From owner-chemistry@ccl.net Fri Dec 16 04:13:01 2005
From: "Noel O Boyle no228^-^cam.ac.uk" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Looking for Extended Huckel codes / ATP protonation state
Message-Id: <-30342-051216040623-697-lky+hEg5/08k3IUVy/1BDw/./server.ccl.net>
X-Original-From: "Noel O'Boyle" <no228]~[cam.ac.uk>
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Date: Fri, 16 Dec 2005 09:06:14 +0000
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Sent to CCL by: "Noel O'Boyle" [no228/a\cam.ac.uk]
Linux4Chemistry is alive and well, as you would have found if you
Googled it. The web site was never at www.linux4chemistry.com though. 

The current website for Linux4Chemistry is:
 http://www.redbrick.dcu.ie/~noel/linux4chemistry/

Comments, suggestions and volunteer editors welcome. :-)

Regards,
 Noel.

On Thu, 2005-12-15 at 14:01 -0500, Andrew D. Fant fant{=}pobox.com
wrote:
> Sent to CCL by: "Andrew D. Fant" [fant]_[pobox.com]
> John McKelvey jmmckel|a|attglobal.net wrote:
> > Sent to CCL by: John McKelvey [jmmckel[A]attglobal.net]
> > Try www.linux4chemistry.com for YAEHMOP  [Yet Another Extended Huckel 
> > Molecular Orbital Program].. 
> 
> linux4chemistry.com appears to be defunct.  The good news is that YAeHMOP is a 
> sourceforge project and can be found at  http://yaehmop.sourceforge.net/ .
> 
> Happy Holidays,
> 	Andy
>


From owner-chemistry@ccl.net Fri Dec 16 07:27:01 2005
From: "Eduardo Lemos de Sa edulsa#,#quimica.ufpr.br" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: convolution/deconvolution softwares - summary
Message-Id: <-30343-051216054757-10679-sVf7SkGw2sT8ozDhdV32+w++server.ccl.net>
X-Original-From: Eduardo Lemos de Sa <edulsa],[quimica.ufpr.br>
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Sent to CCL by: Eduardo Lemos de Sa [edulsa * quimica.ufpr.br]
Dear CCLers

Late week I transmited an email to CCL list and got some replies. Special
thanks for Andras Borosy and Vincent Xianlong Wang.

They suggested:

The one I know is Origin from OriginLab that can do
this job. It is a commerical software, but you can try
its demo version.


and

In PASCAL, BASIC or ForTran see: Numerical Recipes (http://www.nr.com), in
=

MatLab-like see: Octave(http://www.octave.org/)




Most of these solutions involves commercial softwares (demo versions are
avaliable) or using Numerical Receipes (books are also avaliable, in
parts, to download). Octave (free to UNIX users) is the cheapest/better
solution.


I wish to all a Happy Christmas and a Prosper New Year


Eduardo
 

Eduardo Lemos de Saá
Dep. Química - Universidade Federal do Paraná
P. Box 19081 - Curitiba / PR / Brazil
ZIP 81531-990
fax: +55(41)3361-3186
fone: +55(41) 3361-3300


From owner-chemistry@ccl.net Fri Dec 16 08:37:00 2005
From: "Eduardo Lemos de Sa edulsa++bohr.quimica.ufpr.br" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: software to convolution/deconvolution - summary
Message-Id: <-30344-051216063452-30335-vJiL/gGK9oFU/oCQHQ6T6Q .. server.ccl.net>
X-Original-From: Eduardo Lemos de Sa <edulsa%x%bohr.quimica.ufpr.br>
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Date: Fri, 16 Dec 2005 11:40:27 +0100
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Sent to CCL by: Eduardo Lemos de Sa [edulsa- -bohr.quimica.ufpr.br]
Dear CCLers

Late week I transmited an email to CCL list and got some replies. Thanks 
for
Andras Borosy and Vincent Xianlong Wang.

They suggested:

The one I know is Origin from OriginLab that can do
this job. It is a commerical software, but you can try
its demo version.


and 


In PASCAL, BASIC or ForTran see: Numerical Recipes (http://www.nr.com), in =

MatLab-like see: Octave(http://www.octave.org/)




Most of these solutions involves commercial softwares (demo versions are 
avaliable) or using Numerical Receipes (books are also avaliable, in 
parts, to download).


