Setting up Jaguar Input Files for Scans
- Overview
- Examples
To create an input file for a coordinate scan, you set up an input file with the coordinates defined as variables and the variable values defined as described below. For a relaxed scan, the job must be a geometry optimization; for a rigid scan, it must be an energy calculation.
Defining variables in the coord section
You can define a variable in the geometry input (as described in Variables and Dummy Atoms in Jaguar Z‑Matrix Input), or you can define variables in the coord section. Using the coord section allows you to define variables that are not part of the Z matrix geometry input. To define a variable in the coord section, add the variable name after the # sign in the coordinate definition. For example, the following input file section defines a coordinate HCCH as the torsion angle between H1, C1, C2, and H2.
&coord H1 C1 C2 H2 # HCCH &
The values taken by a variable are defined in a zvar section.
Defining variable values
To specify the values that a variable will take in a scan, you can assign a list of values to the variable in the format at number-list, or you can assign the initial value as either number or from number, and use two specifications from the following list, in the order given:
tonumber—specify the final value of the coordinatebynumber—specify the step sizeininteger—specify the number of steps
Here, integer means an appropriate integer and number means an appropriate real number. If you specify the initial and final values, they are always among the values set. For example, varying a coordinate from 0 to 120 by a step size of 30 takes 5 steps: 0, 30, 60, 90, and 120.
As an example, to vary the angle HCCH over the values {0, 30, 60, 90, 120, 150, 180}, you could use any one of the following lines:
HCCH = from 0 to 180 by 30 HCCH = 0 to 180 in 7 HCCH = from 0 by 30 in 7
You can also set a coordinate to a set of specific values using the word at. With this format, the values of the scanned coordinate do not have to be evenly spaced. For example, this line would vary the angle HCCH over the values {0, 30, 60, 70, 80, 90, 120, 150}:
HCCH = at 0 30 60 70 80 90 120 150
You can define up to five scan coordinates at once. The first scan coordinate will be in the innermost loop—that is, the scanner will run through all values of the first scan coordinate before updating the others, and so on, finally looping last over the last scan coordinate.
Relevant keywords
For each geometry in the scan, the default initial guess for the wave function and the default initial Hessian are taken from the previous geometry. You can change this behavior using the scanguess and scanhess keywords in the gen section of the input file.
By default, the scan increments are applied to the final geometry from the previous scan step, thus minimizing the number of geometry optimization steps in a relaxed scan required to optimize the new structure. Sometimes this can have the effect of biasing a relaxed scan such that a number of scan points optimize to the same local minimum for other parts of the structure. In these cases you can set scangeo=1 so that the scan increments are applied to the input geometry. The danger here is the possibility of steric clashes, especially for torsional scans around bonds connecting bulky substituents.
Static vs dynamic constraints
The scan values can be treated as static constraints. In the following example, the HCCH angle is to be scanned over the values {0, 30, 60, 90, 120, 150, 180}. In a relaxed scan (scangeo=1), 7 geometry optimizations are initialized using the input geometry, with the HCCH angle fixed at the specified scan values. In a consecutive relaxed scan (scangeo=0), the final geometry of the previous scan step is used in the geometry optimization of the following scan step, with the HCCH angle fixed to be the value specified for that step.
&zvar HCCH = from 0 to 180 by 30 & &coord H1 C1 C2 H2 # HCCH &
If you want the scan values to be treated as dynamic constraints, adding #dc or #DC after the coordinate instead:
&coord H1 C1 C2 H2 #dc HCCH &
In a relaxed scan (scangeo=1) with dynamic constraints, 7 geometry optimizations are initialized with the input geometry, and the optimization proceeds until the target scan value is reached. In a consecutive relaxed scan (scangeo=0) with dynamic constraints, the final geometry of the previous scan step is used in the geometry optimization of the following scan step, and the optimization proceeds until the target scan value of that step is reached. Specifying dynamic constraints in scans allows you to scan over coordinates contained in rings.
Static and dynamic scan variables can be used together in a calculation containing multiple scan variables. For example,
&zvar HCCH = from 0 to 180 by 30 CC = from 1.3 to 1.6 by 0.1 & &coord H1 C1 C2 H2 #dc HCCH C1 C2 # CC &
Coordinate Scan Examples
Example: Rigid scan of the HOH bond angle of water at the B3LYP-D3/6-31G** level of theory
&gen basis=6-31G* dftname=B3LYP-D3 & &zmat O1 0.0000000000000 0.0000000000000 0.0000000000000 H2 0.8433914458129 0.5372996083468 0.0000000000000 H3 -0.8433914458129 0.5372996083468 0.0000000000000 & &zvar a = 95 to 135 in 5 & &coord H3 O1 H2 # a &
$SCHRODINGER/jaguar run -jobname=scan_rigid_0001 scan-rigid-0001.in
Example: Rigid scan of the HOOH dihedral angle of hydrogen peroxide at the B3LYP-D3/6-31G** level of theory
&gen dftname=B3LYP-D3 basis=6-31G** & &zmat O1 -0.6791109812330 -0.2086276018900 -0.1786617245197 O2 0.6194421815655 0.2950564853165 0.2566520350204 H3 -0.5999103884802 -1.1465423448357 -0.0660695206196 H4 1.0772607858205 0.4551112774238 -0.5578529633853 & &zvar d = 100.66 to 460.66 in 13 & &coord H4 O2 O1 H3 # d &
$SCHRODINGER/jaguar run -jobname=scan_rigid_0002 scan-rigid-0002.in
Example: Relaxed scan of the HOOH dihedral angle of hydrogen peroxide at the B3LYP-D3/6-31G** level of theory. Optimizations run sequentially and use the optimized geometry from the previous step
&gen igeopt=1 dftname=B3LYP-D3 basis=6-31G** & &zmat O1 -0.6791109812330 -0.2086276018900 -0.1786617245197 O2 0.6194421815655 0.2950564853165 0.2566520350204 H3 -0.5999103884802 -1.1465423448357 -0.0660695206196 H4 1.0772607858205 0.4551112774238 -0.5578529633853 & &zvar d = 100.66 to 460.66 in 13 & &coord H4 O2 O1 H3 # d &
$SCHRODINGER/jaguar run -jobname=scan_relaxed_0001 scan-relaxed-0001.in