Subject: Summary: Xmol on O2 SGI

From: Danilo Gonzalez <[email-masked]>
Date: Tue, 09 Dec 1997 16:24:07 -0400

Hi!!

I received many answer about the following question:

***********************************************************************
        I trying to run XMOL on a SGI O2, but when I run it, an error
message
"Wrong Architecture" appears.
        Can anybody help me to solve this problem?
***********************************************************************

In summary, XMOL not run in IRIX 6.X, the solution in only run XMOL in
machine with IRIX 5.X, and run via remote display....    ;^(
Other possibility is to use other alternative program how VMD

ay way, I put it all the answer received.... Thanks again!

*****************

Xmol 1.3.1 has been compiled under old IRIX (even before 5.3) in the
COFF
executable format. Newer IRIX-es (starting with 6.1) no longer support
this format; the executable standard is now ELF. You have to go back to
IRIX 5.3 to run xmol. To make sure type this command:

file xmol

Hope this helps,
Robert Fraczkiewicz
University of Texas Medical Branch

*************************

Dear Fdo Danilo Gonzalez Nilo,

According to my experience, this is because the difference in the IRIX
version. You know SGI O2 runs IRIX6.3 which is very unique. So, try to
compile XMOL on SGI O2 again. Good luck.

Arthur

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
_/   Arthur Wang                     Doctoral Candidate     _/
_/   Molecular Design Lab                                   _/
_/   Institute of Physical Chemistry, Peking University     _/
_/   Beijing 100871, P.R.China                              _/
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**********************************

Hi,

        The short answer is that you can't run Xmol on an O2.  The SGI
version of Xmol uses the COFF executable format which is not supported
by
versions of IRIX after 5.3 .  Last I heard Xmol was not still being
developed so it is unlikely that it will become available for new
machines
and operating system versions.

                                Dave Young
                                [email-masked]

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

          Live long and maintain marketable job skills.

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

***********************

Hi Danilo,

the problem we all have is that there has been a big change in the
operating
system of SGI. The result is that executable programs which had been
compiled
to the old COFF format are no longer supported since IRIX 6.2 (or 6.0
?).
As you will probably have IRIX 6.4 (or eventually 6.2) you can no longer
execute
programs in this old COFF format.
By the way, you can check your version by entering "/sbin/uname -r" and
will
probably get an output like "6.2" or "6.4".

Unfortunately the XMol crew doesn't want to spread their program's
source code
(which one could compile for nearly any operating system that is derived
from
UNIX). Additionally, they do not recompile their old version of XMol to
the new
ELF executable format.

In order to work around this problem, we use an old SGI workstation
running on
IRIX 4.0.5 for executing this program and do this with the option
"-display=<another.host.that.runs.on.irix.6.2>:0.0". This is by now the
only
way to get at least the graphics output and control panels piped to our
new SGI
INDIGO2, where we can use this program.

Your problem is now that you'd need an SGI machine that runs on an old
IRIX...

Hope this helps (or at least answers your question),

Best Regards,

Michael

**********************************************
* Dr. Michael Schimeczek                     *
* AK Boche                                   *
* FB Chemie der Philipps-Universitaet        *
* Hans-Meerwein-Str.                         *
* D-35032 Marburg/Lahn                       *
* email: [email-masked] *
**********************************************

************************

My guess is you are using the wrong executable on the O2.  Either find
an
executable for the O2 or recompile XMOL on the O2 itself.

--
  Jeffrey L. Nauss, PhD           Telephone: 513-556-0148
  Dir. Molec. Model. Serv.        Fax:       513-556-9239
  Department of Chemistry         e-mail: [email-masked]
  University of Cincinnati        URL http://www.che.uc.edu/~nauss

***********************

Hi,

usually you get an error message like this if you try to run an MIPS4
(R8K/R10K)
executable on a MIPS2 machine (R4K/R5K). In this case you need to
recompile
XMOL for your machine architecture. Normally a MIPS2 executable should
run on a
MIPS4 machine.

Regards

Stefan

Disclaimer: All opinions expressed here are mine, not my employers.

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*****************************

Hola

Tambien tenemos una SGI O2 y queremos instalar xmol. De momento xmol lo
tenemos funcionando sin ningun problema en estaciones IBM RS600. No se
como
se resuelve tu problema, pero si lo logras te agradeceria que me lo
contases.

Un saludo

Luis Carballeira
Quimica-Fisica
Universidad de Vigo, Galicia
Espana

*********************************

Hi !

As far as I know, xmol only runs with irix 5.3. Everything higher won't
work;
If there will be a version running on any irix higher than this, please
tell me !

