|
|
| From: |
jstewart (+ at +) fai.com (Dr. James Stewart) |
| Date: |
Thu Nov 11 16:03:15 1993 |
| Subject: |
Re: Orbital Plotting Packages |
The standard package DENSITY will draw M.O.s, total density, difference maps,
etc, for a cross-section (not the 3-D surface) for systems calculated by
MOPAC. DENSITY is available through QCPE.
Jimmy
From: cole %-% at %-% sail.labs.tek.com (Samuel Cole)
Message-Id: <9311111606.AA06996 -x- at -x- sail.labs.tek.com>
To: msrag -8 at 8- csv.warwick.ac.uk
Subject: Orbital Plots
Cc: cole &$at$& sail.labs
Status: R
Dear Dr. Butter,
The CAChe system is able to produce orbital surface plots from MOPAC,
as well as extended Hueckel theory and ZINDO (an INDO program).
CAChe runs on a Macintosh computer equipped with a coprocessor card.
You may wish to contact our salesperson in the UK, Alan Day, at
628-486000 or 628-899239 for more information.
Regards,
Sam Cole
Senior Chemist
CAChe Scientific
cole()at()sail.labs.tek.com
(503)627-2308
From: Jeffrey J Gosper
Message-Id: <13254.9311111619 at.at molnir.brunel.ac.uk>
Subject: Re: Orbital Plotting Packages
To: msrag at.at csv.warwick.ac.uk (Dr D Buttar)
>
> I have been asked by a colleague if there are any graphic packages
> that interface with mopac. Ideally a program that will plot the
> orbitals produced by the mopac program.
> Any information on such packages would be much appreciated.
>
> Many Thanks,
> David Buttar.
>
We use ChemX (ChemQM) which interfaces to denpot (QCPE) this generates
a wire mesh of orbitalis.
If you come up with others please summaries to the net or mail me directly.
>
>
Dear David,
The following package could easily be adapted to plot the mo's. Either
the formats for the basis sets and mos could be converted to be consistent with
this program, or the input subroutine to this program could be directly altered
to read your files. You will see that this program is on an ftp site, but I
have not yet generally announced it. You are welcome to it if it helps your
needs.
Dennis
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PROGRAM MOPLOT2
FOR ORBITAL AND DENSITY PLOTS FROM
LINEAR COMBINATIONS OF SLATER OR GAUSSIAN TYPE ORBITALS
Version 2.0
June 1993
Author: Dennis L. Lichtenberger
Department of Chemistry
University of Arizona
Tucson, Arizona 85721
email: dlichten "-at-" ccit.arizona.edu
Program MOPLOT2 is extremely flexible in providing different methods for
calculating and displaying the spatial distributions of orbital wavefunctions
that are expressed in terms of linear combinations of Slater or Gaussian type
basis functions. Although a large number of options are offered by this
program, the input required for a single specific display is actually quite
small. The purpose is to obtain displays that are suitbable for publication.
The program provides the following output: ASCII displays of contours in
planes and three-dimensional grids; contour line drawings of planes; surface
projections of planes; three-dimensional surface plots; and three-dimensional
grid values for display by other programs, such as PSI88.
The program is actually a collection of programs written in fortran,
all of which execute on SGI, CONVEX, and VAX computers. The line drawings may
be in HPGL, Tektronix, or VGA formats. The HPGL formats can be converted to a
variety of other formats, including postscript.
The routine for Slater wavefunction input is presently consistent with
the Fenske-Hall (version 5.1) format. The Gaussian functions are cartesian.
Other wavefunctions may be converted to these formats, or the routines SFCALC
and GFCALC may be altered for convenience. The only limitation at the present
time is the lack of f orbitals, which will be added when a need develops.
