From owner-chemistry@ccl.net Wed Jul 13 03:50:03 2005
From: "CCL" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: clustering computers in windows system
Message-Id: <-28879-050713034628-5895-gJKokDZHWSap5rm98+rrIw_+_server.ccl.net>
X-Original-From: may abdelghani <may01dz_+_yahoo.fr>
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Sent to CCL by: may abdelghani <may01dz_+_yahoo.fr>
Hello, CLLers
it is possible to clustering 10 or 11 computers in a
way to works( all this 10 or 11 computers) like a only
one computer but have 10 or 11 processors(
like-station. I think that this is possible in UNIX
system, but it is a possible in windows one? what is a
necessary hardware/software, that I need to do this
operation?
best regrds


	

	
		
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From owner-chemistry@ccl.net Wed Jul 13 04:20:19 2005
From: "CCL" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: summary : DOS
Message-Id: <-28880-050713041854-18731-gJKokDZHWSap5rm98+rrIw{=}server.ccl.net>
X-Original-From: Dufaure Corinne <corinne_dufaure{=}yahoo.fr>
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Sent to CCL by: Dufaure Corinne <corinne_dufaure{=}yahoo.fr>
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Hi,
Thanks to everyone who replied to my original question about DOS.The answers are given below. I finally installed gaussSum with the help of Noel O'Boyle who wrote the program and that I particularly thank.

Regards,
Corinne

 
On Tue, 2005-04-12 at 14:06, Corinne, , DUFAURE wrote:
> hello everybody,
> who can help me to draw the density of states of a cluster?
> I know about the theory but I have a problem to do it in practise : 
which software...
> 
> thanks.
> C.
 ******************
Check http://www.sg-chem.net

AOMix can generate the DOS plot data from numerous quantum-chemistry
packages.

Best regards,

Serge Gorelsky

 
 ******************************************
 
What program are you using to do the cluster calculation? If it's
Gaussian or GAMESS you can use http://gausssum.sf.net.

Otherwise you may have luck with http://www.sg-chem.net/aomix/.

Noel








		
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<DIV>
<DIV>
<DIV>
<DIV>
<DIV><TT><TT>Hi,</TT></TT></DIV>
<DIV><TT><TT>Thanks to everyone who replied to my original question about DOS.The answers are given below. I finally&nbsp;installed gaussSum with the help of Noel O'Boyle who wrote the program and that I particularly thank.<BR><BR>Regards,</TT></TT></DIV>
<DIV><TT><TT>Corinne</TT></TT></DIV>
<DIV><TT><TT><BR>&nbsp;</DIV></TT></TT>
<DIV><TT>On Tue, 2005-04-12 at 14:06, Corinne, , DUFAURE wrote:<BR>&gt; hello everybody,<BR>&gt; who can help me to draw the density of states of a cluster?<BR>&gt; I know about the theory but I have a problem to do it in practise : <BR>which software...<BR>&gt; <BR>&gt; thanks.<BR>&gt; C.</TT></DIV>
<DIV><TT></TT>&nbsp;******************</DIV>
<DIV>Check <A href="http://www.sg-chem.net/" target=_blank>http://www.sg-chem.net</A><BR><BR>AOMix can generate the DOS plot data from numerous quantum-chemistry<BR>packages.<BR><BR>Best regards,<BR><BR>Serge Gorelsky<BR></DIV>
<DIV>&nbsp;</DIV>
<DIV><TT></TT>&nbsp;******************************************</DIV>
<DIV><TT></TT>&nbsp;</DIV>
<DIV><TT>What program are you using to do the cluster calculation? If it's<BR>Gaussian or GAMESS you can use <A href="http://gausssum.sf.net/" target=_blank>http://gausssum.sf.net</A>.<BR><BR>Otherwise you may have luck with <A href="http://www.sg-chem.net/aomix/" target=_blank>http://www.sg-chem.net/aomix/</A>.<BR><BR>Noel<BR><BR><BR></DIV></TT></DIV></DIV></DIV></DIV><p>
		<hr size=1> 
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From owner-chemistry@ccl.net Wed Jul 13 08:03:24 2005
From: "CCL" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: Oscillator strength in TD-DFT
Message-Id: <-28881-050713051531-3674-gJKokDZHWSap5rm98+rrIw]^[server.ccl.net>
X-Original-From: =?ks_c_5601-1987?B?sejA5bno?= <biomimic]^[kaist.ac.kr>
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Sent to CCL by: =?ks_c_5601-1987?B?sejA5bno?= <biomimic]^[kaist.ac.kr>
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region u3:st=3D"on"><st1:country-region
w:st=3D"on"><font size=3D2 color=3Dnavy face=3D=B9=D9=C5=C1><span =
lang=3DEN-US style=3D'font-size:
 10.0pt;color:navy'><u4:country-region =
u5:st=3D"on">Korea</span></font></st1:country-region></u4:country-region>=
</u2:country-region><font
color=3Dnavy><span lang=3DEN-US style=3D'color:navy'> Advanced <u2:place =
u3:st=3D"on"><u2:PlaceType u3:st=3D"on"><st1:place =
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w:st=3D"on"><st1:PlaceType =
w:st=3D"on">Institute</u2:PlaceType></st1:place></st1:PlaceType></st1:Pla=
ceType>
 of <u2:PlaceName u3:st=3D"on"><st1:PlaceName =
u7:st=3D"on"><st1:PlaceName =
w:st=3D"on">Science</u2:PlaceName></u2:PlaceName></u2:place></st1:PlaceNa=
me></st1:place>
&amp; Technology (KAIST)<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><u2:address =
style=3D"BACKGROUND-POSITION: left bottom; BACKGROUND-IMAGE: =
url(res://ietag.dll/#34/#1001); BACKGROUND-REPEAT: =
repeat-x"><u2:Street><font
size=3D2 color=3Dnavy face=3D=B9=D9=C5=C1><span lang=3DEN-US =
style=3D'font-size:10.0pt;color:navy'><u2:address =
style=3D"BACKGROUND-POSITION: left bottom; BACKGROUND-IMAGE: =
url(res://ietag.dll/#34/#1001); BACKGROUND-REPEAT: =
repeat-x"><u2:Street>373-1</u2:Street></u2:address></u2:Street></u2:addre=
ss>,</span></font><font
color=3Dnavy face=3D"Times New Roman"><span lang=3DEN-US =
style=3D'font-family:"Times New Roman";
color:navy'>&nbsp;</span></font><font color=3Dnavy><span lang=3DEN-US
style=3D'color:navy'> Guseong-Dong, Yuseong-Ku, Taejeon, 305-701, =
<u2:country-region u3:st=3D"on"><u2:place =
u3:st=3D"on"><st1:country-region u8:st=3D"on"><st1:place =
u8:st=3D"on"><st1:country-region
w:st=3D"on"><st1:place =
w:st=3D"on">Korea</u2:place></u2:country-region></st1:place></st1:country=
-region></st1:place></st1:country-region><o:p></o:p></span></font></p>

