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Date: Fri, 21 Jan 2000 06:54:22 +0200
From: Maija Lahtela <mlahtela@csc.fi>
To: chemistry@ccl.net
Subject: Programming exercise in chemistry
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Dear CCLers,

We are planning a course "Fortran 90/95 for chemists" and I am looking for
exercises in field of chemistry to be solved with the Fortran. 
I have the book of Etter " Structured FORTRAN 77 for Engineers and
Scientists", but there is only one application in chemistry (temperature
conversion).
If you have ideas about exercises, I look forward to hear about them.


Yours,

Maija Lahtela-Kakkonen


***************************************
Maija Lahtela-Kakkonen
Researcher
CSC-Center for Scientific Computing
Tekniikantie 15 a D
P.O.Box 405
FIN-02101 ESPOO FINLAND
TEL 358-9-4572079
FAX 358-9-4572302
E-MAIL mlahtela@csc.fi
***************************************


From chemistry-request@server.ccl.net  Fri Jan 21 11:56:50 2000
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From: Thomas Sommerfeld <Thomas.Sommerfeld@urz.uni-heidelberg.de>
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Subject: symmetry detection/generation
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Dear CCLers,

can anyone point me to a program or preferably to two
subroutines/functions that 

(a) detect symmetries: given a set of Cartesian coordinates 
                       _and_ an accuracy threshold, the point
	               group and sets of equivalent centers      
	               are returned (using a fairly large threshold
		       one should be able to find configurations
		       that are "close" to some symmetry.

(b) generate symmetry equivalent centers:
          given any point group and one point the number and coordinates
          of the symmetry equivalent points should be returned.

Both routines should also work for non-Abelian point groups.

Similar routines can probably be found in most quantum chemistry and
x-ray packages, but I would greatly prefer a simple stand-alone
solution. 

Thanks a lot.

------------------------------------------------------------------------------
Thomas Sommerfeld                                       Tel:   +49 6221 545264
Theoretische Chemie, Universitaet Heidelberg            Fax:   +49 6221 545221
Im Neuenheimer Feld 229, 69120 Heidelberg, Germany         
Email: Thomas.Sommerfeld@urz.uni-heidelberg.de


From chemistry-request@server.ccl.net  Fri Jan 21 09:52:33 2000
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Date: Fri, 21 Jan 2000 14:47:41 +0100 (MET)
From: Jens Antony <antony@dina.kvl.dk>
To: CHEMISTRY@ccl.net
Subject: Summary: Unused basis function in g98?
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Dear CCL!

A few days ago I posted a question concerning the difference of the HF
results on the Cd2+ ion between Gaussian98 and Gaussian94. It turned out
that it was caused by the fact that Gaussian98 automatically checks the
basis set for linear dependency and reduces the expansion space if
necessary. Below as summary two replies and the original question.

Thanks for the help and interest of all replicants.

Jens

---------- Original question ----------

Comparing the HF energies of Gaussian98 with Gaussian94, DALTON, and
MOLCAS we observe a difference of about 0.01 a.u. with Gaussian94,
DALTON, and MOLCAS having the same lower energy. We see this for the
Cd ion and for cadmium containing molecules.

We use the Gen keyword to invoke Kelloe and Sadlej's contracted basis for
Cd (Theor Chim Acta (1995) 91: 353). Looking into the output with Pop=Full
we find that Gaussian98 apparently does not use basis function no. 4 of
s-type. It occurs for revisions A5 and A7 on both LINUX and SGI machines.

Is this a bug in g98 and if so when does it occur?

---------- Reply from Karl K. Irikura ----------

Dear Jens,

G98 may have decided that the basis has a linear dependency and to
delete one function.  You can try turning this off using IOP(3/32=2).

Good luck!

Karl

---------- Reply from Douglas J. Fox (Gaussian support) ----------

There are indeed checks for linear dependencies on the basis set and you
have an unusual case in that you have a near linear dependency in the core
functions. The more common occurance of such dependencies is in diffuse
functions where little or no change in the energy can be detected. For HF
energies you can generally include these functions by turning down the
threshold for discarding basis functions with IOP(3/59=5), the default is
4, or turn off checking as you did with IOP(3/32=2).

