From owner-chemistry@ccl.net Fri Apr 5 08:24:00 2013 From: "sobereva sobjubao:_:yahoo.com.cn" To: CCL Subject: CCL:G: Electron Density cubic grid generation Message-Id: <-48533-130405041253-22181-+4ZjaptIjBvKQ6Z7i0CcvQ-*-server.ccl.net> X-Original-From: sobereva Content-Type: multipart/alternative; boundary="-381987588-515870243-1365149549=:60236" Date: Fri, 5 Apr 2013 16:12:29 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao-x-yahoo.com.cn] ---381987588-515870243-1365149549=:60236 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Gabriel Carvalho, =A0 AFAIK, there is no directly way to convert aux file to wfn file. wfn file c= an only be generated by the ab initio programs based on Gauss functions. Th= e method for obtaining wfn file via Gaussian and GAMESS-US=A0is described a= t the beginning of Chapter 4 of the manual. =A0 If you have any question about Multiwfn, please feel free to directly conta= ct me via the E-mail address given in Multiwfn website. =A0 Best wishes, =A0 Tian Lu=20 --- On Thu, 4/4/13, Gabriel Urquiza urquizagabes ~ gmail.com wrote: > From: Gabriel Urquiza urquizagabes ~ gmail.com Subject: CCL:G: Electron Density cubic grid generation To: "Lu, Tian " 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 j= ust 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 Dear Tian Lu, Thank you very much for your information, I think this might be exactly wha= t I'm looking for, however, I'm puzzled about the content of these .wfn fil= es. 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 b= enzene 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=A0 2013/4/3 sobereva sobjubao_-_yahoo.com.cn Sent to CCL by: sobereva [sobjubao\a/yahoo.com.cn] Hi, Please have a try Multiwfn (http://multiwfn.codeplex.com). You can use eith= er .fch or .wfn/.wfx file generated by Gaussian as input file for generatin= g 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 co= mmands (the texts after the double slashes are comments): E:\H2O.wfn =A0 =A0// The file path 5 =A0 // Main function 5 1 =A0 // Electron density 3 =A0 // 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 othe= r options to set up the grid, especially by option 4, you can directly spec= ify the grid spacings in X,Y,Z manually 2 =A0 // Export the grid data to density.cub in current folder For more about generating grid data in Multiwfn, please check Section 3.6 o= f 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 wrote: > From: Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br > Subject: CCL:G: Electron Density cubic grid generation > To: "Lu, Tian " > 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 > > > > -=3D This is automatically added to each message by the > mailing script =3D- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the *_* sign. You > can also> > E-mail to subscribers: CHEMISTRY*_*ccl.net > or use: > =A0 =A0 =A0> > E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net > or use > =A0 =A0 =A0> =A0 =A0 =A0> =A0 =A0 =A0> > > -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY]^[ccl.net or use: =A0 =A0 =A0E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use =A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0---381987588-515870243-1365149549=:60236 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Gabriel Carvalho,
 
AFAIK, there is no directly way to convert aux file to wfn file. wfn f= ile can only be generated by the ab initio programs based on Gauss function= s. The method for obtaining wfn file via Gaussian and GAMESS-US is des= cribed 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.co= m <owner-chemistry[-]ccl.net> wrote:

From: Gabriel Urquiza urquizagabes ~ gmail.com &l= t;owner-chemistry[-]ccl.net>
Subject: CCL:G: Electron Density cubic gri= d generation
To: "Lu, Tian " <sobjubao[-]yahoo.com.cn>
Da= te: 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. I= t'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 gau= ssian .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 a= part from this difficulty with the filetypes, my doubt seems like its solve= d!


Attentiously


Gabriel Carvalho 


2013/4/3 sobereva sobjubao_-_yahoo.com= .cn <owner-chemistry]^[ccl.net>


Sent to CCL by: so= bereva [sobjubao\a/yahoo.com.cn]
Hi,

Please have a try Multiwfn (http://= multiwfn.codeplex.com). You can use either .fch or .wfn/.wfx file gener= ated by Gaussian as input file for generating cube file of electron density= . This program provides rather flexible ways to set up grid. For example, t= o 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 dou= ble slashes are comments):

E:\H2O.wfn    // The file path<= BR>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 Multiwf= n, 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 C= arvalho gabrielcarvalho%quimica.ufpb.br <owner-chemistry*_*ccl.net> wrote:

>= ; From: Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br <owne= r-chemistry*_*cc= l.net>
> Subject: CCL:G: Electron Density cubic grid generatio= n
> To: "Lu, Tian " <sobjubao*_*yahoo.com.cn>
> Date: Wednesday, April 3, 201= 3, 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 gau= ssian
> "cubegen" utility but it
> doesn't neccessarily generat= es cubic grids, and I need those
> to be cubic
> because the ot= her 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 vox= els 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!
>
>
> Ga= briel Aires Urquiza Carvalho
>
> gabrielcarvalho#,#quimica.ufpb.br<= BR>> Programa de Ps-Graduao em Qumica
> Departamento de Qumica
= > Universidade Federal da Paraba - Brazil
>
>
>
>= ; -=3D This is automatically added to each message by the
> mailing s= cript =3D-
> To recover the email address of the author of the messag= e,
> please change
> the strange characters on the = top line to the *_* sign. You
> can also>
> E-mail to subscr= ibers: CHEMISTRY*_*ccl.net
> or use:
>      >
> E-m= ail to administrators: CHEMISTRY-REQUEST*_*ccl.net
> or use
>      >      >     &= nbsp;>
>
>



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