From wrankin@ee.duke.edu  Mon Jun  8 10:41:03 1998
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Date: Mon, 8 Jun 1998 10:40:54 -0400 (EDT)
From: "William T. Rankin" <wrankin@ee.duke.edu>
To: chemistry@www.ccl.net
Subject: Re: fortran Compiler for Linux Box. Options?
In-Reply-To: <199806080520.BAA21982@www.ccl.net>
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> What would you recommend? I know the subject has come up in the past,
> but compilers are improved all the time, and I would like a follow
> up on people's experience and recommendations. I will summary to the
> list.
> 
> I am willing to go freeware, but I would spend the money on
> a good Fortran compiler to gain the performance. (I also believe
> there is no freeware fortran compiler for f90 code!)

I picked up some information form The Portland Group, who markets
auto-parallelizing FORTRAN compilers for Linux.  You may want to
look them up at http://www.pgroup.com/

Now having said that, I will point out that even with the best
tools, simply running a compiler over existing serial FORTRAN
codes will most likely not produce highly scalable parallel code
without some sort of programmer direction from within the source. 

Your milage may vary of course.

You may also wat to look at the Bert77 optimiation tools from
Paralogic (http://www.plogic.com/), although they deal mainly
with distributed "Beowulf style" cluster computing.

Good luck,

-bill




From rivelino@ufba.br  Mon Jun  8 16:50:16 1998
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Date: Mon, 8 Jun 1998 17:47:18 -0300 (GRNLNDST)
From: Roberto Rivelino de Melo Moreno <rivelino@ufba.br>
To: CHEMISTRY@www.ccl.net
Subject: Re: CCL:ONE Electron Molecule.
In-Reply-To: <199806080731.IAA12006@rs5.csrsrc.mi.cnr.it>
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		Dear Dario,

You can find such a reference in the following papers:

	E. A. Hylleraas, Z. f. Phys. 71, 739 (1931).
			 	     51, 150 (1928).		
	G. Jaffe, Z. f. Phys. 87, 535 (1934).
	E. Teler, Z. f. Phys. 61, 458 (1930).			     	
	P. M. Morse and E. C. G. Stueckelberg, Phys Rev. 33, 932 (1929).
	J. E. Lennard-Jones, Trans. Faraday Soc. 24, 668 (1929)

R. Rivelino M. Moreno
Universidade Federal da Bahia
Instituto de Fisica
Salvador Bahia Brazil



From ep7@dent.okayama-u.ac.jp  Tue Jun  9 01:49:45 1998
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Dear Sir:

        Sometimes, L appear in optimized structural parameters.  I try to
understand about L and to calculate some ion.  However, I can not
understand it.
        I am sorry, please some example send me and please explain it.

        Thank you.


From joubert@ext.jussieu.fr  Mon Jun  8 03:36:35 1998
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To: chemistry@www.ccl.net
From: Laurent Joubert <joubert@ext.jussieu.fr>
Subject: Summary : Postdocs in computational chemistry : WWW sites or
 newsgroups ?



Deart Netters,

Last week, I asked this question on the CCL :

"I'm looking for a postdoctoral position in computational chemistry.
I already know the "job offered list" of the CCL, but I would like to know
if there are other sites or newsgroups of interest concerning postdoctoral
positions in this area of physical chemistry."

Thank you all very much for responding.

Here are the internet sites or newsgroups of interest concerning
postdoctoral positions :

1 ) http://ellington.pharm.arizona.edu/~bear/index.html#job

2 ) Please see http://www.ks.uiuc.edu/~sergei/jobs/.
Most noticable are the newsgroup bionet.jobs.offered,
Science magazine professional network, HUM-MOLGEN.

