The zvar, zvar2, and zvar3 Sections of the Jaguar Input File
- Overview
- Examples
The zvar section should contain equations setting the values of any variables in the zmat section, in the same units used for the zmat section. Here is a sample zvar section:
&zvar ycoor=0.753108 zcoor=0.454006 &
For an optimization, to constrain (freeze) all bond lengths or angles set to a particular variable, you should add a # sign to the end of the zvar section equation setting that variable. Similarly, to request Hessian refinement of a coordinate whose value is determined by a variable setting in the zvar section, add an asterisk (*) to the end of the equation that sets the variable value in the zvar section. For example, the zvar section
&zvar ycoor=0.753108# zcoor=0.454006 &
would freeze all ycoor values to 0.753108 during an optimization job.
Certain types of transition-state optimizations require that you enter two or three geometries (see Transition-State Optimizations for details). For these jobs, you can specify variables for the second and/or third geometries in the zvar2 and zvar3 sections. If no zmat2 or zmat3 sections exist, these variables are used in combination with the zmat section to define the second and third geometries.
The equation that defines a variable can also specify a range of values for coordinate scans. You can assign a list of values to the variable in the format at number-list, or you can assign the initial value, specified by number or from number, and two values from the following list, in the order given in the list:
- The final value of the coordinate, specified by
tonumber - The step size, specified by
bynumber - The number of steps, specified by
ininteger
Here, integer means an appropriate integer and number means an appropriate real number. See Setting up Jaguar Input Files for Scans for information and examples.
Geometry Optimization Examples
Example: B3LYP-D3/6-31G** geometry optimization of pyrimidine in redundant internal coordinates. The geometry is specified as a Z-matrix. A dummy atom and constraints are used to maintain symmetry
&gen igeopt=1 dftname=b3lyp basis=6-31G* ip11=2 & &zmat H1 C2 H1 d1 N3 C2 d2 H1 a1 N4 C2 d2 N3 a1 H1 180 C5 N3 d3 C2 a2 H1 180.0 C6 N4 d3 C2 a2 H1 180.0 X7 C2 1.0 H1 90.0 N3 -90.0 C8 C2 d4 X7 90.0 H1 180.0 H9 C8 d5 C6 a3 N4 180.0 H10 C6 d6 C8 a4 H9 0.0 H11 C5 d6 C8 a4 H9 0.0 & &zvar d1 = 1.09 d2 = 1.33 d3 = 1.33 a1 = 120.0 a2 = 120.0 a3 = 120.0 a4 = 120.0 d4 = 2.75 d5 = 1.09 d6 = 1.09 &
$SCHRODINGER/jaguar run -jobname=opt_zmatwdummy_0001 opt-zmatwdummy-0001.in
Example: B3LYP-D3/6-31G** geometry optimization of pyrimidine in internal coordinates specified in a Z-matrix. A dummy atom and constraints are used to maintain symmetry
&gen igeopt=1 intopt=2 dftname=b3lyp basis=6-31G* ip11=2 & &zmat H1 C2 H1 d1 N3 C2 d2 H1 a1 N4 C2 d2 N3 a1 H1 180 C5 N3 d3 C2 a2 H1 180.0 C6 N4 d3 C2 a2 H1 180.0 X7 C2 1.0 H1 90.0 N3 -90.0 C8 C2 d4 X7 90.0 H1 180.0 H9 C8 d5 C6 a3 N4 180.0 H10 C6 d6 C8 a4 H9 0.0 H11 C5 d6 C8 a4 H9 0.0 & &zvar d1 = 1.09 d2 = 1.33 d3 = 1.33 a1 = 120.0 a2 = 120.0 a3 = 120.0 a4 = 120.0 d4 = 2.75 d5 = 1.09 d6 = 1.09 &
$SCHRODINGER/jaguar run -jobname=opt_zmatsymm_0002 opt-zmatwdummy-0002.in
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