molproView

molproView is a simple formatter for Molpro output files. It works by interpreting the XML markup in the output, and then translating it into an HTML formatted page. Molecular models are displayed using the Jmol toolkit.

Start using molproView here, or look at an example here. See below for more detailed instructions.

Use

1. Via a web browser

   The URL should point to dir/molproView/molproView.php where dir is the server directory in which the source tarball was unpacked. If the server is running Apache or compatible software, the trailing /molproView.php can sometimes be omitted. The resulting page prompts for the URL of the Molpro output file.

2. Via a shell script

   molproView file | URL

   URL should point to a Molpro output file produced with the -X or --xml-output option of molpro (usually having suffix .xml).

   If molproView has been installed in such a way that the configured web server has access to local files, a relative or absolute path pointing to the output file can be used instead of URL.

3. Direct production of html without a server

   Any Molpro output file with suffix .xml can be converted to html by copying it to the molproView source directory and typing make. If it is viewed in place, the Jmol models will work, but if it is copied elsewhere is is likely that they will not. Features that require the Jmol applet to read auxiliary files (ie surface plotting) will not work, unless the html file is itself served through an http server.

Features

• All results (energies, properties).
• The input data for the job.
• Geometries, displayed using a configurable 3-dimensional model.
• 3-dimensional isosurface plots of molecular orbitals and electron densities, where these have ben calculated by Molpro's CUBE facility.
• Intermediate points in geometry optimizations, either individually or as a complete trajectory. Graphical convergence of energy in geometry optimization.
• Generation of restart input files using the geometry at any chosen point in a geometry optimization within the job.
• Normal modes and frequencies, including graphical display of normal coordinates.
• Tables, including optional presentation as 2-dimensional plots using Google Chart.

The following features are still to be added.

• Display of Molpro variables in explicit SHOW commands.
• Download of individual tables as html or csv.
• Visualization of electrostatic potential on density isosurface.

Installation

1. You need a web server that has support for PHP, including the XSL extension (PHP version 5 or higher).
2. If the web server is running on the local workstation, it is convenient to configure it such that it has read access to the user file system. If this is done, then it is possible for the user to specify a file name instead of a URL, without the need to export the file to be viewed to a web server. However if this is done, it is important that the web server serves only the local machine, or is configured with restricted access, otherwise all user files will become visible externally through molproView!
3. Download the source code from here, and unpack it somewhere in the web server.
4. Type cd molproView; make which will complete the installation, including downloading Jmol from sourceforge.
5. Edit the molproView script, changing the definition of urlserver to the URL of this directory, and adjusting if necessary the definition of browser.
6. Copy molproView to a directory in the user's PATH.

Licence