3 ) http://hackberry.chem.niu.edu:70/1/ChemJob
http://www.nature.com/ (see international jobs)
http://www.nextwave.org/http://quantum.chem.ndsu.nodak.edu/acs/openings.html

4 ) http://quantum.chem.ndsu.nodak.edu/acs/openings.html
http://psy.anu.edu.au/academia/chm.htm

5 ) You could have a look at CCP5. This is part of the Daresbury labs in
the UK.
They send out job ads to anyone who is subscribed.
The guy you should write to is M. Leslie. His Email is:
m.leslie@dl.ac.uk

Alternatively, you could do a search on the web or look up the DL web page:
www.dl.ac.uk

6 ) http://arrakis.iimatercu.unam.mx/ (they are looking for postdoc fellows
in a supercomputer center in Mexico)

7 ) http://www.unb.ca/chem.html (see "Ajit Thakkar" who has a vacancy in
his lab - send him a CV (ajit@unb.ca))

8 ) A three year post-doctoral position is available immediately or
starting any time up to Dec 1st 1998 with Dr. Popelier in the
Chemistry Department of UMIST, Manchester.
The project is fully funded by EPSRC and is entitled
"Rigorous Chemical Interpretation of Atomic Contributions in
Accurate Intermolecular Potentials."
The project resorts under the heading of Computational/Theoretical
Chemistry and essentially combines two theories that have
matured independently over the last two decades : "Atoms in
Molecules" (Bader) and "Distributed Mutipoles and Spherical
Tensors" (Stone).
The results are expected to yield genuine insight into
the atom-atom contributions of intermolecular potentials and
will pave the way more accurate Molecular Dynamics modelling.
Although the work is mainly academic, industrial interest
will be sought.

The candidate can have any nationality but must apply for a work
permit if not a citizen of the European Union. The candidate
must have experience in ab initio calculations and/or intermolecular
potentials. Experience in programming , preferentially FORTRAN
is required. Knowledge of "Atoms in Molecules" would be a
great advantage but not essential.

If you are interested send your CV + two references on your behalf
to :
Dr.P.Popelier, Dept.of Chemistry, UMIST, M60 1QD
Manchester, UK

For more details please contact Dr. Popelier at
"pla@umist.ac.uk" or call  44-(0)161-200 45 11.


8 ) (In french) :
http://garp.univ-bpclermont.fr/guilde/Emploi.html
http://www.abg.asso.fr/

Laurent Joubert





***********************************************************
Laurent JOUBERT (PhD student)

Ecole Nationale Superieure de Chimie de Paris
Laboratoire d'Electrochimie et de Chimie Analytique
11, rue Pierre et Marie Curie
75231 PARIS CEDEX 05- FRANCE
Tel : (33) 1-55-42-63-91
Fax : (33) 1-44-27-67-50

E-Mail : joubert@ext.jussieu.fr
Web page : http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/Laurent
***********************************************************




From jaouad@csc.fi  Tue Jun  9 05:29:45 1998
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	Tue, 9 Jun 1998 07:13:20 +0300 (EET DST)
Date: Tue, 9 Jun 1998 07:12:43 +0300 (EET DST)
From: Jaouad El-Bahraoui <jaouad@csc.fi>
Reply-To: Jaouad El-Bahraoui <jaouad@csc.fi>
To: Melissa Petersen <tgakmp@sg10.chem.tue.nl>
cc: chemistry@www.ccl.net
Subject: Re: Gaussain 94 Error Message
In-Reply-To: <9806051821.ZM4742@sg10.chem.tue.nl>
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Hi Melissa and CCl's
A while ago I asked the below question:


Does any one know how to solve this kind of problem in g94, I use the
version E.2

 Density matrix breaks symmetry, PCut= 1.00D-04
 Density matrix has no symmetry -- integrals replicated.
 Density matrix breaks symmetry, PCut= 1.00D-04
 Density matrix has no symmetry -- integrals replicated.


