Jaguar Geometry Scans

Geometry scans are a series of jobs run with input files that vary only in the value of one or more variables used to define an internal or Cartesian coordinate in the input structure. You can perform a “relaxed scan,” finding minimum-energy geometries while holding one or more coordinates fixed to various values, or a “rigid scan”, varying only the scan coordinates. To scan over a coordinate, you must first define the coordinate as a variable, then define the values that the coordinate must take. The maximum number of points per coordinate is 360. You can set up scans from Maestro using the Rigid Coordinate Scan Panel or the Relaxed Coordinate Scan Panel, or you can create an input file with the appropriate sections as described in Geometry Scan Keywords in the Jaguar Input File.

When an internal coordinate is scanned, the last atom in the coordinate definition is the atom that is moved, along with any other atoms that are attached to it. Jaguar will not allow you to scan the distance between two atoms in a ring. This is because it is not possible to change the distance coordinate without changing some other coordinate. Bond angles can be scanned through 0° and 180°, though the scan may not start at these values.

Jaguar Scan Results

The results of scan jobs started from Maestro are incorporated into the Project Table. Each scan point is added as a separate entry to the table, with the energy and scan coordinates as properties. The properties are labeled with an r for distance coordinates, a for angles, and d for dihedrals. Cartesian coordinates are labeled with the atom name and x, y, or z. If you want to submit a particular scan point to Jaguar for refinement, you can select the corresponding entry as the source of job input. You can use the plot facility to display plots of the energy as a function of a particular coordinate, for example.

If the calculation for any point fails to converge, this point is skipped and the calculation proceeds to the next point. The failure is noted in the output.

For one- and two-dimensional scans, Jaguar writes .grd files, which can be read by Maestro and displayed in the Plot Coordinate Scan Results Panel. To open this panel, click the Tasks button and browse to Structure Analysis → Plot Coordinate Scan. You can also open this panel from the Workflow Action Menu for the entry group of the scan job. The panel displays interactive plots and interactive contour plots. You can use any kind of scan except at scans, i.e. scans that supply a list of coordinate values.

If you generated surfaces in the scan job, the surfaces are incorporated along with the structures at each point.

If you want to make use of the Jaguar input files for individual scan points, you can extract them from the file jobname.steps.in, which is written to the working directory whenever a scan is performed. This file contains the geometry specifications for each geometry in the scan, along with the calculated energies, keywords, and forces. Each input section in the jobname.steps.in file terminates with the string END_OF_INPUT., which you can use to determine where to split the file.

Restarting Jaguar Scans

Single-processor scan jobs store a record of their progress, by writing scanindex=n in the gen section of the restart file for scan jobs. If you want to restart a scan job that stopped prematurely, you can use the restart file to restart the scan.

Distributed scan jobs run the scan as a set of single-point calculations, and collate the results when each point is done. If any subjob fails, you should delete the output file for the failed subjobs, and then you can restart the distributed scan job. The completed points are skipped (on the basis of the existence of the output file), and the remaining points are run.