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From: David Young <youngd2@mail.auburn.edu>
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To: chemistry@ccl.net
Subject: Benchmarks and Software
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Hi,

	I would like to point out that this conversation on benchmarks is
a bit one dimensional.  There are some very popular (profitable) chemistry
software packages that do poorly on benchmarks but sell because of other
factors such as ease of use or functionality.  You really need to look at
a list of criteria when choosing a software package.  Some of them would
be

Benchmarks of efficiency

Cost

Ease of use in general

Suitability for a particular class of chemical systems.

Robustness - what percentage of the time does the job fail to execute even
though the inputs are in accordance with the manual?

Functionality - does it compute the properties you need?

	Once you have this information, you still might get a program that
does very poorly on several of the criteria in order to address the
criteria that is your highest priority.  Many people classify ease of use
as the one they have used before thus preserving their five year
investment of previous time rather than investing another 2 weeks to learn
to use another program that would be considered much easier to use.

	That said, now consider benchmarks specifically.  The best model
to follow would probably be the one used for CPU benchmarks.  These fall
into three categories.

1.  Benchmarks done by an independent organization.
2.  Benchmarks that require that the code be unaltered and compiled
without options.
3.  Benchmarks in which almost anything is fair game as long as the final
answer is correct.

In the case of chemistry software, you have to worry about the chemical
systems in the benchmark set.  A program that does very well on a set of
organic molecules may perform miserably or even completely fail to run
with a set of transition metals.  Computer hardware is also a big factor. 
One program may do better on PCs while another does better on machines
with vector math units.  Ideally you would want a break down of all of
these factors and one big number at the end. 

	Who does the benchmarks is also a question.  Academics may not
have a suitable selection of hardware to test codes on and may not wish to
publish poor results for fear that the writer of the codes may be a future
reviewer.  National labs are becoming more tightly tied to industry, thus
creating political problems.  Industrial workers don't want to spend so
much effort unless there is a way to profit from it.  Ideally an
independent organization (perhaps privately held company) would get
hardware manufacturers to give them hardware and charge them a fee besides
to do the benchmarks, then they would charge each software company a fee
to do their benchemarks, then the benchmarks would be published or on the
web free.  Perhaps a company that already benchmarks CPUs should hire a
chemist to develop and run these tests on the same machines.  I wonder if
they could get enough money from the project to pay the chemist and add to
profits besides?  Perhaps the fee they charge should be based on the
selling price of the software.

                                Dave Young
                                youngd2@mail.auburn.edu

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

          Live long and maintain marketable job skills.

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


From chemistry-request@server.ccl.net  Thu Apr 22 14:36:08 1999
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Date: Thu, 22 Apr 1999 11:23:57 -0700
To: "Merethe Sjovoll" <msj@fskru5.hre.hydro.com>,
        chemistry@www.ccl.net
From: David Gallagher <dgallagher@fujitsu.com>
Subject: Re: CCL:Estimation of vapour pressure of organic liquids and
  solids
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Hi Merethe,

Take a look at:

QSPR Prediction of Vapor Pressure from Solely Theoretically-Derived
Descriptors, C. Liang & D. Gallagher; J. Chem Inf. & Comp Sci. Vol 38,
Number 2 pages 321-324

Abstract
	To date, most reported quantitative structure-property relationship (QSPR)
methods to predict vapor pressure rely on, at least, some empirical data,
such as boiling points, critical pressures, and critical temperatures.
This limits their usefulness to available chemicals, and incurs the time
and expense of experimentation. A model to predict vapor pressure from only
computationally derived molecular descriptors, allowing study of
hypothetical structures, is described here.  Several multi-linear
regressions and artificial neural network analyses were tested with a range
of descriptors (e.g. topological and quantum mechanical) derived solely
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WATOC'99: 1-6 August, 1999
=======================

Full information about the scientific program and registration information 
is now available from the following sources

1. The Royal Society of  Chemistry  WATOC pages at
http://www.chemsoc.org/watoc99/.  An Acrobat file
is available for downloading from http://www.chemsoc.org/pdf/watoc99.pdf
which contains full program information  and registration details.
(Version  3 or 4 of the Acrobat reader will be needed to print this document,
and this is available from http://www.adobe.com/prodindex/acrobat/readstep.html

Please note the key dates: 17 May for "early bird registrations"
21 June for normal registrations. Completed registrations should be
returned to 

Mrs Paula Whelan, WATOC99, 
The Royal Society of Chemistry, 
Burlington House, London, W1V 0BN
UK. 

