CCL:G: Electron Density cubic grid generation
- From: sobereva <sobjubao~~yahoo.com.cn>
- Subject: CCL:G: Electron Density cubic grid generation
- Date: Fri, 5 Apr 2013 16:12:29 +0800 (CST)
Dear Gabriel Carvalho,
AFAIK, there is no directly way to convert aux file to wfn file. wfn file can
only be generated by the ab initio programs based on Gauss functions. The method
for obtaining wfn file via Gaussian and GAMESS-US is described at the
beginning of Chapter 4 of the manual.
If you have any question about Multiwfn, please feel free to directly contact me
via the E-mail address given in Multiwfn website.
Best wishes,
Tian Lu
--- On Thu, 4/4/13, Gabriel Urquiza urquizagabes ~ gmail.com
<owner-chemistry[-]ccl.net> wrote:
> From: Gabriel Urquiza urquizagabes ~ gmail.com
<owner-chemistry[-]ccl.net>
Subject: CCL:G: Electron Density cubic grid generation
To: "Lu, Tian " <sobjubao[-]yahoo.com.cn>
Date: Thursday, April 4, 2013, 11:47 PM
Dear Eva (is that how should I call you?)
Thank you very much for your tip! It's been helping along perfectly. It's just
what I need, plus it's faster than I hoped, and the best of it is that it's
opensource, that's a plus. Once more, thank you very much.
Attentiously
Gabriel Carvalho
P.S. Would you know a program to convert from mopac .aux format to gaussian
.wfn?
2013/4/3 Gabriel Urquiza <urquizagabes]^[gmail.com>
Dear Tian Lu,
Thank you very much for your information, I think this might be exactly what I'm
looking for, however, I'm puzzled about the content of these .wfn files. I've
checked a few of them on the examples page and the overall layout didn't seem to
ring any bells. I have currently a gaussian .chk file of a benzene as well as
its corresponding input, how do I go from that to a .wfn? Is there a fast and
reliable way to do that?
Thanks once more for the tip, I'll keep going through the manual but apart >
from this difficulty with the filetypes, my doubt seems like its solved!
Attentiously
Gabriel Carvalho
2013/4/3 sobereva sobjubao_-_yahoo.com.cn <owner-chemistry]^[ccl.net>
Sent to CCL by: sobereva [sobjubao\a/yahoo.com.cn]
Hi,
Please have a try Multiwfn (http://multiwfn.codeplex.com). You can use either .fch or
.wfn/.wfx file generated by Gaussian as input file for generating cube file of
electron density. This program provides rather flexible ways to set up grid. For
example, to generate the cube file of electron density for H2O.wfn, after
booting up Multiwfn you only need to input following commands (the texts after
the double slashes are comments):
E:\H2O.wfn // The file path
5 // Main function 5
1 // Electron density
3 // There will be about 1728000 grids in total, and the grid spacings in
X,Y,Z are exactly identical, namely cubic grid. You can also choose other
options to set up the grid, especially by option 4, you can directly specify the
grid spacings in X,Y,Z manually
2 // Export the grid data to density.cub in current folder
For more about generating grid data in Multiwfn, please check Section 3.6 of the
manual and the examples given in Section 4.5.
Tian Lu
--- On Wed, 4/3/13, Gabriel Aires Urquiza Carvalho
gabrielcarvalho%quimica.ufpb.br <owner-chemistry*_*ccl.net> wrote:
> From: Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br
<owner-chemistry*_*ccl.net>
> Subject: CCL:G: Electron Density cubic grid generation
> To: "Lu, Tian " <sobjubao*_*yahoo.com.cn>
> Date: Wednesday, April 3, 2013, 2:37 AM
>
> Sent to CCL by: "Gabriel Aires Urquiza Carvalho"
> [gabrielcarvalho**quimica.ufpb.br]
> Dear CCL subscribers,
>
>
> Is there any way I could get volumetric data of electron
> density in the form
> of a cubic voxelized grid? I have tried the gaussian
> "cubegen" utility but it
> doesn't neccessarily generates cubic grids, and I need those
> to be cubic
> because the other programs I'm using for my analysis can
> only cubic binary
> inputs and I'd rather not go through rewritting their code
> unless I really
> have to.
>
> It doesn't have to write the voxels in binary, I can convert
> them to a binary
> stream as an extra step in the process by writing a minor
> Fortran utility, I
> just need something to generate the voxels for me, in a
> cubic arrangement.
