Jaguar Geometry Scans

Geometry scans are a series of jobs that calculate the energy of a molecule at different values of one or more internal or Cartesian coordinates. Jaguar supports several approaches to coordinate scans, which differ in whether the non-scanned coordinates are optimized and in how the starting geometry for each scan point is generated. You can scan up to five coordinates simultaneously, with a maximum of 360 points per coordinate. 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 Setting up Jaguar Input Files for Scans and Geometry Scan Keywords in the Jaguar Input File.

Types of Coordinate Scans

Jaguar offers four approaches to coordinate scans, which differ in their speed, the quality of the geometries they produce, and the types of coordinates they can scan.

Rigid scan. Jaguar performs a single-point energy calculation at each set of coordinate values, without optimizing any coordinates. Each scan point is generated directly from the initial geometry. Rigid scans are the fastest type and can be distributed across multiple processors. They are useful for quick estimates of energy profiles or for surveying the effect of multiple coordinates, but the geometries at each scan point are not equilibrium structures. Set up rigid scans in Maestro from the Rigid Coordinate Scan Panel.

Relaxed scan. Jaguar performs a geometry optimization at each set of coordinate values, holding the scan coordinates fixed (as static constraints) while optimizing all other coordinates. Each scan point starts from the initial geometry. This scan type can be distributed across multiple processors and produces more reasonable geometries than rigid scans. Set up relaxed scans in Maestro from the Relaxed Coordinate Scan Panel.

Consecutive relaxed scan. As with a standard relaxed scan, Jaguar optimizes the geometry at each scan point while holding the scan coordinates fixed. However, each scan point starts from the optimized geometry of the previous point rather than from the initial geometry. This produces the most realistic geometries but requires sequential execution, so it cannot be distributed across processors. In Maestro, set up a consecutive relaxed scan from the Relaxed Coordinate Scan Panel by selecting previous optimized geometry for the Generate starting geometries from options in the Scan tab.

Dynamic relaxed scan. A relaxed scan in which one or more scan coordinates use dynamic (target) constraints instead of static constraints. With static constraints, the scan coordinate is set to its target value before the optimization begins, which can cause steric clashing or extreme strain. With dynamic constraints, the geometry starts from its current coordinates and is gradually pulled toward the target value during optimization. Dynamic constraints are required for scanning coordinates that are part of a ring. In Maestro, set up a dynamic relaxed scan from the Relaxed Coordinate Scan Panel by clearing the Fixed Value checkbox for one or more coordinates in the Scan tab. Dynamic constraints can be combined with either starting geometry option. For details on setting up dynamic constraints in the input file, see Static vs dynamic constraints.

Scan type	Calculation	Starting geometry	Can scan ring coordinates	Tutorial
Rigid	Single-point energy	Initial geometry	No	Rigid and Relaxed Coordinate Scans
Relaxed	Geometry optimization	Initial geometry	No	Rigid and Relaxed Coordinate Scans
Consecutive relaxed	Geometry optimization	Previous optimized geometry	No	Rigid and Relaxed Coordinate Scans
Dynamic relaxed	Geometry optimization	Initial or previous optimized geometry	Yes	Dynamic Relaxed Coordinate Scans

When an internal coordinate is scanned with static constraints, the last atom in the coordinate definition is the atom that is moved, along with any other atoms that are attached to it. With static constraints, Jaguar does not allow you to scan the distance between two atoms in a ring, because it is not possible to change the distance coordinate without changing some other coordinate. To scan coordinates in a ring, use dynamic constraints instead. 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.