5.3. Interfaces to External Programs

ABCluster provides programming interfaces so you can write your own interfaces for any computational chemistry programs. Now we will see how to do this.

When isomer and geom is running, it will generate a geometry with a long name like x-34. You do not need to know its exact name but just need to know that x is generated automatically by ABCluster, and 34 means this is the 34th calculation. In ABCluster, this name is represented by $xxx$. This geometry will be saved in standard XYZ format, a file called x-34.xxxxxyz, represented by $inp$. Then, commands between the two >>>> will be run one by one. Finally, the optimized geometry and energy should be written in XYZ format to a file called x-34.ooooout (The title line is the energy), represented by $out$. Then isomer will read optimized geometry and energy from $out$ and save it, launching next search. This mechanism is shown below.

_images/api.png

Now let’s see how we let isomer work with Gaussian. For the following commands:

1>>>>
2xyz2gaussian optfile $inp$ > $xxx$.gjf
3g16 < $xxx$.gjf > $xxx$.log 2>/dev/null
4gaussian2xyz $xxx$.log > $out$
5>>>>

  1. xyz2gaussian uses the structure $inp$ generated by isomer and optfile to generate a Gaussian input file named $xxx$.gjf.

  2. Call Gaussian to perform the local optimization and output to $xxx$.log.

  3. gaussian2xyz extracts optimized structure and its energy from Gaussian output file $xxx$.log and save them to $out$.

Tip

In summary, your task is to write programs or scripts that can transform the XYZ format geometry $inp$ into the format that the external program understands, and perform the calculation, then extract optimized geometry and its energy from program output and save them in another XYZ file $out$ (title line being the energy).

Tip

You can read the interfaces provided in misc to better understand how to write your own interfaces.