2. Information about  WATOC, including how to join and  get  £100 off
the registration fees,  is available at http://www.ch.ic.ac.uk/watoc/. This
discount also applies to  RSC members (http://www.rsc.org/members/join.htm)

3. Anyone having difficulty in printing off the registration pages can get 
GIF image versions from http://www.ch.ic.ac.uk/watoc/

4. Abstracts of talks and posters submitted electronically can be
searched and viewed from http://www.chemsoc.org/cgi-bin/fx.exe?DB=chemwatoc&P=watoc

Please note that abstracts received on paper will only be available via the printed
conference abstracts book.
From chemistry-request@server.ccl.net  Fri Apr 23 07:29:42 1999
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From: "Stefan Fau" <fau@chemie.uni-marburg.de>
To: "Jirka Kozelka" <kozelka@citi2.fr>
Cc: "CCL" <chemistry@ccl.net>
Subject: RE: HOMO-LUMO gap in Pt(II)
Date: Fri, 23 Apr 1999 13:28:48 +0200
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Dear Jirka,

modeling a complex in solution by SCF calculations in the gas phase 
contains two errors: You neglect correlation and solvent effects.

Normally reaction energies are more sensitive to correlation than the 
geometry. I would not be surprised if this holds for HOMO-LUMO gaps too. 
By the way, DFT methods include correlation effects and are only slightly 
more expensive than HF calculations.

The HOMO -> LUMO transition is accompanied by a change of the charge 
distribution. Since the solvent can be polarized by the solute, your 
ground and excited state energies are lowered (by different amounts) 
in the presence of a solvent. 

There are two methods for inclusion of solvents, explicitly including 
the solvent molecules into the calculation (expensive!) and using a 
polarizable continuum as a model for the solvent (cheaper). 

Stefan
______________________________________________________________________
Dr. Stefan Fau
Fachbereich Chemie, AK Frenking
Philipps-Universität Marburg
35032 Marburg, Germany
fau@chemie.uni-marburg.de

> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On
> Behalf Of Jirka Kozelka
> Sent: Thursday, April 22, 1999 9:01 PM
> To: chemistry@www.ccl.net
> Subject: CCL:HOMO-LUMO gap in Pt(II)
> 
> 
> Dear CCL-members,
> 
> I have carried out a number of SCF calculations on Pt(II) complexes with
> chloride, amine, and phosphine ligands, using Gaussian 94 and 98, with
> different basis sets, and find consistently HOMO-LUMO gaps of 0.3-0.4
> Hartrees, i.e., 65000-90000 cm-1. This is roughly 3 times the excitation
> energies of spin-allowed d-d bands seen in
> solutions of these species. The difference seems too big to me to be
> explained by electron relaxation. I would very much appreciate comments
> and/or explications on/of this apparent discrepancy.
> We have seen that the bond lengths and dipole moment coming from HF
> calculations are quite wrong for these compounds, and one has to apply 
> correlated methods to get these quantities right. But can it be that the
> difference in energies of the HF HOMO/LUMO one-electron orbitals is so
> far from the excitation energy?
> 
> I shall summarize the answers.
> 
> Thanks,
> 
> Jirka Kozelka
> 
> -- 
> Jirka Kozelka
> Universite Rene Descartes
> URA CNRS 400
> 45 rue des Saints-Peres
> 75270 Paris 06
> FRANCE
> Tel. +331 42 86 21 75
> Fax  +331 42 86 83 87
> E-mail: kozelka@citi2.fr
> -= This is automatically added to each message by mailing script =-
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> 
> 
> 
> 

From chemistry-request@server.ccl.net  Fri Apr 23 10:14:06 1999
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Reply-To: horsfield@fecit.co.uk
To: chemistry@ccl.net
Subject: Non-adiabatic MD: multiple configurations?
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I am attempting to repeat the calculations of Gersonde and Gabriel (J.
Chem. Phys. vol 98 (3), p 2094 (1993)) in which the photodissociation of
Cl2 in Xe is discussed.

I am attempting to describe the electronic degrees of freedom using a
simple one particle model (tight binding), but have found a problem which
I fear is fundamental. Since my background is in DFT, I am not well versed
in multiple configuration interactions, hence the following question.

Excited states within the model are created by promoting an electron from
a low lying level to an empty higher lying level. When the interactions
are weak I believe this is a reasonable description. But when they are
weak, I suspect the model breaks down.

Consider the Cl2 dimer. It is unstable with respect to dissociation when
placed into an excited state. Thus, on being excited by a photon the atoms
begin to separate. As this happens, the HOMO-LUMO splitting decreases
until they become nearly degenerate. Thus it is no longer possible to
distinguish the excited from the unexcited states. No transition between
states is observed to take place. This is a problem should the two atoms
meet up again some time later as it is not clear what state they should go
into - ground state or excited state.

I suspect that the root of the problem is that when the HOMO-LUMO
splitting is very small it no longer makes sense to work with a single
particle picture - it takes no energy to move between configurations, thus
they will mix freely.