Here I present the summary of responses, and by the way I want to thanks
all who gives me a little of his time to solve my problem.

all the Best
Jaouad

***************************************************************************
                            summary
***************************************************************************

On Fri, 5 Jun 1998, Melissa Petersen wrote:

> Hi Jaouad,
> 
> I have just joined the computational chemistry list and I noticed that you
> posted a message on 25 May concerning an error that you got in g94 i.e.
> "Density Matrix breaks symmetry"
> 
> I have also been experiencing this problem. Could you tell me if you have
> received any replies? I was not able to find any replies in the message
> archives.
> 
> Thanks in anticipation.
> Melissa Petersen
> 
> ********************************************************************************
> ********************************************************************************
> Catalysis Research Unit
> Department of Chemical Engineering
> University of Cape Town
> Private Bag, Rondebosch, 7701
> Cape Town
> South Africa
> 
> Email: melissa@chemeng.uct.ac.za
> or    tgakmp@sg10.chem.tue.nl
> ****************************************************************************************************************************************************************


>From hofmann@thkin.pci.uni-leipzig.de Tue Jun  9 06:53:38 1998
Date: Mon, 25 May 1998 16:23:42 +0100 (GDT)
From: hofmann@thkin.pci.uni-leipzig.de
To: Jaouad El-Bahraoui <jaouad@csc.fi>
Subject: Re: CCL:G:G94 problem.....

Hi!

Your problem may be a numerical one.

 Density matrix breaks symmetry, PCut= 1.00D-04
 Density matrix has no symmetry -- integrals replicated.
 Density matrix breaks symmetry, PCut= 1.00D-04
 Density matrix has no symmetry -- integrals replicated.

It arises if the integrals must be the same in a certain symmetry, but
they are not. So one hint is to tell the scf-procedure to calculate
integrals with respect to symmetry: scf=(intrep)

This can be keyword  connected to scf=(symm). This one frozens 
configurations and is a powerful tool to get crazy things.
Be careful.

Alex



-------------------------------------------------------------------------
|                                    |                                  | 
| Alexander Hofmann                  | Phone (office) +49-341-97-36337  |
| Wilhelm-Ostwald-Institut fuer      | Fax   (office) +49-341-97-30099  | 
| Physikalische und Theoretische     |                                  |
| Chemie                             |                                  | 
| Augustusplatz 10-11                | hofmann@thkin.pci.uni-leipzig.de |
|                                    |                                  |
| D-04109 Leipzig                    | http://www.uni-leipzig.de/~quant |
|                                    |      /hofmann/alex.html          |
-------------------------------------------------------------------------


>From danne@rscqc2.anu.edu.au Tue Jun  9 06:53:49 1998
Date: Tue, 26 May 1998 01:42:04 +1000
From: Danne R Rasmussen <danne@rscqc2.anu.edu.au>
To: Jaouad El-Bahraoui <jaouad@csc.fi>
Subject: Re: CCL:G:G94 problem.....

a few options:  

a) if you are reading in a guess (using guess=read or guess=check) then
don't,
b) try using SCF=novaracc i.e. use best integral accuracy at all steps in
the SCF,
c) if you are doing DFT try SCF=vshift and/or SCF=(vshift,novaracc),
d) if you are using many diffuse functions in a large molecule try using a
different basis set; diffuse functions can cause convergence problems due to
linear dependence etc,
e) (risky) if you think you should have symmetry but keep running into
problems (i.e. all the above failed) try modifying PCut in the G94 source
and recompiling l502 [PCut=1.0D-03 will do it but you risk getting false
symmetry].  you can put your special l502.exe in your own home directory
(e.g. ~/g94/l502.exe) and modify GAUSS_EXEDIR to include ~/g94 earlier in
the path than the $root/g94 directory then your own l502.exe will be used
instead of the default executable.  

good luck,

danne

>From Krys.Radacki@ac.rwth-aachen.de Tue Jun  9 06:53:55 1998
Date: Mon, 25 May 1998 21:11:30 +0200
From: Krzysztof Radacki <Krys.Radacki@ac.rwth-aachen.de>
To: Jaouad El-Bahraoui <jaouad@csc.fi>
Subject: Re: CCL:G:G94 problem.....