This has drawbacks for geometry optimizations and post-HF calculations
where near linear dependencies can change with geometry or cause numerical
problems with correlation expansions and integrals over the MO basis.

Also while the total energy is affected it is likely that this energy
defect will be evident in all molecular systems as the core orbitals don't
interact strongly on bonding. Thus relative energies are likely to be
unaffected.

Dependencies in core functions are uncommon and while you have checked the
Sadlej publication it is possible that there is an error there. You might
want to look at the uncontracted atomic calculation and associated
eigenvectors to see how well than energy compares with the contracted
value.



From chemistry-request@server.ccl.net  Fri Jan 21 12:05:53 2000
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I am interested using Charmm to study systems of large molecules in
water.
I am using the academic version of Charmm, which lacks a molecule
building interface.  My question is, what is the best way to build
molecules
for this version?

J Clohecy
orac@fuse.net



From chemistry-request@server.ccl.net  Fri Jan 21 13:04:38 2000
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From: "Feller, David F" <david.feller@pnl.gov>
Subject: Linear Dependency and Gaussian 98: A cautionary tale
To: "'CHEMISTRY@ccl.net'" <CHEMISTRY@ccl.net>
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One change in Gaussian 98 that had escaped our notice until
yesterday was that it will "automatically handle" linear dependency
in basis sets.  What this means is that a rectangular transformation
is performed to eliminate eigenvectors of the overlap matrix with
eigenvalues below some threshold.  The default threshold in G98
seems to be 1.0E-5.  To the best of my knowledge, in previous versions 
of Gaussian all basis functions were retained, no matter how small
their eigenvalues.  In particularly severe cases this caused convergence
failure in the SCF. 

Eliminating eigenvectors has both positive and negative consequences.  
The principal advantage is that the code will operate more robustly.  The
disadvantage is that users find *significant* energy differences between
calculations run with earlier versions of Gaussian (or other codes) and
Gaussian 98.  Like us, they may not have been aware of this change
in Gaussian 98.

In the G98 output file, you will see a line such as:
One-electron integrals computed using PRISM.
NBasis=    95 RedAO= T  NBF=    95
NBsUse=    92 1.00D-04 NBFU=    92

The variable NBUse is the actual number of basis functions used.
In this case 3 were elminated.  John Montgomery sent us the 
IOP code necessary to override this new feature.  It is iop(3/32=2)
which should appear on the same line as the level of theory,
basis set, etc.

Dave 

P.S. Thanks to Michel Dupuis, Kirk Peterson and John Montgomery
for unraveling the mystery.

David Feller                                | d3e102@emsl.pnl.gov 
Environmental Molecular Sciences Lab., K8-91| Box 999
Pacific Northwest National Laboratory       | Richland, WA 99352 
                                            | Fax: 509-375-6631

From chemistry-request@server.ccl.net  Fri Jan 21 13:24:15 2000
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From: "Feller, David F" <david.feller@pnl.gov>
Subject: Linear dependency/G98 (followup)
To: "'CHEMISTRY@ccl.net'" <CHEMISTRY@ccl.net>
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I just noticed Jens Antony's mail on this same topic and read
Doug Fox's reply.  I think Doug is correct in stating that most
linear dependency arises from the presence of diffuse functions
in basis sets, but it would be an oversimplication to imply that
this is the only case where it arises or that the consequences
of eliminating vectors is small.

The case that brought this issue to our attention was a calculation
on the argon atom.  If you use the (s,p) functions taken from the
correlation consistent cc-pV5Z set, you will obtain the following
SCF energies:
Ar Atom E(SCF)
-526.817342 (G94, MOLPRO, MELDF, etc.)
-526.813116 (G98)

As you can see, the difference in this case is more than 4 millihartrees
for a single atom.

