The CCP1 GUI Project - Interfaces
From it's inception, the CCP1GUI has been designed to work with a
range of different underlying computational codes. For many of the
supported codes, provided the code is already installed on the target
system, using them should be as simple as using the Job
Submission tool in the Job tab of the relevant editor to
point the ccp1gui at the binary that should be used.
For some of the codes however, various hoops have to be jumped
through to get them working properly. Often these are just the
standard issues around getting the code to work on a particular
platform, but in some cases they may be slightly more involved.
The following sections describe what needs to be done for each of
Molden is a package for displaying Molecular Density from the Ab
Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the
Semi-Empirical packages Mopac/Ampac, it also supports a number of
other programs via the Molden Format.
The CCP1GUI can use Molden to generate the data required to
visualise molecular orbitals from the data in a GAMESS-UK output
file. This functionality is useful for when the orbital in question
was not explicitly written out to the GAMESS-UK punch file as part of
the calcualtion (which is where the CCP1GUI usually expects to find
the information about the orbitals).
To access this functionality within the CCP1GUI, use the
File option that will appear under the main Views menu
when a GAMESS-UK calculation has been completed from within the
Molden is available from the website at http://www.cmbi.ru.nl/molden/molden.html.
For use by the CCP1GUI, however, the standard Molden is not
suitable and a couple of small changes need to be made to the source
code before Molden is compiled.
The changes need to be made to the file wrinfo.f
and are required to:
- to allow output of fields other than densities
- to output in a formatted file that the GUI can read
A diff out put showing the changes as made to a copy of version 4.6 of
Molden is below:
software/molden> diff molden4.6/wrinfo.f molden4.6.ccp1gui/wrinfo.f
< call inferr('Only Normal Density Can be Written!',0)
> > cc call inferr('Only Normal Density Can be Written!',0)
> > cc return
> > write(6,*)'Writing 3d field (not normal density)'
> > open(unit=21,form='formatted',file='3dgridfile',
< write(21) natoms
< write(21) (nat(i),i=1,natoms)
< write(21) adjus
> > write(21,*) natoms
> > write(21,*) (nat(i),i=1,natoms)
> > write(21,*) adjus
> > write(21,*)(xyz(j,i),j=1,3)
< write(21) px, py, pz, cx, cy, cz, r(1),r(2),r(3),
< & npts1,npts2,npts3,iplat
> > 100 format(a5,3f20.5)
> > write(21,100) 'p', px, py, pz
> > write(21,100) 'c', cx, cy, cz
> > write(21,100) 'v1', v1
> > write(21,100) 'v2', v2
> > write(21,100) 'r',r(1),r(2),r(3)
> > write(21,*) npts1,npts2,npts3,iplat
< write(21)(denn((i-1)*mx3d2 + j),j=1,npts1*npts2)
> > write(21,*)(denn((i-1)*mx3d2 + j),j=1,npts1*npts2)
Once these changes have been made, Molden should be compiled and
installed as usual.
The CCP1GUI will look for a file called molden.exe
(under Windows) or molden (under Linux/Mac) in the
system path, so you will need to make sure that the folder where this
file lives in in your system path.
Molpro is a complete system of ab initio programs for molecular
electronic structure calculations, designed and maintained by
H.-J. Werner and P. J. Knowles, and containing contributions from a
number of other authors. As distinct from other commonly used quantum
chemistry packages, the emphasis is on highly accurate computations,
with extensive treatment of the electron correlation problem through
the multiconfiguration-reference CI, coupled cluster and associated
methods. Using recently developed integral-direct local electron
correlation methods, which significantly reduce the increase of the
computational cost with molecular size, accurate ab initio
calculations can be performed for much larger molecules than with most
The Molpro website can be found at: http://www.molpro.net/ and a copy
can be obtained by contacting the developers.
Using Molpro with the CCP1GUI
The CCP1GUI expects to find an executable called
molpro in the system path. Alternatively, the tools in
the Job Submission tool in the Job tab can be used to
point the CCP1GUI at the desired binary.
Unfortunately, the visualisation toolkit used by the CCP1GUI (VTK) provides a version of the library
libexpat.so that is not compatible with the python XML
tools used by the CCP1GUI to read the Molpro XML output. This
incompatiblity causes the CCP1GUI to throw a segmentation violation on
Linux systems on starting.
The work-around for this is to force the CCP1GUI to load the system
libexpat.so before the VTK one. This is accomplished
by setting the LD_PRELOAD environment variable as shown below:
NB: the above is bash-shell syntax and should be changed if
you use t/csh
This command should either be executed before the CCP1GUI is
started, or should be placed in the ccp1gui.sh script
usd to start the CCP1GUI.
is a chemical toolbox designed to speak the many languages of chemical
data. It's an open, collaborative project allowing anyone to search,
convert, analyze, or store data from molecular modeling, chemistry,
solid-state materials, biochemistry, or related areas. The CCP1GUI can
use OpenBabel to extend the number of different file formats that it
supports for reading and writing.
page of the OpenBabel Wiki has instructions on how to download or
build OpenBabel on Windows, Macintosh and Linux platforms. Whichever
platform you are installing on, make sure that you also install the
Python bindings. There are brief notes for the different platforms below:
There is a separate download of the Python bindings for Windows. This
is labelled as the Python Module on the website, so make sure
that you download this (whether or not you also download the Windows
There are various options for installing on Mac OSX listed on the
OpenBabel website. You can test whether the route you've used has
installed the Python bindings by firing up the python interpreter and
importing openbabel, as shown below.
fred:~ foo$ python|
Python 2.5 (r25:51918, Sep 19 2006, 08:49:13)
[GCC 4.0.1 (Apple Computer, Inc. build 5341) on darwin
Type "help", "copyright", "credits" or "licence" for more information.
>>> import openbabel
If this completes without an error then your Python bindings are
installed. If some form of import error is generated, then you may
need to install OpenBabel from source as described in the Linux/Unix
There are often RPMs available for OpenBabel, and sometimes, it's
also possible to find RPM files for the Python bindings (e.g. under
Fedora/Redhat, there is an RPM called openbabel-python that
provides this functionality).
In cases where this is not available, you will need to compile
OpenBabel from source (instructions here),
however make sure that you also follow the section titled Install
the Python bindings globally, as this is required in order for the
CCP1GUI to be able to access OpenBabel.
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