From chemistry-request@ccl.net Tue Jun  7 09:02:16 2005
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Date: Tue, 7 Jun 2005 20:57:14 +0800 (HKT)
From: ChiYung Yam <yamcy _+_ yangtze.hku.hk>
To: chemistry _+_ ccl.net
Subject: Bismutite (Bi2O2CO3)
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Dear all,

I am trying to do some calculations on Bi2O2CO3 nanotubes. However
I can't find the structure of that compound. Does anyone know the
structure of Bi2O2CO3 nanotubes? Thanks.

Best regards,
ChiYung Yam


From chemistry-request@ccl.net Tue Jun  7 05:00:09 2005
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From: Chimica Teorica <teoricach _+_ unito.it>
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To: "Ojwang, J.G.O." <j.g.o.ojwang _+_ tue.nl>, chemistry _+_ ccl.net
Subject: Re: CCL:Single point calculation in CRYSTAL03
References: <AA85ED879728134DB941020C04A2515203F295A4 _+_ stex2.campus.tue.nl>
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"Ojwang, J.G.O." wrote:
> 
> Dear all,
> Is there anyone with an idea on how to perform single point calculation in CRYSTAL03 without geometry optimisation of the internal coordinates, something like freezing the atoms while expandinbg the lattice.


Dear Ojwang, J.G.O.,

the default choice of CRYSTAL03 is a single point calculation.
Optimization of internal coordinates is requested by the keyword
OPTCOORD
(the program checks if there are internals degrees of freedom).
See http://www.crystal.unito.it => tutorials => Total energy single
point

You can modify the lattice parameters for each single point run, 
keeping constant the internal (fractionary) coordinates of the atoms.

In case of molecular crystals, the keyword MOLEXP allows
modification of the lattice parameters, keeping constant the
internal coordinates and the fractionary coordinate of the
barycentre of each molecule. 

Regards,

CRYSTAL support team Torino


From chemistry-request@ccl.net Tue Jun  7 11:36:19 2005
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Date: Tue, 07 Jun 2005 09:16:50 -0500
From: Aaron Deskins <ndeskins_at_purdue.edu>
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There seem to be so many people bombarding the forum with questions, 
that I'm almost embarrased to ask this. I'm looking for a review of term 
symbols- particularly molecular. Can anyone recommend a review article 
or book? My old physical chemistry text only discusses atomic term symbols.

Any help is appreciated.

Aaron Deskins
Chemical Engineering
Purdue University


From chemistry-request@ccl.net Tue Jun  7 13:13:12 2005
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Date: Tue, 07 Jun 2005 18:37:34 +0200
From: Pablo Echenique Robba <pnique/at/unizar.es>
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To: CCL list <chemistry/at/ccl.net>
Subject: existence of HF-SCF solutions
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Hello everybody.

What I wanted to know is whether someone could indicate to me where may 
I find a discussion on the existence of solutions of the HF-SCF 
iterative procedure. I first enumerate briefly what I know:

1) The HF equations HAVE solutions (Lieb and Simon, 1977).
2) Any solution of the HF equations is an extremal, with no indication 
about its being a maximum, a saddle point or a minimum whatsoever.
3) The SCF method DOES NOT always converge. Of course, when it does 
converge, the wave function that results is indeed a solution of the HF 
equations. Again, with no indication about its being a maximum, a saddle 
point or a minimum.

My two questions are related to point 3:

a) When does the SCF converge?
b) How do we know, if it converged, that it did it to a minimum (and not 
to a maximum or to a saddle point)?

I would thank very much any hint to articles or books discussing this. I 
mean, further than the typical "we hope it converge because our basis 
sets and our starting point are so good".

 Pablo Echenique.

-- 

------------------------------------
  Pablo Echenique Robba

  Departamento de Fisica Teorica
                &
  Instituto de Biocomputacion y
  Fisica de los Sistemas Complejos
  BIFI

  Universidad de Zaragoza
  50009 Zaragoza
  Spain

  Tel.:    34 976761260
  E-mail:  pnique/at/unizar.es
------------------------------------



From chemistry-request@ccl.net Tue Jun  7 14:28:06 2005
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From: "Gustavo, Alberto, Mercier" <gamercier*at*yahoo.com>
To: chemistry*at*ccl.net
X-Web-Message-Number: 050607142236-23745
Subject: W:5d vs 6d Functions; Gaussian vs Gamess-US
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HI!

I need some clarification in the differences that GAMESS-US and GAUSSIAN handle 5d (spherical) vs 6d (cartesian) atomic orbitals.

I have not used Gaussian and many years, but in Gamess the output is a bit peculiar.

