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The CCP1 GUI Project - Interfaces

Introduction

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 the codes.

Molden

Intro

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 CCP1GUI.

Installation

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
62,63c62,64
<           call inferr('Only Normal Density Can be Written!',0)
<           return
---
> > cc          call inferr('Only Normal Density Can be Written!',0)
> > cc          return
> >           write(6,*)'Writing 3d field (not normal density)'



66c67
<       open(unit=21,form='unformatted',file='3dgridfile',
---
> >       open(unit=21,form='formatted',file='3dgridfile',

69,71c70,72
<       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

73c74
<          write(21)(xyz(j,i),j=1,3)
---
> >          write(21,*)(xyz(j,i),j=1,3)

75,76c76,82
<       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

78c84
<          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

Intro

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 other programs.

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.

Problems

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:

export LD_PRELOAD=/usr/lib/libexpat.so

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.

OpenBabel

Intro

OpenBabel 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.

The Installation 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:

Windows 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 OpenBabel GUI).
Mac OSX

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 section below.

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.

Return to the CCP1GUI homepage

 
 
   
 
For more information about the work of the Computational Chemistry Group please contact Paul Sherwood p.sherwood@dl.ac.uk or Bill Smith w.smith@dl.ac.uk
 
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