>
> Thanks in advance!
>
>
> Gabriel Aires Urquiza Carvalho
>
> gabrielcarvalho#,#quimica.ufpb.br
> Programa de Ps-Graduao em Qumica
> Departamento de Qumica
> Universidade Federal da Paraba - Brazil
>
>
>
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---381987588-515870243-1365149549=:60236
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
<table cellspacing="0" cellpadding="0"
border="0" ><tr><td valign="top"
style="font: inherit;"><DIV>Dear Gabriel
Carvalho,</DIV>
<DIV> </DIV>
<DIV>AFAIK, there is no directly way to convert aux file to wfn file. wfn
file can only be generated by the ab initio programs based on Gauss functions.
The method for obtaining wfn file via Gaussian and GAMESS-US is
described at the beginning of Chapter 4 of the manual.</DIV>
<DIV> </DIV>
<DIV>If you have any question about Multiwfn, please feel free to directly
contact me via the E-mail address given in Multiwfn website.</DIV>
<DIV> </DIV>
<DIV>Best wishes,</DIV>
<DIV> </DIV>
<DIV>Tian Lu </DIV>
<DIV><BR><BR>--- On <B>Thu, 4/4/13, Gabriel Urquiza
urquizagabes ~ gmail.com
<I><owner-chemistry[-]ccl.net></I></B>
wrote:<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT:
5px; MARGIN-LEFT: 5px"><BR>From: Gabriel Urquiza urquizagabes ~
gmail.com <owner-chemistry[-]ccl.net><BR>Subject: CCL:G:
Electron Density cubic grid generation<BR>To: "Lu, Tian "
<sobjubao[-]yahoo.com.cn><BR>Date: Thursday, April 4, 2013,
11:47 PM<BR><BR>
<DIV id=yiv894493646>
<DIV dir=ltr>Dear Eva (is that how should I call you?)
<DIV><BR></DIV>
<DIV><BR></DIV>
<DIV>Thank you very much for your tip! It's been helping along perfectly.
It's just what I need, plus it's faster than I hoped, and the best of it is that
it's opensource, that's a plus. Once more, thank you very much.</DIV>
<DIV><BR></DIV>
<DIV>Attentiously</DIV>
<DIV><BR></DIV>
<DIV><BR></DIV>
<DIV>Gabriel Carvalho</DIV>
<DIV><BR></DIV>
<DIV>P.S. Would you know a program to convert from mopac .aux format to
gaussian .wfn?</DIV></DIV>
<DIV class=yiv894493646gmail_extra><BR><BR>
<DIV class=yiv894493646gmail_quote>2013/4/3 Gabriel Urquiza <SPAN
dir=ltr><<A href="http://us.mc152.mail.yahoo.com/mc/compose?to=urquizagabes]^[gmail.com";
rel=nofollow target=_blank ymailto="mailto:urquizagabes]^[gmail.com";>urquizagabes]^[gmail.com</A>></SPAN><BR>
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px
0.8ex; PADDING-LEFT: 1ex" class=yiv894493646gmail_quote>
<DIV dir=ltr>
<DIV>Dear Tian Lu,</DIV>
<DIV><BR></DIV>Thank you very much for your information, I
think this might be exactly what I'm looking for, however, I'm puzzled about the
content of these .wfn files. I've checked a few of them on the examples page and
the overall layout didn't seem to ring any bells. I have currently a gaussian
.chk file of a benzene as well as its corresponding input, how do I go from that
to a .wfn? Is there a fast and reliable way to do that?