-------------- How to retrieve MOPLOT2 ----------
MOPLOT2 is available from the archives of Computational Chemistry List on
anonymous ftp on www.ccl.net [128.146.36.48] in the directory:
/pub/chemistry/moplot2
If you are on the UNIX machine, it is easiest to retrieve the compressed tar
archive as:
% ftp www.ccl.net (or ftp 128.146.36.48)
Login: anonymous
Password: Your_email_address
ftp> cd /pub/chemistry/moplot2
ftp> binary
ftp> get moplot2.tar.Z
ftp> quit
Then, execute command:
zcat moplot2.tar.Z | tar xvof -
which will unpack the archive and restore directories and files.
The total size is about 6.5 Mbyte.
If you do not use UNIX and do not have tar and uncompress utilities,
you can retrieve files individualy. They are located under
/pub/chemistry/moplot2/moplot2
directory.
Received: from localhost for djh $#at#$ ccl.net
by xipe.ccl.net (8.6.1/920428.1525) id LAA00266; Thu, 11 Nov 1993 11:46:45 -0500
Date: Thu, 11 Nov 1993 11:46:45 -0500
Message-Id: <199311111646.LAA00266(-(at)-)xipe.ccl.net>
To: msrag %-% at %-% csv.warwick.ac.uk
Subject: Re: Orbital Plotting Packages
Status: R
My apologies if I'm the Nth person to suggest this, but you might
try XMol from the Minnesota Supercomputer Ceter. From the README
file for XMol:
XMol is available for DECstation, Silicon Graphics IRIS-4D, SPARCstation,
and Sun-3 architectures. We are currently assessing the prospect of
an RS/6000 version of XMol. MSCI is making this release of XMol publicly
available to anyone through internet ftp access.
HOW TO GET XMOL VERSION 1.3.1
Make a directory to contain the XMol files, and 'cd' into that
directory.
Perform an 'ftp' to 'ftp.msc.edu'.
Enter 'anonymous' as username.
Enter your e-mail address as password (eg., user : at : school.edu).
Enter the following commands at the ftp prompt:
cd pub/xmol
binary
mget README xmol.tar xmol.arch
----
quit
...where "arch" is the architecture type of your machine: mips,
sgi, sun3, or sun4.
--
David J. Heisterberg (djh "-at-" ccl.net) Gee, it's so beautiful, I gotta
The Ohio Supercomputer Center give somebody a sock in the jaw.
Columbus, Ohio -- Little Skippy (Percy Crosby)
From: jxh - at - ibm12.biosym.com (Joerg Hill)
Message-Id: <9311111643.AA16814 %! at !% ibm12.biosym.com>
To: msrag %-% at %-% csv.warwick.ac.uk
Subject: Orbital Plotting
Status: R
The graphical user interface from Biosym, called Insight II, provides the
desired capabilities. It can generate orbital plottings from data produced
by mopac.
Joerg-R. Hill
From: "JEREMY WALTON"
Subject: MOPAC plotting program
To: "msrag"
Status: R
Hi David,
I saw your enquiry about the above on the comp chem mailing list. IRIS
Explorer is a visualisation package for Unix workstations that can be used
to (among other things) display MOPAC plot files, as well as molecular
configurations. I can give you more info about its availability and
features if you're interested.
Cheers,
Jeremy
Jeremy Walton,
NAG Ltd, Oxford UK
From: "Cory C. Pye"
Message-Id: <9311111702.AA08057.,at,.riemann.math.mun.ca>
To: msrag "-at-" csv.warwick.ac.uk
Subject: Orbital Plotting Packages
Status: R
I posted a similar inquiry several months ago. What follows is a summary that
was posted to the list.
Subject: Plotting ab initio molecular orbitals
Here is a summary of responses as promised.
**********************Original Inquiry - Me******************************
Hello fellow netters,
I am looking for a program which can plot molecular orbitals, given a
geometry, basis set, and final SCF coefficients. My requirements are
1) Preferably SGI Indigo with output to either the screen or printer
(postscript, dvi). Alternatives: VAX 4500, Apollo DN10000, (VIC-20 :-))
2) Ability to use any basis set given to it. (Not absolutely necessary)
3) Ability to use any atom defined within the basis set. (necessary)
4) Hopefully, public domain or shareware (I'm a grad student => $ = 0)
5) Easy to install.