Dave

David Feller                                | d3e102@emsl.pnl.gov 
Environmental Molecular Sciences Lab., K8-91| Box 999
Pacific Northwest National Laboratory       | Richland, WA 99352 
                                            | Fax: 509-375-6631

From chemistry-request@server.ccl.net  Fri Jan 21 13:31:47 2000
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Date: Fri, 21 Jan 2000 17:25:43 +0000
From: Laurence Cuffe <Laurence.Cuffe@ucd.ie>
Subject: G98 on an SGI problems
To: CHEMISTRY@ccl.net
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We have compiled g98 on an  SGI Origin 2000 computers with 
IRIX64 ver. 6.5.x Operating System 
According to bldg98.log  the compilation of the
 source was successful. However, we are unable to run any
 Model Chemistry (method/basis set) except for the default one:
 HF/STO-3G. 
Changing basis set results in error
Standard basis: ????? (5D,7F)
Changing method results in error 
Unrecognized post-SCF IPrc10 in PutPrc
Putting in the route from the log file of a g98 job run on a different 
system results in successfully completed jobs.
This leads us to believe that the problem is with the compiled 
version of the link1 code. Has anyone encountered similar problems
and if so have they any fixes.
Hopping to hear from you
LaurenceCuffe
University Colege Dublin
Ireland

From chemistry-request@server.ccl.net  Fri Jan 21 14:48:26 2000
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Hi CCL members,

I am looking for some kinetic data of H-abstraction reactions of 
methoxy radical/t-butoxy radical with methyl amine or any alkyl-amines. 

I appreciate every response.

--Sree Rao  (voleti@wsunix.wsu.edu)


From chemistry-request@server.ccl.net  Fri Jan 21 17:58:45 2000
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Date: Fri, 21 Jan 2000 16:54:07 -0500
To: chemistry@ccl.net
From: Sompop Sanongraj <ssanongr@mtu.edu>
Subject: polarizability
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Hi all
Can anyone point me out " what's the unit of polarizability that is
obtained from frequency calculation?"? I try to find from the manual but I
didn't see they have explained about the unit. It tell you about the
polarizability tensors. I don't know how to relate to the typical unit of
polarizability such as 10^-24 cm^3. 
Thanks
sompop 
Sompop Sanongraj
208 Church Street
Hancock MI 49930.

TEL: (906) 482 9377


From chemistry-request@server.ccl.net  Fri Jan 21 20:10:47 2000
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Hi Sompop,

In a classical picture, it can be shown that an atom has 

polarizability (alpha) ~ 4 (pi) (epsilon_o) (radius)^3

epsilon_o = 8.85419 x 10^-12   F m^-1 ( F = Farad)
               = 8.85419 x 10^-12   C^2 m^-2 N^-1

In MKS system, it gives unusual unit C^2 m N^-1 for polarizability. 
It is also expressed in volume polarizability: 

(alpha) / 4 (pi) (epsilon_o) 

which has units of m^3. In CGS units, where 4 (pi) (epsilon_o) = 1, 
the unit of polarizability is cm^3.

The polarizability increases with the number of electrons in the 
molecules, or with the volume of charge distribution.

For example the polarizability of CH_4 is 2.6 x 10^-24 cm^3
                                           of CCl_4 is 11.2 x 10^-24 cm^3


Jamal Uddin




On 21 Jan 00, at 16:54, Sompop Sanongraj wrote:

> Hi all
> Can anyone point me out " what's the unit of polarizability that is
> obtained from frequency calculation?"? I try to find from the manual but I
> didn't see they have explained about the unit. It tell you about the
> polarizability tensors. I don't know how to relate to the typical unit of
> polarizability such as 10^-24 cm^3. 
> Thanks
> sompop 
> Sompop Sanongraj
> 208 Church Street
> Hancock MI 49930.
> 
> TEL: (906) 482 9377
> 
> 
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To Admins
> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net
> 
> 
> 
> 
> 



From chemistry-request@server.ccl.net  Fri Jan 21 21:26:54 2000
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Date: Fri, 21 Jan 2000 20:23:28 -0500 (EST)
From: AM <amasunov@shiva.hunter.cuny.edu>
To: kcharoen@theochem.tu-muenchen.de
cc: sctkc@mucc.mahidol.ac.th, noy@atc.atccu.chula.ac.th, chemistry@ccl.net
Subject: Re: BSSE should not affect gradient
In-Reply-To: <3888DBB6.9E4E0C27@bigfoot.com>
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Dear Teerakiat,
 BSSE does affect gradients and equilibrium geometry (pushes molecules
apart). This way you get stronger attraction compare to single point
BSSE.
 CP optimizer (shell script submitting bunch of G98 jobs) with analitical
gradients was recently developed. For download, description, and
references look at
http://stark.udg.es/~perico/bbopt.html
For a script for GAMESS-US, contact me.