I wish to all a Happy Christmas and a Prosper New Year


Eduardo


From owner-chemistry@ccl.net Fri Dec 16 10:15:00 2005
From: "Wai-To Chan chan.:.curl.gkcl.yorku.ca" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: convergence of optimization for heme Fe3+
Message-Id: <-30345-051216100946-30988-ThcdQnd3Wzx1uaJYddw8lA!=!server.ccl.net>
X-Original-From: Wai-To Chan <chan]_[curl.gkcl.yorku.ca>
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Date: Fri, 16 Dec 2005 10:21:44 -0500 (EST)
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Sent to CCL by: Wai-To Chan [chan||curl.gkcl.yorku.ca]
Vlad Cojocaru [Vlad.Cojocaru * eml-r.villa-bosch.de] wrote:

<<<<<<<<<<<
 Dear CCLers,
I have been trying to optimize the geometry of a heme group that has
Fe3+ (both in low and high spin states - mult=2, mult=6).  For this
purpose I use GAMESS with the input shown below. However, the
onvergence is not achieved and the energy fluctuates widely (as shown
in the output sample below). I am not an expert in QM calculations, so I
was wondering if somebody could give me a hint how to deal with this or
let me know if my input needs to be changed in any way?
The result is very similar for MULT=2.
Best wishes
vlad
>
>>>>>>>>>>>>>>>>>

	 As suggested in the other reply to your post using convergence methods
other than the default DIIS may help. Give a try to the use of the damping 
method with DIIS turned off by setting

$SCF DAMP=.TRUE. NOCONV=.TRUE. $END

in a single point energy calculation first. 

   Damping is not as efficient as DIIS and chance is your SCF won't converge. 
But if the SCF iteration shows improvement (no wide oscillation) you may repeat the 
calculation from the previous unconverged MOs as the initial guess
with a larger number of SCF cycles specified. 

   If convergence is achieved you may experiment with switching back to the 
default DIIS method using the converged MOs as initial guess to speed up 
the SCF step in the geometry optimization. 

   The wide energy fluctuation clear shows that tha this is a difficult system
for SCF to converge. When dealing with such systems it is  
prudent to examine the orbitals closely. Look out for signs of trouble
like very narrow HUMO-LUMO gap or incorrect order of eigenvalues
in the initial guesss and the converged MOs as well.

Wai-To Chan


From owner-chemistry@ccl.net Fri Dec 16 17:36:00 2005
From: "Grzegorz Bakalarski grzesb(!)biogeo.uw.edu.pl" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: OT:Fedora Core 3 or 4 and Gaussian - exec problem
Message-Id: <-30346-051216122006-3464-QlbAE0VdIWvL1uzbkJXZog===server.ccl.net>
X-Original-From: Grzegorz Bakalarski <grzesb!^!biogeo.uw.edu.pl>
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Sent to CCL by: Grzegorz Bakalarski [grzesb|*|biogeo.uw.edu.pl]
Dear All,

I'm sorry for slightly off topic and again gaussian query!

I feel it is rather linux query so more off-topicism and again I'm sorry.

The situation is a following: 

I have few linux workstations: one with very new SuSE 10.0,
one with Fedora Core 3 and one with Fedora Core 4 (unfortunately
Fedora is not supported by gaussian, but I cannot change
it to SuSE due to other issues).
I have also PGI Fortran compiler v. 6.05.
Also I have source codes for various gaussian relases
(since G98 E.2 up to G03 D.1 - we are on maintenance).

Compilation on Fedora machines as well as on SuSE machine
goes smoothly without any problems.

One SuSE machine execution of a test job goes like a charm.