6) Ab initio data (DFT & semiemp. would be an interesting bonus)
7) geometry: Cartesian or z-matrix(preferred)
I am thinking along the lines of the program PSI/88 which I have found
very useful. The code, however is heavily optimized and probably
difficult to extend to arbitrary bases and atoms. It can handle atoms
H-Ar and bases STO-3G, 3-21G, 6-31G with and without diffuse and
polarization functions. I have used this on a VAX 4500.
There is a program xpsi of which I am aware (basically the above with
application of f2c and using PEX libraries) if I am not mistaken.
Alternatively, somebody could tell me the status of PEX on the SGI, and
if free, an ftp site where one could obtain this. This of course does
not solve my problem of wishing to print molecules with atoms larger
than Ar.
I suspect that there may be some Explorer modules or some extension of
programs like xmol which may be able to do this. Remember, free is the
key word. I do not want to envision the idea of writing it myself,
except as a last resort, since I program in OSIPE-Fortran ('Fortran++')
and I would probably have to learn C (C++) to take advantage of the
full capabilities of X/Motif, GL, or PEX.
Please send replies to cory &$at$& riemann.math.mun.ca (as in header) or if
this fails try cory (+ at +) kean.ucs.mun.ca
cory ^at^ morgan.ucs,mun.ca
cory' at \`zeus.chem.mun.ca
cory-0at0-bohr.chem.mun.ca
I will try to post a summary.
*************************Responses to my query***********************
In no particular order: (with some minor editing)
Note: I have used <> to insert my comments.
EXPLORER
---------------------------------------------------------------------
From: jjv5 <-at-> retina.chem.psu.edu (Jim Vincent)
(Dr. ?) Omer Casher has developed Explorer modules for doing lots of stuff with
Gaussian and Mopac output. He said he will probably be putting them in the
public domain. Details will be posted to comp.graphics.explorer in about two
weeks. He will be showing the modules at SIGGRAPH in California. You might
want to just check in on that group in a while.
I will be gettin the modules as soon as they become available. If you
like I can tell you more about what they do after I use them a little.
Jim Vincent
jjv5 at.at retina.chem.psu.edu
SciAn
---------------------------------------------------------------------
From: vazquez at.at iqm.unicamp.br (Pedro A M Vazquez)
Hello:
Take a look the SciAn package from fsu. I'm sending to you
the README file from where you can get more info. guada (+ at +) iqm.unicamp.br
has done some little programs to interface SciAn to mopac and g92
outputs.
Regards
Pedro
[ README file from SciAn deleted:]
Some highlights kept:
SciAn currently runs on two platforms:
1) Silicon Graphics 4D workstations
2) IBM RISC/System 6000 workstations
SciAn will run only on IBM RISC/System 6000 workstations that have 3-D
graphics accelerators that provide GL compatibility. SciAn also requires
a Z-buffer.
If you would like to obtain SciAn, please send electronic mail to
scian-info # - at - # scri.fsu.edu, if you haven't already done so. You can also
request to be put on the SciAn mailing list, which will keep you informed
of updates.
SciAn is normally distributed via anonymous ftp from ftp.scri.fsu.edu. If
you do not have access to anonymous ftp, send us mail, and we'll try to
figure out some other way to get you the program. It is much easier to
get the program through ftp, however, and it's certainly easier to get
updates that way.
The SciAn program and documentation are located in the SciAn subdirectory
of the pub directory. To get into that directory, enter
cd pub/SciAn
In that directory, you will find a README file (which is this document
)
and several subdirectories.
The release subdirectory contains the release versions of SciAn. Obtaining
SciAn from this directory is described in section 3.2.
(stuff deleted)
The documentation subdirectory contains documentation for SciAn. Obtaining
and printing it is described in section 3.3.
