for
Bader charge allocation, J. Comp. Chem. 28, 899-908 (2007).

 * W. Tang, E. Sanville, and G.

Henkelman A grid-based Bader analysis algorithm without
lattice bias, J. Phys.: Condens. Matter 21, 084204 (2009).

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed
compiling, find bugs
proactively, and fine-tune applications for
parallel performance.
See why Intel Parallel Studio got high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

4

Will do. I just got a positive response from the software developers below, they are also sharing they source code on their website. see below:

That would be great. As long as you keep the author list and the references that describe the algorithm (which are listed in the source), it can be incorporated into another code. It would also be nice if improvements to the algorithm could be updated in a derived code, but this is not a requirement. We’re all for a community improvement of these tools. - Graeme

There’s no need to incorporate their code. I think the best way is to write a plugin (of engine type) which will call ‘bader’ application, installed system-wide or within Avogadro ‘bundle’, or even simply load its output file
The only problem is to figure out, how to visualize results :slight_smile:

— On Thu, 4/1/10, Konstantin Tokarev wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 3:53 AM
Great idea! Please, submit it to
feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” :

I was wondering if it would be possible and useful to
implement Bader analysis in Avogadro. There is several
minimization algorithms implemented already which makes
Avogadro evolve beyond simple visualization program, why not
implement Bader analysis? It needs charge density Gaussian
like cube file. There is standalone program for it, of
course, but integration into Avogadro GUI would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A.

Arnaldsson, and H. Jónsson, A fast and robust
algorithm for Bader decomposition of charge density, Comput.
Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny, R.

Smith, and G. Henkelman An improved grid-based algorithm for
Bader charge allocation, J. Comp. Chem. 28, 899-908 (2007).

 * W. Tang, E. Sanville, and G.

Henkelman A grid-based Bader analysis algorithm without
lattice bias, J. Phys.: Condens. Matter 21, 084204 (2009).

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed
compiling, find bugs
proactively, and fine-tune applications for
parallel performance.
See why Intel Parallel Studio got high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

5

Or you just think of calculated bond orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” jasius_1@yahoo.com:

Will do. I just got a positive response from the software developers below, they are also sharing they source code on their website. see below:

That would be great. As long as you keep the author list and the references that describe the algorithm (which are listed in the source), it can be incorporated into another code. It would also be nice if improvements to the algorithm could be updated in a derived code, but this is not a requirement. We’re all for a community improvement of these tools. - Graeme

— On Thu, 4/1/10, Konstantin Tokarev wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 3:53 AM
Great idea! Please, submit it to
feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” :

I was wondering if it would be possible and useful to
implement Bader analysis in Avogadro. There is several
minimization algorithms implemented already which makes
Avogadro evolve beyond simple visualization program, why not
implement Bader analysis? It needs charge density Gaussian
like cube file. There is standalone program for it, of
course, but integration into Avogadro GUI would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A.

Arnaldsson, and H. Jónsson, A fast and robust
algorithm for Bader decomposition of charge density, Comput.
Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny, R.

Smith, and G. Henkelman An improved grid-based algorithm for
Bader charge allocation, J. Comp. Chem. 28, 899-908 (2007).

 * W. Tang, E. Sanville, and G.

Henkelman A grid-based Bader analysis algorithm without
lattice bias, J. Phys.: Condens. Matter 21, 084204 (2009).

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed
compiling, find bugs
proactively, and fine-tune applications for
parallel performance.
See why Intel Parallel Studio got high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

6

pretty much. or tabulated values, or a value for the selected atoms only. I think this would be very exciting application

— On Thu, 4/1/10, Konstantin Tokarev annulen@yandex.ru wrote:

From: Konstantin Tokarev annulen@yandex.ru
Subject: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Thursday, April 1, 2010, 5:26 AM
Or you just think of calculated bond
orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” jasius_1@yahoo.com:

Will do. I just got a positive response from the
software developers below, they are also sharing they source
code on their website. see below:

That would be great. As long as you keep the
author list and the references that describe the algorithm
(which are listed in the source), it can be incorporated
into another code. It would also be nice if improvements to
the algorithm could be updated in a derived code, but this
is not a requirement. We’re all for a community improvement
of these tools. - Graeme

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 3:53 AM
Great idea! Please, submit it to
feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” :

I was wondering if it would be
possible and useful to
implement Bader analysis in Avogadro. There
is several
minimization algorithms implemented already
which makes
Avogadro evolve beyond simple visualization
program, why not
implement Bader analysis? It needs charge
density Gaussian
like cube file. There is standalone program
for it, of
course, but integration into Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A.