Cheers

CR

 _________________________________________________________________
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|  Christian Rummey                                               |
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|  Universitaet Wuerzburg                                         |
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***********************

There is only one problem: IRIX-6.x does not longer support
COFF binaries:

$ file /usr/local/bin/xmol
/usr/local/bin/xmol:    MIPSEB COFF executable (paged) - version 2.40

There are no chances to get a newer version of xmol ( i had a
correspondence
with the developers of xmol).
You have to use other programs.

Ciao
Bernd Melchers

--
Bernd Melchers             | [email-masked]
Freie Universitaet Berlin  | "We don't write software, we compose it."
AG Macromelecular Modelling - Prof. Dr. E.W. Knapp
for more information see http://www.chemie.fu-berlin.de/~melchers

**********************

Nobody can help you. IRIX 6.3 (which is the only operating system O2 is
capable of running reliably at the moment) does not support COFF
executables. The only way to make Xmol run under 6.3 is to recompile
it using one of the ELF executable formats 6.3 supports. However,
since Xmol is not supported or developed anymore, and the source
code is not publicly available, this is not possible. Tough luck...

Regards,

/Serge.P

*********************

  I'm afraid there is not much you can do about it. As you know, part of

  Xmol is distributed as an executable and this has been compiled for
  different SGI machines, the newest of them being IRIX 5.x

  As far as I know, the Minnesota team who created Xmol do not plan to
  upgrade anymore and there we have 1.3.1.1 (if I remember well) as the
latest
  version, which does not work on IRIX 6.x machines, thus including SGI
O2.

  My suggestion would be: install Xmol in an older machine and then run
it
  from your O2 setting the proper DISPLAY.

  If anyone else comes up with a Xmol version for IRIX 6.x please let me
know,
  I would also be extremelly interested on it ([email-masked]).
Cheers.

  German
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http://www.ri.ac.uk/DFRL/G.Sastre
 Instituto de Tecnologia Quimica                 e-mail:
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                                            oo0 0oo

**********************

Hi Danilo,

I think that happens because you are running IRIX 6.2 or higher. Xmol
is not supported for those platforms. I have not heared that anyone was
still working on it, so it seems unlikely that it will work in the near
future.

Cheers,
Roelant

****************************

Hi,

the problem you have is that IRIX 6.x does not support the elf binary
format any more. Since XMol is not available in the right format (coeff)

you'll have to choose another molecular viewer. You can try VMD
(http://www.ks.uiuc.edu/Research/vmd/), that's what I use.

Cheers,
       Dominik

--

------------------------------------------------------------------
Dominik Horinek
Institut fuer physikalische und theoretische Chemie
Universitaet Regensburg
Universitaetsstr. 31, 93053 Regensburg, Deutschland
email: [email-masked]
------------------------------------------------------------------
**************************

Hello,

  The reason XMol doesn't work on the O2 is that is was compiled for
IRIX 4.  IRIX 6, which the O2s use, doesn't support those binaries any
more.  Since XMol is no longer updated and source isn't available, you
will have to use other programs.  The one I know the most (because I
helped develop it) is VMD at http://www.ks.uiuc.edu/Research/vmd/ .
Other good, free ones I've heard of are MOLMOL and gOpenMol, which you
should be able to find with a net search program.

                                                Andrew Dalke
                                                [email-masked]

******************

        XMOL will not run on an O2. The executable was compiled for an
entirely different binary architecture on earlier SGI's.

        Here, we have O2s, Indigo 2s and and Indigo. The only computer
that will run XMOL is the Indigo.

        As far as I know, there are no plans to update the executable.
There has been much discussion in CCL about this; there are alternate
packages for many situations.

                                                Dan Strahs

**********************

--
Fdo. Danilo González Nilo
University of Santiago de Chile, Faculty of Chemistry and Biology,
Computational Chemistry Lab.
Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108
URL   : http://quimbio.usach.cl/~danilo/
E-mail: [email-masked]
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

---

From: Naoko Akiya <[email-masked]>
Date: Tue, 9 Dec 1997 15:22:38 -0500 (EST)

Long, long time ago, I posted the following question:

> I have a question regarding the open shell calculation with DFT.  I am
> trying to calculate the energy of a transition state structure.
> Although the structure is designated as a singlet in the input, it is
> "partially" open shell.  How can I account for this in the calculation
> using DFT methods?

Below is the summary of all the responses I received.  I hope you will
find them useful.  Sorry for not posting the summary in a timely manner.

Naoko

=====

   The simplest approach to such a situation would be to move to a
UB3LYP singlet wavefunction.  This does not completely solve the problem
but it does allow for alpha and beta densities to differ and thus you
can approximate an open-shell singlet at one extreme and a conventional
closed shell singlet with alpha = beta at the other.  You will need to
use GUESS=Mix for such calculations to break the spin symmetry and explore
if there is a UHF singlet type solution.

  Also you would do well to run a STABLE=OPT calculation on the TS
structure you find to see if you have a lower lying SCF solution.  Should
you find one you would need to re-optimize to find that TS structure so
you should use a checkpoint file with this calculation to start the
optimization with the right wavefunction, Guess=Read.