In the "release" subdirectory (enter cd release to get to the directory)
you will find several files. They will all have names of the form
scianXXX.tar.Z, where XXX is the version number of SciAn. For example, the
file scian060.tar.Z contains SciAn version 0.60.
PLTORB
-----------------------------------------------------------------------
From: "System Manager, and VAX Gopher"
You didn't specify which package you're using to obtain the input for
the plotting program, but there is a package PLTORB that is distributed
with GAMESS that may do what you want. It can be used with GaussianXX
output, providing you can get Gaussian to choke out the data in an ascii
format. GAMESS will punch an input deck for it. The program only does
Contour plots, not 3d.
I've read the code in PSI/88, and while I haven't taken action on it yet
(I too am a grad student, and have a minimal amount of time to spend on
side projects at this point), the code seems easy to extend to arbitrary
bases. The simplest action would be to add code for the specific basis
sets you're using.
Finally, QCPE has some older programs that may be modifiable, in the sense
that if you write a new graphics interface to them, the core plotting
routines are already present.
-fred
MOPLOT 2.0
-----------------------------------------------------------------------
Message 1:
From: DLICHTEN at.at CCIT.ARIZONA.EDU
I have developed a series of programs that come very close to your
request. They allow virtually any Gaussian or Slater basis set and any vector
coefficients, with alterations of the density matrix, etc. if you so desire.
The original program MOPLOT was written in 1970 and only allowed single plane
plots. This program has been available from QCPE for many years. The new
MOPLOT version 2.0 does three dimensional grids as well. The
output can be sent through the plotting routines of PSI88 if desired, or
plotted with routines that are provided. Right now the graphics is a choice of
hewlett-packard, tectronix or VGA for the PC. It is easy to incorporate other
graphics. All the programs are in fortran 77 and run on both unix and vax
systems without alteration.
The disadvantage is that the code is probably not designed for ease of
use with your wavefunctions, and you may want to alter the Gaussian subroutine
to read in your wavefunctions more easily. I would be interested in having
other users extend the code for their applications. If you are interested I
will make the code available on a FTP site.
Dennis L. Lichtenberger
Professor of Chemistry
Department of Chemistry
University of Arizona
Tucson, AZ 85721
unnamed
--------------------------------------------------------------------------
From: "Terry R. Coley"
I have something that will do this. It runs on a Silicon graphics
and creates output suitable for viewing in AVS. It is currently
difficult to install and maintain, however. I am in the process of
cleaning it up. In a few months I will make it freely available.
Check with me after a few months if you are still interested and
I'll give you a status update.
- Terry | Parallelograms
terry \\at// wag.caltech.edu 818-395-2723 | PO Box AA
Caltech, M/S 139-74 | Pasadena, CA 91102
Pasadena, CA 91125 | 818-577-5515 Voice/FAX
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In addition, I received a couple of requests. If I have omitted anyboby,
then please e-mail and I will add your suggestions to this file and
repost in a few weeks.
At this point I would like to thank everybody who responded. I am in
the process of obtaining some of the software. I will share with
anybody my experiences with the application of the software to problems
in the 'real' world, via private e-mail. If enough are interested, I may
present a critical review of software if the respective authors allow
this. (Provided I have time, of course)
-Cory Pye
Message 7:
>From modrego%cc.unizar.es;at;garfield.cs.mun.ca Thu Aug 12 10:28 GMT 1993
X400-Received: by mta iris-dcp in /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Thu,
12 Aug 1993 12:29:10 UTC+0200
X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Thu,
12 Aug 1993 12:29:00 UTC+0100
Date: Thu, 12 Aug 1993 09:59:00 -0230
From: Javier Modrego
Subject: Plottin M.O.'s
To: cory -x- at -x- riemann.math.mun.ca
Content-Identifier: 552
Content-Transfer-Encoding: 7BIT
Conversion: Prohibited
X400-Content-Type: P2-1984 (2)
X400-Mts-Identifier: [/PRMD=iris/ADMD=mensatex/C=es/;930812122900]
X400-Originator: modrego()at()cc.unizar.es
X400-Recipients: non-disclosure:;
In the summary about your recent question on Plotting MO's somebody pointed
out that it should be easy to include more basis sets in PSI88. In fact this is
no necesary, at least if you use Gaussian-XX. You can request a Cube=orbitals
calculation, then you can feed the data (after reformating the output) into
the second part of PSI88 (PSICON) which reads a cube of data in order to
construct the plotting. Gaussian can calculate the value of the wavefunction
in an arbitrary grid of points, but PSI, as it is, only can read an orthogonal
grid with the same number of points in each direction. I think this is the
only restriction.If you only use one program you can modify the READ's in
psicon to make it able to read the data from Gaussian directly.