Arnaldsson, and H. Jónsson, A fast and
robust
algorithm for Bader decomposition of charge
density, Comput.
Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny,

R.

Smith, and G. Henkelman An improved
grid-based algorithm for
Bader charge allocation, J. Comp. Chem. 28,
899-908 (2007).

 * W. Tang, E. Sanville, and

G.

Henkelman A grid-based Bader analysis
algorithm without
lattice bias, J. Phys.: Condens. Matter 21,
084204 (2009).

Download Intel® Parallel Studio
Eval
Try the new software tools for
yourself. Speed
compiling, find bugs
proactively, and fine-tune
applications for
parallel performance.
See why Intel Parallel Studio got
high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

7

I think it would be reasonable to add bader output format to OpenBabel, and add new property for OBBond like ‘fractional order’

01.04.10, 06:36, “Jonas Baltrusaitis” jasius_1@yahoo.com:

pretty much. or tabulated values, or a value for the selected atoms only. I think this would be very exciting application

— On Thu, 4/1/10, Konstantin Tokarev wrote:

From: Konstantin Tokarev
Subject: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 5:26 AM
Or you just think of calculated bond
orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” :

Will do. I just got a positive response from the
software developers below, they are also sharing they source
code on their website. see below:

That would be great. As long as you keep the
author list and the references that describe the algorithm
(which are listed in the source), it can be incorporated
into another code. It would also be nice if improvements to
the algorithm could be updated in a derived code, but this
is not a requirement. We’re all for a community improvement
of these tools. - Graeme

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 3:53 AM
Great idea! Please, submit it to
feature request tracker

31.03.10, 18:16, “Jonas Baltrusaitis” :

I was wondering if it would be
possible and useful to
implement Bader analysis in Avogadro. There
is several
minimization algorithms implemented already
which makes
Avogadro evolve beyond simple visualization
program, why not
implement Bader analysis? It needs charge
density Gaussian
like cube file. There is standalone program
for it, of
course, but integration into Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman, A.

Arnaldsson, and H. Jónsson, A fast and
robust
algorithm for Bader decomposition of charge
density, Comput.
Mater. Sci. 36, 254-360 (2006).

 * E. Sanville, S. D. Kenny,

R.

Smith, and G. Henkelman An improved
grid-based algorithm for
Bader charge allocation, J. Comp. Chem. 28,
899-908 (2007).

 * W. Tang, E. Sanville, and

G.

Henkelman A grid-based Bader analysis
algorithm without
lattice bias, J. Phys.: Condens. Matter 21,
084204 (2009).

Download Intel® Parallel Studio
Eval
Try the new software tools for
yourself. Speed
compiling, find bugs
proactively, and fine-tune
applications for
parallel performance.
See why Intel Parallel Studio got
high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

8

But to my understanding Bader is not getting calculated by Qm programs. They just supply charge density files as cubes and then math needs to be done by avogadro

Jonas

— On Thu, 4/1/10, Konstantin Tokarev annulen@yandex.ru wrote:

From: Konstantin Tokarev annulen@yandex.ru
Subject: Re: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Thursday, April 1, 2010, 7:11 AM
I think it would be reasonable to add
bader output format to OpenBabel, and add new property for
OBBond like ‘fractional order’

01.04.10, 06:36, “Jonas Baltrusaitis” jasius_1@yahoo.com:

pretty much. or tabulated values, or a value for the
selected atoms only. I think this would be very exciting
application

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 5:26 AM
Or you just think of calculated bond
orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” :

Will do. I just got a positive
response from the
software developers below, they are also
sharing they source
code on their website. see below:

That would be great. As long as you
keep the
author list and the references that
describe the algorithm
(which are listed in the source), it can be
incorporated
into another code. It would also be nice if
improvements to
the algorithm could be updated in a derived
code, but this
is not a requirement. We’re all for a
community improvement
of these tools. - Graeme

— On Thu, 4/1/10, Konstantin
Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel]
Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010,
3:53 AM
Great idea! Please, submit it
to
feature request tracker

31.03.10, 18:16, “Jonas
Baltrusaitis” :

I was wondering if it
would be
possible and useful to
implement Bader analysis in
Avogadro. There
is several
minimization algorithms
implemented already
which makes
Avogadro evolve beyond simple
visualization
program, why not
implement Bader analysis? It
needs charge
density Gaussian
like cube file. There is
standalone program
for it, of
course, but integration into
Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman,

A.

Arnaldsson, and H. Jónsson,
A fast and
robust
algorithm for Bader
decomposition of charge
density, Comput.
Mater. Sci. 36, 254-360
(2006).

 * E. Sanville, S.

D. Kenny,

R.

Smith, and G. Henkelman An
improved
grid-based algorithm for
Bader charge allocation, J.
Comp. Chem. 28,
899-908 (2007).

 * W. Tang, E.

Sanville, and

G.

Henkelman A grid-based Bader
analysis
algorithm without
lattice bias, J. Phys.:
Condens. Matter 21,
084204 (2009).

Download Intel®
Parallel Studio
Eval
Try the new software
tools for
yourself. Speed
compiling, find bugs
proactively, and
fine-tune
applications for
parallel performance.
See why Intel Parallel
Studio got
high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing
list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма
есть. Спама

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

9

Bader is written in F90. Avogadro for Windows is compiled with MSVC => it isn’t possible to include Fortran code (or I’m wrong?). On Unices there isn’t any problem to install bader into /usr/local/bin. So my proposal will be don’t touch code that works, and use it as external application

01.04.10, 07:56, “Jonas Baltrusaitis” jasius_1@yahoo.com:

But to my understanding Bader is not getting calculated by Qm programs. They just supply charge density files as cubes and then math needs to be done by avogadro

Jonas

— On Thu, 4/1/10, Konstantin Tokarev wrote:

From: Konstantin Tokarev
Subject: Re: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 7:11 AM
I think it would be reasonable to add
bader output format to OpenBabel, and add new property for
OBBond like ‘fractional order’

01.04.10, 06:36, “Jonas Baltrusaitis” :

pretty much. or tabulated values, or a value for the
selected atoms only. I think this would be very exciting
application

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 5:26 AM
Or you just think of calculated bond
orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” :

Will do. I just got a positive
response from the
software developers below, they are also
sharing they source
code on their website. see below:

That would be great. As long as you
keep the
author list and the references that
describe the algorithm
(which are listed in the source), it can be
incorporated
into another code. It would also be nice if
improvements to
the algorithm could be updated in a derived
code, but this
is not a requirement. We’re all for a
community improvement
of these tools. - Graeme

— On Thu, 4/1/10, Konstantin
Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel]
Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010,
3:53 AM
Great idea! Please, submit it
to
feature request tracker

31.03.10, 18:16, “Jonas
Baltrusaitis” :

I was wondering if it
would be
possible and useful to
implement Bader analysis in
Avogadro. There
is several
minimization algorithms
implemented already
which makes
Avogadro evolve beyond simple
visualization
program, why not
implement Bader analysis? It
needs charge
density Gaussian
like cube file. There is
standalone program
for it, of
course, but integration into
Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman,

A.

Arnaldsson, and H. Jónsson,
A fast and
robust
algorithm for Bader
decomposition of charge
density, Comput.
Mater. Sci. 36, 254-360
(2006).

 * E. Sanville, S.

D. Kenny,

R.

Smith, and G. Henkelman An
improved
grid-based algorithm for
Bader charge allocation, J.
Comp. Chem. 28,
899-908 (2007).

 * W. Tang, E.

Sanville, and

G.