<DIV><BR></DIV>
<DIV>Thanks once more for the tip, I'll keep going through the manual but
apart from this difficulty with the filetypes, my doubt seems like its
solved!</DIV>
<DIV><BR></DIV>
<DIV><BR></DIV>
<DIV>Attentiously</DIV>
<DIV><BR></DIV>
<DIV><BR></DIV>
<DIV>Gabriel Carvalho <BR></DIV></DIV>
<DIV class=yiv894493646gmail_extra><BR><BR>
<DIV class=yiv894493646gmail_quote>2013/4/3 sobereva <A href="http://sobjubao_-_yahoo.com.cn/"; rel=nofollow
target=_blank>sobjubao_-_yahoo.com.cn</A> <SPAN
dir=ltr><<A href="http://us.mc152.mail.yahoo.com/mc/compose?to=owner-chemistry]^[ccl.net";
rel=nofollow target=_blank ymailto="mailto:owner-chemistry]^[ccl.net";>owner-chemistry]^[ccl.net</A>></SPAN>
<DIV>
<DIV class=yiv894493646h5><BR>
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px
0.8ex; PADDING-LEFT: 1ex" class=yiv894493646gmail_quote><BR>Sent
to CCL by: sobereva [sobjubao\a/<A href="http://yahoo.com.cn/";
rel=nofollow
target=_blank>yahoo.com.cn</A>]<BR>Hi,<BR><BR>Please
have a try Multiwfn (<A href="http://multiwfn.codeplex.com/"; rel=nofollow
target=_blank>http://multiwfn.codeplex.com</A>;). You can use either
.fch or .wfn/.wfx file generated by Gaussian as input file for generating cube
file of electron density. This program provides rather flexible ways to set up
grid. For example, to generate the cube file of electron density for H2O.wfn,
after booting up Multiwfn you only need to input following commands (the texts
after the double slashes are comments):<BR><BR>E:\H2O.wfn
// The file path<BR>5 // Main function 5<BR>1
// Electron density<BR>3 // There will be about
1728000 grids in total, and the grid spacings in X,Y,Z are
exactly identical, namely cubic grid. You can also choose other options to set
up the grid, especially by option 4, you can directly specify the grid spacings
in X,Y,Z manually<BR>2 // Export the grid data to density.cub
in current folder<BR><BR>For more about generating grid data in
Multiwfn, please check Section 3.6 of the manual and the examples given in
Section 4.5.<BR><BR>Tian Lu<BR><BR><BR>--- On Wed,
4/3/13, Gabriel Aires Urquiza Carvalho gabrielcarvalho%<A href="http://quimica.ufpb.br/"; rel=nofollow
target=_blank>quimica.ufpb.br</A> <owner-chemistry*_*<A
href="http://ccl.net/"; rel=nofollow
target=_blank>ccl.net</A>> wrote:<BR><BR>>
From: Gabriel Aires Urquiza Carvalho gabrielcarvalho%<A href="http://quimica.ufpb.br/"; rel=nofollow
target=_blank>quimica.ufpb.br</A> <owner-chemistry*_*<A
href="http://ccl.net/"; rel=nofollow
target=_blank>ccl.net</A>><BR>> Subject: CCL:G:
Electron Density cubic grid generation<BR>> To:
"Lu, Tian " <sobjubao*_*<A href="http://yahoo.com.cn/";
rel=nofollow target=_blank>yahoo.com.cn</A>><BR>>
Date: Wednesday, April 3, 2013, 2:37 AM<BR>
<DIV>
<DIV>><BR>> Sent to CCL by: "Gabriel Aires
Urquiza Carvalho"<BR>> [gabrielcarvalho**<A href="http://quimica.ufpb.br/"; rel=nofollow
target=_blank>quimica.ufpb.br</A>]<BR>> Dear CCL
subscribers,<BR>><BR>><BR>> Is there any
way I could get volumetric data of electron<BR>> density in the
form<BR>> of a cubic voxelized grid? I have tried the
gaussian<BR>> "cubegen" utility but it<BR>>
doesn't neccessarily generates cubic grids, and I need those<BR>>
to be cubic<BR>> because the other programs I'm using for my
analysis can<BR>> only cubic binary<BR>> inputs and
I'd rather not go through rewritting their code<BR>> unless I
really<BR>> have to.<BR>><BR>> It doesn't
have to write the voxels in binary, I can convert<BR>> them to a
binary<BR>> stream as an extra step in the process by writing a
minor<BR>> Fortran utility, I<BR>> just need something
to generate the voxels for me, in a<BR>> cubic
arrangement.<BR>><BR>> Thanks in
advance!<BR>><BR>><BR>> Gabriel Aires
Urquiza Carvalho<BR>><BR>> gabrielcarvalho#,#<A
href="http://quimica.ufpb.br/"; rel=nofollow
target=_blank>quimica.ufpb.br</A><BR>> Programa de
Ps-Graduao em Qumica<BR>> Departamento de Qumica<BR>>
Universidade Federal da Paraba -
Brazil<BR>><BR>><BR>><BR>>
-= This is automatically added to each message by the<BR>> mailing
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><BR>> E-mail to
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<DIV>
<DIV>> >
>
><BR>><BR>><BR><BR><BR><BR>-=
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