******************************************************************************
Javier Modrego
Department of Inorganic Chemistry
Facultad de Ciencias
University of Zaragoza
50071 Zaragoza
SPAIN
E-mail: modrego %-% at %-% cc.unizar.es
******************************************************************************
-Cory
From: Rainer Koch
Message-Id: <9311111937.AA18366.,at,.derioc1.organik.uni-erlangen.de>
Subject: Re: Orbital Plotting Packages
To: msrag "at@at" csv.warwick.ac.uk (Dr D Buttar)
Date: Thu, 11 Nov 93 20:37:09 MET
Dear Dr. Buttar
one of the best programs for your friend's purpose is PSI88.
It should be available from QCPE, for the new PC version you may want to
contact also QCPE or Bernd Wiedel (wiedel \\at// organik.uni-erlangen.de) who has
done the portation.
Hope this will be of some help.
Rainer Koch
******************************************************************************
* Rainer Koch *
* Institut fuer Organische Chemie *
* Universitaet Erlangen-Nuernberg *
* Henkestr. 42 *
* 91054 Erlangen *
* Germany *
* *
* E-mail: koch "-at-" organik.uni-erlangen.de *
* Fax: 0049/0-9131-85-6864 *
******************************************************************************
From: Chris Waller
Subject: mopac plots
To: msrag # - at - # csv.warwick.ac.uk
Message-Id:
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Status: R
I am aware of two packages capable of producing MO plots:
(1) SYBYL (Tripos) has a very nice (transparent) interface to
MOPAC. The orbitals may be viewed as wire mesh or MolCad (opaque
or transparent) surfaces.
(2) AVS (marketed by Molecular Simulations as ChemViewer) also
produces very nice graphical representations of molecular
orbitals from MOPAC (and practically any other package). The
interface is not so transparent as SYBYL's.
Chris L. Waller, Ph.D.
Center for Molecular Design
Washington University in St. Louis
waller;at;wucmd.wustl.edu
From: henk()at()qsar.ritox.dgk.ruu.nl
To: msrag[ AT ]csv.warwick.ac.uk
Message-Id: <009756C7.4C0F2290.12095 at.at qsar.ritox.dgk.ruu.nl>
Subject: RE: Orbital Plotting Packages
Status: R
Dr D Buttar writes:
>
> I have been asked by a colleague if there are any graphic packages
>that interface with mopac. Ideally a program that will plot the
>orbitals produced by the mopac program.
> Any information on such packages would be much appreciated.
MOLDEN, available from QCPE, or from its author, Gijs Schaftenaar
(schaft (+ at +) camms1.caos.kun.nl), while not publicly advertised as such, has
the
capability to display MOPAC generated density 'maps', including orbitals. It
was originally written to do this for GAUSSIAN or GAMESS output, but given one
trick, can handle MOPAC output as well.
Hope this helps
==============================================================================
| Henk Verhaar | e-mail: henk ( ( at ) )
qsar.ritox.dgk.ruu.nl |
| Research Institute of Toxicology | |
| Environmental Toxicology Section | phone: +31 30 535338 |
| Utrecht University, the Netherlands | fax: +31 30 535077 |
==============================================================================
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