Preparing Live View documents for the Imperial college Data Repository

This document describes the general principles behind preparing a live view or live preview display of data deposited in the Imperial College Data Repository. Different types of live view can be generated, and each is likely to require different (JavaScript based) software to be invoked.

1. Isosurfaces prepared using CubGen in compressed JVXL format

The files necessary to produce a live view, as illustrated by DOI: 10.14469/hpc/6273. The JSmol molecular viewing Javascript program will be used to generate these isosurface. This is invoked by the index.html template and you do not need to do anything further.

1. The root document, index.html, which contains the Javascript commands to load a JSmol window. An example of this document can be downloaded here (use the right click, Download or save link format, which most browsers support).
2. A stylesheet, table.css An example of this document can be downloaded here
3. A DOI resolver script, needed if the data file has been registered with a repository and issued a DOI identifier. This can be here
4. An XYZ coordinate file for the molecule. An example can be seen here
5. A JVXL compressed isosurface file. An example can be seen here
6. Any required image files, an example of which is here. Use SVG if possible to ensure accurate scaling.

1.1 Generating your JVXL files

1. Open a Checkpoint file (a log file does not contain the wavefunction and cannot be used).
2. Use the option Cube actions/new cube and select the type of cube you want. The options include
   • Molecular orbital,
   • total (electron) density (used also for NCI surfaces),
   • ESP (electrostatic potential),
   • and the density Laplacian.
3. There are also options to add and subtract two cubes, to square a cube and to scale a cube.
4. Next you will have the option of specifying a resolution for the generated cube. In the first instance, use the coarse cube until you are sure the property computed is what you want.
5. When complete, go back to Cube actions and save the cube file for uploading as per above.
6. If the resulting cube file is >100Mbyte in size, it will not be processed by the tool above and you will instead have to produce it using the Java-based Jmol program. The utility above produces three files, a .xyz coordinate file, a .jvxl isosurface file and a .png image file which you can use as desired.

1.2 Actions to publish a live view.

1. Initiate a data deposition, using https://data.hpc.imperial.ac.uk/publish/
2. Complete the title and description boxes and then upload all the files above, other than the root document index.html
3. Now edit the root document index.html to include the various data files in the following manners. Use a text editor, preferably an HTML-aware one.
   1. The coordinate and isosurface files will be transcluded into the root document using the following syntax
      <a href="javascript:displayLocalCub('J6_den.cub.xyz', 'J6_den.cub.jvxl', 'NCI surface')">View NCI surfaces</a>
   2. Image files are included by first determining the URL of the specified image. Thus the image example above can be obtained by "right clicking" the link to the file from the just uploaded file list, which will appear something like:
      https://data.hpc.imperial.ac.uk/resolve/?doi=6273&file=2 Use this URL in invoking the HTML instance, as eg
      <img align="right" alt="" src="https://data.hpc.imperial.ac.uk/resolve/?doi=6273&file=2">
   3. If you want to load a data file directory from the repository rather than uploading a copy as described above, then invoke it as:
      <a href="javascript:show_jmol();javascript:handle_jmol('10.14469/hpc/5085',%20';frame 18;font label 16;zoom 140;spin 3;set echo bottom left;font echo 20 serif bolditalic;color echo green;echo methyl axial, N eq;')">(<i>S</i>,<i>R</i>,<i>S</i>)</a>
      where 10.14469/hpc/5085 is eg the DOI of the (in this case assumed) Gaussian deposited data.
   4. Do not make changes to any other parts of the index.html document unless you are very familiar with its operation!
4. When the index.html document has been appropriately customised with the items above, it can be uploaded to the data set as per above. It should now produce a live display of the files, as specified above.
5. You may find the index.html has to be edited a number of times before the final version is accepted. Take care to label each version with a version number (root document, V5). You cannot delete old version, you can only add new ones.

2. XY plots using the Plotly software.