I am doing UHF computations.

In Gamess I see the following. I don't have Gaussian to experiment.

The matrix of MO coefficients may not be square but rectangular:
MxN where M is the number of basis functions and N is the number of MO's.

When I request 6d (cartesian), M=N and you get the expected square matrix.

When I request 5d (spherical), M>N, and you get less MO's than basis functions. The difference reflects the loss of the redundant functions present when using 6d. It looks like at the time of the SCF Gamess is projecting out the redundant elements, while Gaussian starts with 5d from scratch. The printout reflects the 5d's while in Gamess the printout reflects 6d's but the number of MO's is correct in both cases.

For example:

psi = Cg * (x2-y2)           in Gaussian with output of Cg and (x2-y2) basis.

psi = C1 * (x2) + C2 * (y2)  in Gamess with output of C1 and C2 and x2,y2

so C1 = Cg     and C2 = -Cg

This is my "naive" interpretation of what is going on.

Is this correct?

Thanks!
Gustavo Mercier
gamercier*at*yahoo.com
gustavom*at*baylorhealth.edu



From chemistry-request@ccl.net Tue Jun  7 15:04:40 2005
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Subject: W:gaussian 03 Linda error
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Now we can run g03 on single processor after we updated glibc.
But when we try to run g03l, it always give error like:
/linda-exe/l302.exel: error while loading shared libraries: util.so: cannot
open shared object file: No such file or directory

But acutally util.so is in the right directory, also l302.exel link the
same file:
/home/guser>ldd /auto/g03/linda-exe/l302.exel
	util.so => /auto/g03/util.so (0x40016000)
	libm.so.6 => /lib/i686/libm.so.6 (0x44092000)
	libc.so.6 => /lib/i686/libc.so.6 (0x440b4000)
	libpthread.so.0 => /lib/i686/libpthread.so.0 (0x441ed000)
	libpgc.so => /auto/g03/libpgc.so (0x4423d000)
	/lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
/home/guserg>ls /auto/g03/util.so
/auto/g03/util.so



From chemistry-request@ccl.net Tue Jun  7 15:33:16 2005
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Subject: Monte Carlo and solvent structure ?
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Hi all,
I'm trying to repeat some published research in order to better familia=
rize
with Monte Carlo modeling using BOSS. I'm looking at the solvation of G=
d 3+
in TIP3P waters using the parameters of van Veggel and Reinhoudt ( Chem=
.
Eur. J. 5(1) 1999 p90 ). I'm trying to get a feel for the structure and=

number of waters in the first solvation shell, so with a relatively sma=
ll
simulation I generate the rdf which seems reasonable and compares well =
to
the published data. Here's where I become clueless, how do I determine =
the
number of water molecules in the first solvation shell ? Now the BOSS
output following the rdf spits out "Gamma(R) and Coordination Numbers" =
with
"Actual CN =3D CN x Atom Density" following but I can't figure out what=
 this
is and or what to do with it. My admittedly limited understanding is th=
at
the integral of the rdf can provide this, any help/pointers would be
greatly appreciated.
thanks in advance,
-david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd*at*wustl.edu
voice: (314) 362-8461
fax: (314) 362-9940=

--0__=09BBFA8ADFF659F08f9e8a93df938690918c09BBFA8ADFF659F0
Content-type: text/html; charset=US-ASCII
Content-Disposition: inline
Content-transfer-encoding: quoted-printable

<html><body>
<p>Hi all,<br>
I'm trying to repeat some published research in order to better familia=
rize with Monte Carlo modeling using BOSS. I'm looking at the solvation=
 of Gd 3+ in TIP3P waters using the parameters of van Veggel and Reinho=
udt ( Chem. Eur. J. 5(1) 1999 p90 ). I'm trying to get a feel for the s=
tructure and number of waters in the first solvation shell, so with a r=
elatively small simulation I generate the rdf which seems reasonable an=
d compares well to the published data. Here's where I become clueless, =
how do I determine the number of water molecules in the first solvation=
 shell ? Now the BOSS output following the rdf spits out &quot;Gamma(R)=
 and Coordination Numbers&quot; with &quot;Actual CN =3D CN x Atom Dens=
ity&quot; following but I can't figure out what this is and or what to =
do with it. My admittedly limited understanding is that the integral of=
 the rdf can provide this, any help/pointers would be greatly appreciat=
ed.<br>
thanks in advance,<br>
-david <br>
David Reichert, Ph.D.<br>
Asst. Professor Radiology<br>
Washington University School of Medicine<br>
510 S. Kingshighway, Campus Box 8225<br>
St Louis, MO 63110<br>
<br>
e-mail: reichertd*at*wustl.edu<br>
voice: (314) 362-8461<br>
fax: (314) 362-9940</body></html>=