As far as I know it means that during geometry optimization you have lost
symmetry. Try to start without symmetry (NoSymm flag in command line) 
for example:

#P RHF/6-31++G(d,p) opt=z-matrix Nosymm


regards
Krzys Radacki



>From b_duke@quoll.ntu.edu.au Tue Jun  9 06:54:00 1998
Date: Tue, 26 May 1998 09:09:21 +0930 (CST)
From: Brian Salter-Duke <b_duke@quoll.ntu.edu.au>
To: Jaouad El-Bahraoui <jaouad@csc.fi>
Subject: Re: CCL:G:G94 problem.....

Hi,


1. Check everything. Have you got the right state you want?
2. Do you have an ion? If so do the parent closed shell molecule
and use guess=read to get the starting vectors. Maybe try reading
the coefficients from a smaller basis set.

Cheers, Brian.
-- 
        Associate Professor Brian Salter-Duke (Brian Duke)
School of Mathematical and Physical Sciences, Northern Territory University,
          Darwin, NT 0909, Australia.  Phone (61) (0)8-89466702
e-mail: b_duke@lacebark.ntu.edu.au  or b_duke@quoll.ntu.edu.au


>From Megan.Govender@eskom.co.za Tue Jun  9 06:54:05 1998
Date: Tue, 26 May 1998 06:48:54 +0200
From: Megan Govender <Megan.Govender@eskom.co.za>
To: jaouad@csc.fi, jaouad@csc.fr
Subject: Re: CCL:G:G94 problem.....

Hi....

I also had that same problem optimizing compounds of Uranium some time back...
Are you trying similar calculations?...I used to use opt=fp with 
the nosymm option for these type calculations to get around this
problem. Hope this helps...



Regards
Magan



>From simek@rudjer.irb.hr Tue Jun  9 06:54:20 1998
Date: Wed, 27 May 1998 12:40:11 +0200
From: Visnja Simek <simek@rudjer.irb.hr>
To: Jaouad El-Bahraoui <jaouad@csc.fi>
Subject: Re: CCL:G:G94 problem.....


Do you put "NoSym" in # line in addition to other keywords ?


                              Best regards,
                                               Visnja 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Visnja Simek
Laboratory of Molecular Spectroscopy
Rudjer Boskovic Institute
P.O.B. 1016, Zagreb
CROATIA

Tel: (385-1) 456 09 44
Fax: (385-1) 468 00 84
     (385-1) 468 01 95
E-mail: simek@rudjer.irb.hr
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-


                                 \^ ^/
                                 )@ @(
     +-----------------------oOO--(_)----------------------------------+
     |                 Jaouad El-Bahraoui , Ph.D                       |
     +-----------------------------------------------------------------+
     | Inorganic Chemistry Laboratory        | Tel: +358-9-19140199    |
     | department of Chemistry, P.O. BOX 55  | Fax: +358-9-19140198    |
     | University of Helsinki,FIN-00040      | jaouad@nd.edu           |
     | Helsinki, Finland                     | w3.nd.edu/~jaouad/      |
     +----------------------Oooo--oOO----------------------------------+
                           oooO (   )
                           (   )  ) /
                             \ (  (_/
                               \_)


     --------------------------------------------------------------------
     I know you believe you understand what you think I said, but I am
     not sure you realize that what you heard is not what I meant.
     --------------------------------------------------------------------






From seabra@NPD.UFPE.BR  Tue Jun  9 10:41:30 1998
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 9 Jun 1998 11:36:11 GMT-3
Date: Tue, 09 Jun 1998 11:51:28 -0300
From: Gustavo de Miranda Seabra <seabra@NPD.UFPE.BR>
Subject: dispersion constants
To: chemistry@www.ccl.net
Reply-to: Gustavo de Miranda Seabra <seabra@NPD.UFPE.BR>
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Dear All,

    Could anyone indicate me some references about the caculation of
dispersion (van der Waals) constants (C6 and C8)? Specially, recent
references and references with the calculation of those constants to alkali
and halide atoms would be of great help.