Henkelman A grid-based Bader
analysis
algorithm without
lattice bias, J. Phys.:
Condens. Matter 21,
084204 (2009).

Download Intel®
Parallel Studio
Eval
Try the new software
tools for
yourself. Speed
compiling, find bugs
proactively, and
fine-tune
applications for
parallel performance.
See why Intel Parallel
Studio got
high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing
list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта. Письма
есть. Спама

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

–
Regards,
Konstantin

Здесь спама нет http://mail.yandex.ru/nospam/sign

10

Also, AFAIK Bader analysis can be time consuming for large systems, so it would be reasonable to use properly optimized binary from authors

01.04.10, 07:56, “Jonas Baltrusaitis” jasius_1@yahoo.com:

But to my understanding Bader is not getting calculated by Qm programs. They just supply charge density files as cubes and then math needs to be done by avogadro

Jonas

— On Thu, 4/1/10, Konstantin Tokarev wrote:

From: Konstantin Tokarev
Subject: Re: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 7:11 AM
I think it would be reasonable to add
bader output format to OpenBabel, and add new property for
OBBond like ‘fractional order’

01.04.10, 06:36, “Jonas Baltrusaitis” :

pretty much. or tabulated values, or a value for the
selected atoms only. I think this would be very exciting
application

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 5:26 AM
Or you just think of calculated bond
orders loading?

01.04.10, 05:20, “Jonas Baltrusaitis” :

Will do. I just got a positive
response from the
software developers below, they are also
sharing they source
code on their website. see below:

That would be great. As long as you
keep the
author list and the references that
describe the algorithm
(which are listed in the source), it can be
incorporated
into another code. It would also be nice if
improvements to
the algorithm could be updated in a derived
code, but this
is not a requirement. We’re all for a
community improvement
of these tools. - Graeme

— On Thu, 4/1/10, Konstantin
Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: [Avogadro-devel]
Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010,
3:53 AM
Great idea! Please, submit it
to
feature request tracker

31.03.10, 18:16, “Jonas
Baltrusaitis” :

I was wondering if it
would be
possible and useful to
implement Bader analysis in
Avogadro. There
is several
minimization algorithms
implemented already
which makes
Avogadro evolve beyond simple
visualization
program, why not
implement Bader analysis? It
needs charge
density Gaussian
like cube file. There is
standalone program
for it, of
course, but integration into
Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G. Henkelman,

A.

Arnaldsson, and H. Jónsson,
A fast and
robust
algorithm for Bader
decomposition of charge
density, Comput.
Mater. Sci. 36, 254-360
(2006).

 * E. Sanville, S.

D. Kenny,

R.

Smith, and G. Henkelman An
improved
grid-based algorithm for
Bader charge allocation, J.
Comp. Chem. 28,
899-908 (2007).

 * W. Tang, E.

Sanville, and

G.

Henkelman A grid-based Bader
analysis
algorithm without
lattice bias, J. Phys.:
Condens. Matter 21,
084204 (2009).

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–
Regards,
Konstantin

–
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Konstantin

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–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

–
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11

This is beyond my understanding, I think having Bader implemented and associated with Avogadro GUi would be utmost useful. How it’s done - I will let you decide. Most importantly, Bader developers don;t mind and are happy to see their code reused and/or optimized if needed

— On Thu, 4/1/10, Konstantin Tokarev annulen@yandex.ru wrote:

From: Konstantin Tokarev annulen@yandex.ru
Subject: Re: Re: Re: Re: [Avogadro-devel] Bader analysis
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Thursday, April 1, 2010, 8:21 AM
Also, AFAIK Bader analysis can be
time consuming for large systems, so it would be reasonable
to use properly optimized binary from authors

01.04.10, 07:56, “Jonas Baltrusaitis” jasius_1@yahoo.com:

But to my understanding Bader is not getting
calculated by Qm programs. They just supply charge density
files as cubes and then math needs to be done by avogadro

Jonas

— On Thu, 4/1/10, Konstantin Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: Re: Re: [Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010, 7:11 AM
I think it would be reasonable to add
bader output format to OpenBabel, and add
new property for
OBBond like ‘fractional order’

01.04.10, 06:36, “Jonas Baltrusaitis” :

pretty much. or tabulated values, or a
value for the
selected atoms only. I think this would be
very exciting
application

— On Thu, 4/1/10, Konstantin
Tokarev
wrote:

From: Konstantin Tokarev
Subject: Re: Re:
[Avogadro-devel] Bader
analysis
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Thursday, April 1, 2010,
5:26 AM
Or you just think of calculated
bond
orders loading?