At this point I get lost. Does this analysis really solve the problem of
what state the system is in? Or would there still be ambiguity even if
configurations were allowed to mix?

Cheers,

Andrew

  +----------------------------------------------------+
   Andrew Horsfield       e-mail: horsfield@fecit.co.uk 
     FECIT, 2 Longwalk Road, Stockley Park, Uxbridge,   
          Middlesex UB11 1AB, United Kingdom.           
   phone: +44-(0)181-606-4653  FAX: +44-(0)181-606-4422 
  +----------------------------------------------------+

From chemistry-request@server.ccl.net  Sat Apr 24 07:31:15 1999
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Date: Sat, 24 Apr 1999 12:08:37 +0100 (BST)
From: Xiaogang Wang <xgwang@emu.thchem.ox.ac.uk>
To: chemistry@server.ccl.net
Subject: source code of Szabo and Ostlund's book
Message-ID: <Pine.LNX.3.96.990424120543.24251I-100000@emu.thchem.ox.ac.uk>
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Dear CCLers,

Does somebody have a copy of the FORTRAN source code, from the Ostlund 
and Szabo textbook, for  performing a two electron STO SCF calculation ? 

I know somebody has put up this question before, but I cannot find the
answer. 

Thanks!
Xiaogang

-------------------------------------------------------
Xiaogang Wang
Physical and Theoretical Chemistry Laboratory
University of Oxford          | Tel: 44-1865-275159(O), 44-1865-711623(H)
South Parks Road              | Fax: 44-1865-275400
Oxford OX1 3QZ                | Email:xgwang@emu.thchem.ox.ac.uk
UK

On leave from
Open Laboratory of Bond Selective Chemistry
University of Science and Technology of China | Fax: 86-551-3602969
Hefei, 230026                                 | Email: xgwang@ustc.edu.cn
China
-------------------------------------------------------


From chemistry-request@server.ccl.net  Sat Apr 24 09:06:17 1999
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Date: Sat, 24 Apr 1999 08:35:06 +36000
From: Richard Wood <dmpc@hugh.chem.uic.edu>
To: Xiaogang Wang <xgwang@emu.thchem.ox.ac.uk>
cc: chemistry@server.ccl.net
Subject: Re: CCL:source code of Szabo and Ostlund's book
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I have the book.  The code runs on pages 418-428.

Richard

On Sat, 24 Apr 1999, Xiaogang Wang wrote:

> Dear CCLers,
> 
> Does somebody have a copy of the FORTRAN source code, from the Ostlund 
> and Szabo textbook, for  performing a two electron STO SCF calculation ? 
> 
> I know somebody has put up this question before, but I cannot find the
> answer. 
> 
> Thanks!
> Xiaogang
> 
> -------------------------------------------------------
> Xiaogang Wang
> Physical and Theoretical Chemistry Laboratory
> University of Oxford          | Tel: 44-1865-275159(O), 44-1865-711623(H)
> South Parks Road              | Fax: 44-1865-275400
> Oxford OX1 3QZ                | Email:xgwang@emu.thchem.ox.ac.uk
> UK
> 
> On leave from
> Open Laboratory of Bond Selective Chemistry
> University of Science and Technology of China | Fax: 86-551-3602969
> Hefei, 230026                                 | Email: xgwang@ustc.edu.cn
> China
> -------------------------------------------------------
> 
> 
> -= This is automatically added to each message by mailing script =-
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> 
> 
> 
> 
From chemistry-request@server.ccl.net  Sat Apr 24 09:12:40 1999
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	Sat, 24 Apr 1999 14:08:38 +0100 (BUD)
Date: Sat, 24 Apr 1999 14:08:38 +0100
From: Karpati Tamas <toma@iris.inc.bme.hu>
To: Stefan Fau <fau@chemie.uni-marburg.de>
cc: Jirka Kozelka <kozelka@citi2.fr>, CCL <chemistry@ccl.net>
Subject: Re: CCL:HOMO-LUMO gap in Pt(II)
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   Dear Jirka,

   Have you compared the experimental excitation energies 
to those came from CIS calculations? They should be much 
more precise since CIS is developed for this aim, and in fact,
this is the cheepest ab initio tool to perform such a calculation. 
Using Gaussian, you may even take the solvent effects into account.
I would suggest to try this.

Also, in the former days of spectroscopy, semiempirical methods 
were used for predicting electron excitation and ionisation energies.
If everything else fails, i would -at least- try some of them.
Most of them is parametrized on experimental data (IPs, etc.)
Many programs that are dealing with semiempirical calculations
allows you to carry out CIS calculations on semiempirical SCF, as well.
For very large systems -in my opinion- this is the only way.