    Thanks very much,
----------------------------------------------------------------------------
---------------
                      Gustavo de Miranda Seabra
MSc Student in Chemistry                  seabra@npd.ufpe.br
Federal University of Pernambuco                             Brazil
----------------------------------------------------------------------------
---------------



From mn1@helix.nih.gov  Tue Jun  9 16:03:09 1998
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Date: Tue, 9 Jun 1998 16:03:06 -0400 (EDT)
From: "M. Nicklaus" <mn1@helix.nih.gov>
Message-Id: <199806092003.QAA23053@helix.nih.gov>
To: CHEMISTRY@www.ccl.net
Subject: DFT B3LYP/6-31+G(d,p) Convergence Problem
Cc: mn1@helix.nih.gov


Dear CCL'ers,

After optimizing a structure (60 atoms, 37 non-H) at the HF/3-21G* level,
I'm trying to calculate a DFT single point energy at the B3LYP/6-31+G(d,p)
level, reading geometry and initial wave function from the checkpoint file.

After nearly seven days (!) of CPU time on a very fast machine, the job
aborts without having converged, with the following end of the output file:

 Standard basis: 6-31+G(d,p) (6D, 7F)
 There are   818 symmetry adapted basis functions of A   symmetry.
 Crude estimate of integral set expansion from redundant integrals=1.000.
 Integral buffers will be    131072 words long.
 Raffenetti 2 integral format.
 Two-electron integral symmetry is turned on.
   818 basis functions     1345 primitive gaussians
   132 alpha electrons      132 beta electrons
       nuclear repulsion energy      4057.3559996761 Hartrees.
 One-electron integrals computed using PRISM.
 There are  17 eigenvalues of the overlap less than 1.0D-05
 The smallest eigenvalue of the overlap matrix is  1.959D-08
 Initial guess read from the checkpoint file:
 dG-C8-FAAF_01-711_75.49.chk,-1
 Warning!  Cutoffs for single-point calculations used.
 Requested convergence on RMS density matrix=1.00D-04 within  64 cycles.
 Requested convergence on MAX density matrix=1.00D-02.
 Requested convergence on             energy=5.00D-05.
 Restarting both DIIS and incremental Fock formation.
 Restarting both DIIS and incremental Fock formation.
 Restarting both DIIS and incremental Fock formation.
 >>>>>>>>>> Convergence criterion not met.
 SCF Done:  E(RB+HF-LYP) =  -34352969.2846     A.U. after   65 cycles
             Convg  =    0.1924D-03             -V/T = *******
             S**2   =   0.0000
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /sbin/loader.
 Job cpu time:  6 days 21 hours 27 minutes 49.9 seconds.
 File lengths (MBytes):  RWF=  539 Int=    0 D2E=    0 Chk=   30 Scr=    1


Any hints?  TIA

Marc

------------------------------------------------------------------------
 Marc C. Nicklaus                        National Institutes of Health
 E-mail: mn1@helix.nih.gov               Bldg 37, Rm 5B29
 Phone:  (301) 402-3111                  37 Convent Dr, MSC 4255       
 Fax:    (301) 496-5839                  BETHESDA, MD 20892-4255    USA 
      http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
    Laboratory of Medicinal Chemistry, National Cancer Institute,  &
  Center for Molecular Modeling, Ctr. for Information Technology, NIH
------------------------------------------------------------------------


From zuilhof@Sg1.OC.WAU.NL  Tue Jun  9 17:01:51 1998
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Date: Tue, 09 Jun 1998 23:02:04 +0200
From: zuilhof@Sg1.OC.WAU.NL (Han Zuilhof)
Subject: Re: CCL:G:DFT B3LYP/6-31+G(d,p) Convergence Problem
To: "M. Nicklaus" <mn1@helix.nih.gov>, CHEMISTRY@www.ccl.net
Cc: mn1@helix.nih.gov
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Dear Marc,

This frequently has happened to me as well, and a good work-around is
usually the following:
go from HF/3-21G* to B3LYP/3-21G* (just single point), then to
B3LYP/6-31G(d,p) (just single point again), and only finally to
B3LYP/6-31+G(d,p).