01.04.10, 05:20, “Jonas
Baltrusaitis” :

Will do. I just got a
positive
response from the
software developers below, they
are also
sharing they source
code on their website. see
below:

That would be great. As
long as you
keep the
author list and the references
that
describe the algorithm
(which are listed in the
source), it can be
incorporated
into another code. It would
also be nice if
improvements to
the algorithm could be updated
in a derived
code, but this
is not a requirement. We’re all
for a
community improvement
of these tools. - Graeme

— On Thu, 4/1/10,
Konstantin
Tokarev
wrote:

From: Konstantin
Tokarev
Subject: Re:
[Avogadro-devel]
Bader
analysis
To: “Jonas
Baltrusaitis”
Cc: “Avogadro-devel
Devel”
Date: Thursday,
April 1, 2010,
3:53 AM
Great idea! Please,
submit it
to
feature request
tracker

31.03.10, 18:16,
“Jonas
Baltrusaitis” :

I was
wondering if it
would be
possible and useful to
implement Bader
analysis in
Avogadro. There
is several
minimization
algorithms
implemented already
which makes
Avogadro evolve
beyond simple
visualization
program, why not
implement Bader
analysis? It
needs charge
density Gaussian
like cube file.
There is
standalone program
for it, of
course, but
integration into
Avogadro GUI
would be useful,
too

http://theory.cm.utexas.edu/bader/

References:

 *  G.

Henkelman,

A.

Arnaldsson, and H.
Jónsson,
A fast and
robust
algorithm for
Bader
decomposition of charge
density, Comput.
Mater. Sci. 36,
254-360
(2006).

 * E.

Sanville, S.

D. Kenny,

R.

Smith, and G.
Henkelman An
improved
grid-based algorithm for
Bader charge
allocation, J.
Comp. Chem. 28,
899-908 (2007).

 * W.

Tang, E.

Sanville, and

G.

Henkelman A
grid-based Bader
analysis
algorithm without
lattice bias, J.
Phys.:
Condens. Matter 21,
084204 (2009).

Download
Intel®
Parallel Studio
Eval
Try the new
software
tools for
yourself. Speed
compiling, find
bugs
proactively,
and
fine-tune
applications for
parallel
performance.
See why
Intel Parallel
Studio got
high marks
during beta.
http://p.sf.net/sfu/intel-sw-dev

Avogadro-devel mailing

list

Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

–
Regards,
Konstantin

–
Regards,
Konstantin

Яндекс.Почта.
Письма
есть. Спама

–
Regards,
Konstantin

Яндекс.Почта. Письма
есть. Спама

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама

12

On Apr 1, 2010, at 11:52 AM, Jonas Baltrusaitis wrote:

This is beyond my understanding, I think having Bader implemented and associated with Avogadro GUi would be utmost useful. How it’s done - I will let you decide. Most importantly, Bader developers don;t mind and are happy to see their code reused and/or optimized if needed

Before I see more messages about this, I should say that there’s already someone working on directly integrating Bader analysis into Avogadro. There’s a few notes:

  1. Bader analysis is slow. If you use it on a cube (rather than a wavefunction), it also requires a very fine grid.
  2. The code is typically written in F90, so it likely would not be a “core” plugin distributed with Avogadro.
  3. An Avogadro plugin can read AIM output files without directly needing anything in Open Babel (although certainly that works too).

Visualization techniques for AIM/Bader analysis vary. Many times, people want to see the critical points, not just calculated bond orders or charges.

If someone is gung-ho about the project, I can put them in touch with Eric Brown, who has been working on updated QTAIM code and wants to integrate it into Avogadro.

Cheers,
-Geoff