Hope this helps.
Best wishes,

Tamas Karpati
Technical University of Budapest, Hungary
toma@iris.inc.bme.hu

From chemistry-request@server.ccl.net  Sat Apr 24 13:10:00 1999
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Date: Sat, 24 Apr 1999 17:47:19 +0100 (BST)
From: Xiaogang Wang <xgwang@emu.thchem.ox.ac.uk>
Reply-To: Xiaogang Wang <xgwang@emu.thchem.ox.ac.uk>
To: chemistry@server.ccl.net
Subject: whereabouts of source code in Szabo and Ostlund's book 
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Dear CCLers,
 I have got the source code about 2 electron STO SCF calculation
>from the web. I forward a message from one kind CCLer below.

 I want to thank everbody who answered my question.
Xiaogang

-------------------------------------------------------
Xiaogang Wang
Physical and Theoretical Chemistry Laboratory
University of Oxford          | Tel: 44-1865-275159(O), 44-1865-711623(H)
South Parks Road              | Fax: 44-1865-275400
Oxford OX1 3QZ                | Email:xgwang@emu.thchem.ox.ac.uk
UK

On leave from
Open Laboratory of Bond Selective Chemistry
University of Science and Technology of China | Fax: 86-551-3602969
Hefei, 230026                                 | Email: xgwang@ustc.edu.cn
China
-------------------------------------------------------


---------- Forwarded message ----------
Date: Sat, 24 Apr 1999 16:19:51 +0200
From: Alexander Klinsky <alex.klinsky@scientist.com>
To: Xiaogang Wang <xgwang@emu.thchem.ox.ac.uk>
Subject: Re: CCL:source code of Szabo and Ostlund's book

> Does somebody have a copy of the FORTRAN source code, from the Ostlund
> and Szabo textbook, for  performing a two electron STO SCF calculation ?

You can get it with the Hyperchem 5 CDK. There is a free evaluation version
at www.hyper.com. After installation look in the cdk/fortran/szabostl
folder. There is the source code from the book.

Kind regards,

Alexander Klinsky
Department of Applied Theoretical Biochemistry
Insitute of Theoretical Chemistry
University of Vienna
Austria



From chemistry-request@server.ccl.net  Sat Apr 24 14:22:00 1999
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Date: Sat, 24 Apr 1999 20:17:58 +0200 (MDT)
From: "Dr. Peter Burger" <chburger@aci.unizh.ch>
To: chemistry@server.ccl.net
Subject: CCL: optimizer
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Dear CCLers,

I am in search for a freely available (short) geometry optimizer
(for equilibrium & TS opt.), which can read in coordinates, gradients
and energies externally from a file and generate geometry updates.
The idea is to interface the optimizer with a different program that
I am using here in that I would require the source code
(Fortran would be best).

Preferably the optimizer should be capable of handling cartesian
coordinates, Z-matrices and acknowledge applied geometrical constraints.
Different optimization routines/algorithms were obviously a plus.

Many thanks in advance,

Peter

-----------------------------------
Peter Burger
University of Zuerich
chburger@aci.unizh.ch    

From chemistry-request@server.ccl.net  Sat Apr 24 17:05:11 1999
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Date: Sat, 24 Apr 1999 22:01:06 +0100 (BST)
From: "Ivan I. Oleinik" <ivan.oleinik@materials.oxford.ac.uk>
To: "Dr. Peter Burger" <chburger@aci.unizh.ch>
cc: chemistry@server.ccl.net
Subject: Re: CCL:optimizer
In-Reply-To: <Pine.SGI.3.95.990424201743.29458A-100000@rzusgi.unizh.ch>
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Dear Peter,

Could you please summarize the answers. This is very important for my work
but I think, this is the issue that might be of great interest for many
people around.

Ivan.

------------------------------------------------------------------------
Ivan I. Oleinik             E-mail : ivan.oleinik@materials.ox.ac.uk
Department of Materials
University of Oxford
Parks Road
Oxford OX1 3PH                     Tel : +44 (0)1865 283325
United Kingdom                     Fax : +44 (0)1865 273764 
------------------------------------------------------------------------

On Sat, 24 Apr 1999, Dr. Peter Burger wrote:

> 
> Dear CCLers,
> 
> I am in search for a freely available (short) geometry optimizer
> (for equilibrium & TS opt.), which can read in coordinates, gradients
> and energies externally from a file and generate geometry updates.
> The idea is to interface the optimizer with a different program that
> I am using here in that I would require the source code
> (Fortran would be best).
> 
> Preferably the optimizer should be capable of handling cartesian
> coordinates, Z-matrices and acknowledge applied geometrical constraints.
> Different optimization routines/algorithms were obviously a plus.
> 
> Many thanks in advance,
> 
> Peter
> 
> -----------------------------------
> Peter Burger
> University of Zuerich
> chburger@aci.unizh.ch    
> 
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> 
> 
> 