Use
geom=check & guess=read
in every step, and the same checkpoint-file.  I.e. a job like (for a
neutral singlet system):

%chk=marc
%mem=6000000
#p b3lyp/3-21G* geom=check guess=read

marc's structure

0,1

--link1--
%chk=marc
%mem=6000000
#p b3lyp/6-31G(d,p) geom=check guess=read

marc's structure

0,1

--link1--
%chk=marc
%mem=6000000
#p b3lyp/6-31+G(d,p) geom=check guess=read scf=tight

marc's structure

0,1


An approach like this worked in nearly all of my b3lyp/6-31+G(d,p) jobs!

Good luck,
Han

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

At 4:03 PM 6/9/98, M. Nicklaus wrote:
>Dear CCL'ers,
>
>After optimizing a structure (60 atoms, 37 non-H) at the HF/3-21G* level,
>I'm trying to calculate a DFT single point energy at the B3LYP/6-31+G(d,p)
>level, reading geometry and initial wave function from the checkpoint file.
>
>After nearly seven days (!) of CPU time on a very fast machine, the job
>aborts without having converged, with the following end of the output file:
>
> Standard basis: 6-31+G(d,p) (6D, 7F)
> There are   818 symmetry adapted basis functions of A   symmetry.
> Crude estimate of integral set expansion from redundant integrals=1.000.
> Integral buffers will be    131072 words long.
> Raffenetti 2 integral format.
> Two-electron integral symmetry is turned on.
>   818 basis functions     1345 primitive gaussians
>   132 alpha electrons      132 beta electrons
>       nuclear repulsion energy      4057.3559996761 Hartrees.
> One-electron integrals computed using PRISM.
> There are  17 eigenvalues of the overlap less than 1.0D-05
> The smallest eigenvalue of the overlap matrix is  1.959D-08
> Initial guess read from the checkpoint file:
> dG-C8-FAAF_01-711_75.49.chk,-1
> Warning!  Cutoffs for single-point calculations used.
> Requested convergence on RMS density matrix=1.00D-04 within  64 cycles.
> Requested convergence on MAX density matrix=1.00D-02.
> Requested convergence on             energy=5.00D-05.
> Restarting both DIIS and incremental Fock formation.
> Restarting both DIIS and incremental Fock formation.
> Restarting both DIIS and incremental Fock formation.
> >>>>>>>>>> Convergence criterion not met.
> SCF Done:  E(RB+HF-LYP) =  -34352969.2846     A.U. after   65 cycles
>             Convg  =    0.1924D-03             -V/T = *******
>             S**2   =   0.0000
> Convergence failure -- run terminated.
> Error termination via Lnk1e in /sbin/loader.
> Job cpu time:  6 days 21 hours 27 minutes 49.9 seconds.
> File lengths (MBytes):  RWF=  539 Int=    0 D2E=    0 Chk=   30 Scr=    1
>
>
>Any hints?  TIA
>
>Marc
>
>------------------------------------------------------------------------
> Marc C. Nicklaus                        National Institutes of Health
> E-mail: mn1@helix.nih.gov               Bldg 37, Rm 5B29
> Phone:  (301) 402-3111                  37 Convent Dr, MSC 4255
> Fax:    (301) 496-5839                  BETHESDA, MD 20892-4255    USA
>      http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
>    Laboratory of Medicinal Chemistry, National Cancer Institute,  &
>  Center for Molecular Modeling, Ctr. for Information Technology, NIH
>------------------------------------------------------------------------
>
>
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______________________________________________________________________
Han Zuilhof                         |  E-mail:  ZUILHOF@SG1.OC.WAU.NL
Laboratory of Organic Chemistry     |  FAX   :  31-317-484914
Department of Biomolecular Sciences |  phone :  31-317-482367
Wageningen Agricultural University  |
Dreijenplein 8                      |
6703 HB  Wageningen                 |    "Excite a photochemist!"
The Netherlands                     |   