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style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3D2 color=3Dnavy face=3D=B9=D9=C5=C1><span lang=3DEN-US =
style=3D'font-size:10.0pt;color:navy'>E-mail
: <a href=3D"mailto:biomimic]^[kaist.ac.kr" =
title=3D"mailto:biomimic]^[kaist.ac.kr">biomimic]^[kaist.ac.kr</a><o:p></o:p>=
</span></font></p>

<p class=3DMsoNormal =
style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3D2 color=3Dnavy face=3D=B9=D9=C5=C1><span lang=3DEN-US =
style=3D'font-size:10.0pt;color:navy'>TEL.
: +82-42-869-2884<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3D2 color=3Dnavy face=3D=B9=D9=C5=C1><span lang=3DEN-US =
style=3D'font-size:10.0pt;color:navy'>FAX.
: +82-42-869-2810<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
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* * * * * * * * * * * * * * * * * * *</span></font><font color=3Dnavy
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------=_NextPart_000_0000_01C587D1.0F6BBA00--


From owner-chemistry@ccl.net Wed Jul 13 08:33:54 2005
From: "CCL" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: W:change of atom numbering in RasMol
Message-Id: <-28882-050713082754-31088-gJKokDZHWSap5rm98+rrIw|a|server.ccl.net>
X-Original-From: "Maurizio  Ciofalo" <omega|a|unipa.it>


Sent to CCL by: "Maurizio  Ciofalo" <omega|a|unipa.it>
Hi to all.
I have been using rasmol as a graphical interface in a modeling application which I am about to complete. However, rasmol numbers the atoms taken from xyz files starting from atom 0, while mine has to start from atom 1. I also read and experienced that there is no way to change this feature but editing the rasmol code.
Is there anybody who already faced with this challenge?
Thanks to all for your attention.
best regards
Maurizio


From owner-chemistry@ccl.net Wed Jul 13 13:00:49 2005
From: "CCL" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: SUMMARY: Symmetry Breaking During CAS
Message-Id: <-28883-050713125942-32295-gJKokDZHWSap5rm98+rrIw{=}server.ccl.net>
X-Original-From: <gustavo{=}mercury.chem.pitt.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
MIME-Version: 1.0


Sent to CCL by: <gustavo{=}mercury.chem.pitt.edu>
Dear CCL Readers,
        I am sending the summary of the answers I received about my recent
question about symmetry breaking during a CAS calculation. I would
like to say thank you to Antonio M. Marquez Cruz and Wai-To Chan
for their answers.
        Basically I discovered that I don´t know how to perform a CAS
calculation in order to obtain the properties I need. I will study this
type of calculation in more detail and try the suggestions I have
received.
        Sincerely Yours,
                                            Gustavo L.C. Moura
                                    gustavo{=}mercury.chem.pitt.edu