  Douglas J. Fox
  Director of Technical Support
  [email-masked]

=====

What do you mean when you say 'partially open shell'?  Do you have an
unsymmetrical structure that resulted from the Jahn-Teller distortion of a
symmetrical diradical? Or do you expect that your transition structure
possesses a diradical character?  The first thing you may want to do is
checking the restricted DFT -> unrestricted DFT stability (e.g. RB3LYP ->
UB3LYP) (also called as 'triplet stability') of your solution. If the
solution is unstable, the lowest eigenvalue of the stability matrix and
the energy lowering for the stable optimized wavefunction can give you an
idea how significant the diradical character is. Your further actions
depend on these results.

Best regards,
                          Mikhail Gloukhovtsev

If the RHF or R-DFT solution is triplet stable (i.e. RHF->UHF stable),
using the UHF wavefunction should give the same energy as that you
calculated with the RHF one.  However, the triplet instability threshold 
can take place later when the bond breaking becomes more profound.  You
find a comprehensive discussion of this problem in the paper of Schlegel
and Chen:

   First Author: CHEN-W.
  Other Authors: SCHLEGEL-HB*.
  Article Title: EVALUATION OF S-2 FOR CORRELATED WAVE-FUNCTIONS AND SPIN
                 PROJECTION OF UNRESTRICTED MOLLER-PLESSET
                 PERTURBATION-THEORY
 Journal Source: JOURNAL OF CHEMICAL PHYSICS, Volume: 101, Issue: 7, Issue
                 Date: OCT 1, Publication Year: 1994, Pages: 5957-5968
  Document Type: 3: ARTICLE.
  Abstract Ind.: Y
   Subject Cat.: UH: PHYSICS, ATOMIC, MOLECULAR & CHEMICAL.

Hope this helps.

Best regards,
                                    Mikhail

**************************************************************************
*                                                                        *
*   Mikhail Gloukhovtsev, Ph. D., Dr. Sci.                               *
*   Brown Laboratory, Department of Chemistry and Biochemistry           *
*   University of Delaware, Newark, DE 19716                             *
*   Ph. 302-831-0887    Fax (302)-831-6335                               *
*   E-mail [email-masked]  WWW http://planck.duch.udel.edu/~mikhail        *
*                            http://udel.edu/~mng                        *
*                                                                        *
**************************************************************************

=====

        It is not that simple to explan the open shell matter in a few
words. Usually, when a system has any unpaired electron(s), one should
use unrestricted (open shell) method. It is incorrect to work with
closed shell and open shell combination. One should stick on one method
throughout whole calculation.

************************************************************************
* Because the machine, the terminator,         ________      ________  *
*   can learn the value of human life,        |        \    /        | *
*                   maybe we can, too.        |_        \  /        _| *
* ------------------------------------------  __|________\/________|__ *
* Ning Chen                                  |                        |*
* Department of Chemical Engineering         |     M I C H I G A N    |*
* University of Michigan, Ann Arbor, MI48109 |________________________|*
* Phone: (313)-764-8362 (o)                    _|    |_\    /_|    |_  *  
*        (313)-936-3186 (lab)                 |        |\  /|        | * 
* e-amil: [email-masked]            |________| \/ |________| *
* URL: www-personal.engin.umich.edu/~ningchen                          *
************************************************************************       

=====

There was recently a discussion about singlet diradicals ( open shell,
i.e. e.g. 1s(1)2s(1) for helium or 1_Sigma_gerade state of molecular
oxygene etc). In principle you can't do the calculation within
a single determinant ansatz (in Kohn-Sham DFT you use also a single
determinant of Kohn-Sham orbitals to represent the "wave function").
But you can use a trick : you calculate the energy for the triplet (t)
and for the mixed state (m). The energy of the singlet state
is then E(s)=2*E(m)-E(t). But this works only for energies, not
for gradients. Literatur : Tom Ziegler, Arvi Rauk, Evert J. Baerends,
Theoret. Chim. Acta 43 (1977) 261-271. Another problem: I was not able
to do the calculation for the mixed state for molecules more 
complicated than He. I got very (!!!!) sincere convergence problems
and wild oscillations during the course of calculation.
Ciao,
Heinz  
-- 
Dr. Heinz Schiffer                  Phone ++49-69-305-2330                      
Hoechst Research & Technology       Fax   ++49-69-305-81162                     
Scientific Computing, G864          Email [email-masked]         
65926 Frankfurt am Main                   [email-masked]

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  Naoko Akiya                        [email-masked]
  University of Michigan                
  Dept. of Chemical Engineering      phone (313) 764-7121        
  Ann Arbor, MI 48109-2136	     fax   (313) 763-0459
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=