Best,
Artem

>   Question is ..... does BSSE affect gradient ? Is there
>any theory or paper doing on this issue ? I need only
>the answer but some clever man could take this to make
>a publication.

>From nkobko@shiva.hunter.cuny.edu Fri Jan 21 19:15:44 2000
Date: Fri, 21 Jan 2000 18:43:04 -0500 (EST)
From: Nadya Kobko <nkobko@shiva.hunter.cuny.edu>
To: amasunov@shiva.hunter.cuny.edu
Subject: NEW UPDATE of the CP-optimizer (fwd)



---------- Forwarded message ----------
Date: Wed, 19 Jan 2000 15:44:16 +0000
From: Pedro Salvador <perico@stark.udg.es>
To: J. J. Dannenberg <jdannenberg@gc.cuny.edu>,
     Miquel Duran <quel@stark.udg.es>, dtmoore <dtmoore@email.unc.edu>,
     vmrr <vmrr@sauron.quimica.uniovi.es>,
     E.R.Waclawik <E.R.Waclawik@exeter.ac.uk>, klauda <klauda@che.udel.edu>,
     p.j.a.ruttink <p.j.a.ruttink@chem.uu.nl>, woher <woher@ruca.ua.ac.be>,
     AlexWhite <AlexWhite@chem.ih.navy.mil>,
     nkobko <nkobko@shiva.hunter.cuny.edu>, silvia <silvia@stark.udg.es>,
     tomvdk <tomvdk@ruca.ua.ac.be>
Subject: NEW UPDATE of the CP-optimizer


Dear all

Some errors have been detected in the scripts when single atoms are
defined as fragments, because Gaussian doesn't print out the (null)
gradients and second derivatives in some cases.
Therefore, slight changes have been made in some UNIX scripts and
Fortran files.
The main difference is that  for frequency calculations, the
calculations corresponding to every single atom with his own basis set
is skipped and a set of zeros is generated. This situation is also
written out in the log file.

You can download the pacth from this URL (please read also the
patch.readme file):
http://kerr.udg.es/~perico/

thanks for your interest

Best Regards

Pedro


(you've got this e-mail because once you contacted us concernig our
CP-optimizer package. If you don't want to receive information about it
anymore let us know. Sorry for the possible inconveniences)
--
/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\
I Pedro Salvador Sedano             I                              I
\ Ph.D. Student                     I  Butch: You okay?            /
I Universitat de Girona             I  Marcellus: No. I'm pretty   I
/ Institut de Quimica Computacional I       fuckin' far from okay. \
I E-mail: perico@stark.udg.es       I                              I
\ WWW :http://stark.udg.es/~perico  I           Pulp Fiction       /
I Telf: +34 972 418358              I                              I
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From chemistry-request@server.ccl.net  Fri Jan 21 23:36:46 2000
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Date: Sat, 22 Jan 2000 11:35:40 +0800 (CST)
From: Fenglou Mao <mao@linux2.ipc.pku.edu.cn>
To: "CHEMISTRY@www.ccl.net" <CHEMISTRY@server.ccl.net>
Subject: Rasmol front-end to browse molecules.
Message-ID: <Pine.LNX.4.10.10001221130040.13071-100000@linux2.ipc.pku.edu.cn>
MIME-Version: 1.0
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Hi, all,
    I wrote a small rasmol front-end, if you
want to view molecules just like xview or acdsee
to pictures, you can use it: molsee,

     ftp://mdl.ipc.pku.edu.cn/pub/software/molsee/molsee

Sincerely Yours,

FengLou Mao
*******************************
ADD:Mr. FengLou Mao
    Institute of Physical Chemistry
    Peking University
    BeiJing
    P.R.China
Tel:86-10-62756833
Fax:86-10-62751725



