Prepare...

When you choose the Prepare... command from the Tools menu a dialog box will be presented that you can use to specify how to generate a set of jobs.

Three main list fields are presented: the Run field, the coordinates field, and the input options field. In each of these lists you can specify multiple options. When pressing 'OK' ADFjobs will generate the jobs by combining the options in all possible ways.

Select one or more .adf files to run. A .adf file is just a calculation that has been set up using ADFinput before. Alternatively, one may use one of the predefined .adf files as present in the pull-down menu when you press the '+' button. To add a .adf file, use the pulldown menu, or specify a file name in the text field and press return. You may use wild card in the text field, so the default value (*.adf) will expand to all .adf files in the current directory. To remove something from the list, select it and press the '-' button.

When this list is empty, the molecule as found in the .adf files will be used. When one or more sets of coordinates is present in this list, the molecule in the .adf file(s) will be replaced by the molecules as defined in the coordinate files. You may use .adf files, .xyz files, .t21 results files, .mol files, .pdb files or whatever other format ADFinput can use with the 'Import Coordinates' function. By listing multiple files here your .adf files (that you listed in the Run: list box) will all be executed with each of the molecules in turn. Thus, if you specified two run files (for example a Single Point calculation, and a Geometry Optimization), and three molecules, you will end up with 6 jobs.

In this list you may define alternative input options. The corresponding input options in the .adf file will be replaced by the values that you specify here. So if you specify two different basis sets, each job will be replaced by two new jobs, one with each basis set that you specify. You may also specify other things, like integration accuracy and so on. If you specify only one value, that value will be used in all jobs. If you specify multiple values (by repeatedly adding the option) you will generated multiple jobs.

The text field may be used to add additional keywords, or replace existing ones, with the value specified. These options will be added to the list of options by pressing return in the text field. The values will be used as the '-k' argument to the adfprep command. For detailed information about this please check the adfprep documentation.

The final fields will tell the prepare tool where to generate the jobs (the directory is relative to the current directory, and will be created if it does not yet exists). Also one big job will be created that is just a concatenation of all the individual jobs. When running interactively it might be more convenient to run this job instead of all the individual jobs. The results should be identical, the big job will produce files that look as if they have been produced by the individual jobs.