But on Fedora machines (3 or 4 ) I get an error at a very 
begining saying:

 ******************************************
 Gaussian 03:  IA32L-G03RevD.01 13-Oct-2005
                16-Dec-2005
 ******************************************
 %nproc=1
 Will use up to    1 processors via shared memory.
 %mem=20mw
Erroneous write during file extend. write 1896 instead of 4096
Probably out of disk space.
Erroneous write during file extend. write 1896 instead of 4096
Probably out of disk space.
Write error in NtrExt1
Write error in NtrExt1: No such file or directory

Of course the machine has 20GB of disk space and a test job
is HF/3-21G* for water molecule so a diskspace can;t be an issuse.

What is more strange one of Fedora machines had Fedorea Core 2 (or maybe 1)
previously and g03 C.2 has run on it successfuly. I tried to run this version
of G03 as well as G98 E.2 with exactly the same error message.

I tried to debug the problem using strace tool and it showed that
whenever G03 (or G98) tried to open internal files like chk, rwf,
int, d2e which were not present (need not to !!!) it created them and 
then tried to write to them but the count of written blocks did not match.
Typilac strace output looked like:

open("/tmp/Gau-5823.scr", O_RDWR|O_LARGEFILE) = -1 ENOENT (No such file or directory)
open("/tmp/Gau-5823.scr", O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE, 0666) = 6
_llseek(6, 0, [0], SEEK_END)            = 0
fstatfs64(6, 84, {f_type="EXT2_SUPER_MAGIC", f_bsize=4096, f_blocks=4923709, f_bfree=2412286, f_bavail=2162175, f_files=2501856,
f_ffree=2268833, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0
_llseek(6, 0, [0], SEEK_END)            = 0
write(6, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., 524288) = 1064
write(1, "Erroneous write during file exte"..., 91) = 91

Resulting file had always size of 4096 bytes (NB correct one!).

What is really more strange I found a method to run the test job on the Fedora 
machines.
On my SuSE machine I've run the test jobs and generated all 
internal files using % directives (e.g. added the following lines
to an input file:

%chk=wat.chk
%rwf=wat.rwf
%scr=wat.scr
%d2e=wat.d2e
%int=wat.int

)
Then I copied the files to Fedora machine and also modified
input file.
The I've run g03 again and it did the jobs very well ...

I guess there have to be some problem with Fedora config or kernel
settings .....
A system admin of the machine said it is purely vanilla
installation without any security (SE) settings.
I'm not sysadmin and have little knowledge on Fedora linux 
so I ask you for help ..

Thanks for any friendly suggestion!

GB


From owner-chemistry@ccl.net Fri Dec 16 18:11:01 2005
From: "Jorge Seminario seminario^tamu.edu" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: vibrations of an excited electronic state
Message-Id: <-30347-051216114008-32306-O22h6vxy8zCQ9miA47XvhA a server.ccl.net>
X-Original-From: "Jorge Seminario" <seminario:tamu.edu>
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Sent to CCL by: "Jorge Seminario" [seminario^^tamu.edu]
This is a multi-part message in MIME format.

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Dear All,
I am looking for references on the
vibrational spectrum of an
electronic excited state of a molecule.
Is there any experiment?
I would strongly appreciate your help on this
Sincerely
Jorge M. Seminario
Department of Chemical Engineering
Department of Electrical and Computer Engineering
Texas A&M University
3122 TAMU
College Station, TX 77843-3122
Phone and Fax 979-845-3301
seminario++tamu.edu
http://cheweb.tamu.edu/faculty/seminario/

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I am looking for references on =
the</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>vibrational spectrum </FONT><FONT =
face=3DArial=20
size=3D2>of&nbsp;an</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>electronic excited state of a=20
molecule.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Is there any experiment?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I would strongly appreciate your help =
on=20
this</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Jorge M. Seminario<BR>Department of =
Chemical=20
Engineering<BR>Department of Electrical and Computer =
Engineering<BR>Texas=20
A&amp;M University<BR>3122 TAMU<BR>College Station, TX =
77843-3122<BR>Phone and=20
Fax 979-845-3301<BR><A=20
href=3D"mailto:seminario++tamu.edu">seminario++tamu.edu</A><BR><A=20
href=3D"http://cheweb.tamu.edu/faculty/seminario/">http://cheweb.tamu.edu=
/faculty/seminario/</A><BR></FONT></DIV></BODY></HTML>

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