--0__=09BBFA8ADFF659F08f9e8a93df938690918c09BBFA8ADFF659F0--



From chemistry-request@ccl.net Tue Jun  7 16:26:28 2005
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Subject: RE: Query- Term Symbols
Date: Tue, 7 Jun 2005 21:24:49 +0200
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From: "Ojwang, J.G.O." <j.g.o.ojwang-.at.-tue.nl>
To: "Aaron Deskins" <ndeskins-.at.-purdue.edu>, <chemistry-.at.-ccl.net>
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Hi.

Check Haken and Wolf's "Molecular Physics and Elements of Quantum Chemistry"


Regards,
Ojwang JGO
---------------------
Eindhoven University,
The Netherlands
---------------------


-----Original Message-----
From:	Computational Chemistry List on behalf of Aaron Deskins
Sent:	Tue 6/7/2005 4:16 PM
To:	chemistry-.at.-ccl.net
Cc:	
Subject:	CCL:Query- Term Symbols
There seem to be so many people bombarding the forum with questions, 
that I'm almost embarrased to ask this. I'm looking for a review of term 
symbols- particularly molecular. Can anyone recommend a review article 
or book? My old physical chemistry text only discusses atomic term symbols.

Any help is appreciated.

Aaron Deskins
Chemical Engineering
Purdue University


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From chemistry-request@ccl.net Tue Jun  7 18:26:18 2005
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Reply-To: "Alex. A. Granovsky" <gran*at*classic.chem.msu.su>
From: "Alex. A. Granovsky" <gran*at*classic.chem.msu.su>
To: "Brian Salter-Duke" <b_duke*at*octa4.net.au>, <chemistry*at*ccl.net>
References: <200506030511.j535B9ba021246*at*server.ccl.net> <a06200710bec9b5a78948@[155.210.88.109]> <20050606225944.GB3561@bsalterduke1>
Subject: Re: CCL:W:gOpenMol and Gamess MO plotting
Date: Wed, 8 Jun 2005 02:27:22 +0400
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Hi!

the cube option is supported only by the PC GAMESS, not GAMESS (US).

Best regards,
Alex Granovsky

----- Original Message ----- 
From: "Brian Salter-Duke" <b_duke*at*octa4.net.au>
To: <chemistry*at*ccl.net>
Sent: Tuesday, June 07, 2005 2:59 AM
Subject: CCL:W:gOpenMol and Gamess MO plotting


> On Mon, Jun 06, 2005 at 10:19:15AM +0200, Fco. Javier Modrego wrote:
> > At 01:11 -0400 3/6/05, Gustavo, , Mercier wrote:
> > >Hi!
> > >
> > >I am interested in plotting MO's computed using GAMESS-US. I've 
> > >tried several programs with limited succes (molden, molekel, 
> > >orbdraw) and now I am trying gOpenMol.
> > >
> > >Looking at the manual etc I need to generate a cube file that will 
> > >be converted to the plt format read by gOpenMol using a plugin. 
> > >However, it is not clear to me how to generate the cube file using 
> > >GAMESS-US.
> > 
> > Look at the keyword PLTORB in the $CONTRL section of the Gamess' 
> > manual, then as stated in the gOpenMol pages, use Gamess2plt to 
> > convert a Gamess "cube" PUNCH file to a plt file. Otherwise if you 
> > can use a Mac , the program MacMolPlt is the easiest way of doing 
> > what you need.
> 
> I thought that PLTORB and cube were completely different. PLTORB gives a
> 2-dimensional grid but this is calculated in the pltorb graphics program
> > from the data in the PUNCH file. A cube file contains the values in a
> 3-dimension grid that can indeed be translated into a plt file for
> gOpenMol. I do not see how PLTORB in $CONTRL can give you anything that
> can be used by gOpenMol. Am I confused? 
> > 
> > I hope this can help you,
> > 
> >  Dr. F.J. Modrego
> >  Department of Inorganic Chemistry
> >  Facultad de Ciencias
> >  University of Zaragoza
> >  50009 ZARAGOZA
> >  SPAIN
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> -- 
>            Brian Salter-Duke (Brian Duke) b_duke*at*octa4.net.au  
>         Post: 626 Melbourne Road, Spotswood, Vic 3015, Australia.
>    Phone: 03-93992847. Web: http://members.iinet.net.au/~linden1/brian/
> Honorary Researcher, Chemistry, Melbourne Univ, & Med. Chem., Monash Univ.
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