-----------------Original Message--------------------------------------
Dear CCL Readers,
     I have a planar conjugated organic molecule that, on paper, has D2h
symmetry. I am working with the hypothesis that the molecule is a
biradical singlet. I want to perform a CASSCF(2,2) on this molecule
to estimate the biradical character of this molecule. When I
calculate the molecule with the constraint that the molecule has D2h
symmetry, the calculation has severe convergence problems. If I
remove this constraint, the molecule distorts to a C2v symmetry and I
obtain a biradical character ~20%. I checked the orbitals being used
for the CASSCF calculation and they look right (one nonbonding and
another slightly antibonding).
     Is the situation described above correct? Can an organic molecule
have such a symmetry breaking as a result of a CASSCF calculation? Is
the molecule really a C2v system? Any suggestions are welcome.
     Thank you very much in advance for your help.
     Sincerely yours,
                                Gustavo L.C. Moura
                           gustavo{=}mercury.chem.pitt.edu
 --------------------------------------------------------------------------
"Antonio M. Marquez Cruz" <marquez  {=}  us.es>

Hi,

Unless I'm wrong in D2h symmetry group there are not degenerate
representations, so you can discard a symmetry breaking due to a
Jahn-Teller effect.

Are all symmetry equivalent molecular orbitals included in the CAS
active space ? To keep the D2h symmetry in your orbitals your CASSCF
wavefunction must also have this symmetry and you have to include all
symmetry equivalente MOs in the active space.

If this is the case, please double check that your initial orbitals are
what they are supposed to be. I mean, in many cases it is difficult to
be sure that our virtual orbitals are good representations of the
antibonding MO we are looking for.

Hope these comments helps you.

--------------------------------------------------------------------------

   I assume that you removed the D2h symmetry constraint by changing
the original cartesian coordinates just small enough for the program to
recognize
the C2v symmetry.

        If the distortion of the C2v structure from D2h is not too large
I would repeat the optimization starting with the undistorted D2h geometry.
Small deviation from ideal symmtry is not that unusual with CASSCF geometry
optimization
even when it is properly executed.
I would try to avoid the convergence difficulties by changing the symmetry
of the wavefunction instead of the geometry. With GAMESS this can be done by
specifying a lower symmetry than D2h in the $DET or $DRT input card.
With Gaussian I am not sure how this can be done. Perhaps the nosymm
keyword could do
but I am not sure if it is effective in the CASSCF step. If the CASSCF is
based on
UHF unrestricted orbitals I will try to break the symmetry of the UHF
wavefunction.

          If your casscf-optimized C2V geometry is clearly distinctive from
the D2h symmetry you perceive to be correct a possible explanation
is that the active space in your MCSCF wavefunction is not sufficiently
large. A 2-electrons-2-MOs active space is of the minimum size for
diradicals. Your system seems to be more of a diradicaloid than an
open-shell singlet diradical. It may sound surprising but partial diradical
systems may require a larger active space than a pure diradical.
With Gaussian I would design the size of the active space required by
running a UHF calculation on the D2h structure first with guess=mix and
stable=opt
specified. I would then examine the occupancy of the UHF-natural orbitals
(with pop=naturalorbitals). If the fraction occupancies  of the natural
orbitals
beyond the HOMO and the LUMO are significant I would increase the active
space
size accordingly.

Wai-To Chan


From owner-chemistry@ccl.net Wed Jul 13 15:10:48 2005
From: "CCL" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: W:How can I modify the van der waals radii of elements in Gaussian 03?
Message-Id: <-28885-050713150651-21615-gJKokDZHWSap5rm98+rrIw{:}server.ccl.net>
X-Original-From: "Adrian  Villegas" <adriano{:}eps.mcgill.ca>


Sent to CCL by: "Adrian  Villegas" <adriano{:}eps.mcgill.ca>
To: CCL subscribers
> From: Adrin Villegas

Hey folks,
I want to use the CHelpG function in Gaussian 03 in order to calculate
the molecular electrostatic potential of a crystal containing calcium
and derive the corresponding atomic charges.
Unfortunately, the value of the van der waals (vdw) radius for calcium is
not specified in the Gaussian database and, thus, the program crashes before the calculation can be completed. 

Any idea about how to specify/enter the vdw radius of this element in the Gaussian 03 database? (I want to test my calculation using an approximate vdw value for calcium since I could not find the actual value in any major handbook or database containig physical constants/values).

Any piece of information would be greatly appreciated!

Adrin


From owner-chemistry@ccl.net Wed Jul 13 15:09:46 2005
From: "CCL" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: W:How can I modify the van der waals radii of elements in Gaussian 03?
Message-Id: <-28884-050713150651-21615-gJKokDZHWSap5rm98+rrIw%x%server.ccl.net>
X-Original-From: "Adrian  Villegas" <adriano%x%eps.mcgill.ca>


Sent to CCL by: "Adrian  Villegas" <adriano%x%eps.mcgill.ca>
To: CCL subscribers
> From: Adrin Villegas

Hey folks,
I want to use the CHelpG function in Gaussian 03 in order to calculate
the molecular electrostatic potential of a crystal containing calcium
and derive the corresponding atomic charges.
Unfortunately, the value of the van der waals (vdw) radius for calcium is
not specified in the Gaussian database and, thus, the program crashes before the calculation can be completed. 

Any idea about how to specify/enter the vdw radius of this element in the Gaussian 03 database? (I want to test my calculation using an approximate vdw value for calcium since I could not find the actual value in any major handbook or database containig physical constants/values).

Any piece of information would be greatly appreciated!

Adrin