Plotting Keywords in the Jaguar Input File

Overview
Examples

You can generate a plot file, using keywords in the gen section, that contains the values of the density, the spin density, the electrostatic potential, or orbital amplitudes. The data values are tabulated on a rectangular grid (the “box”), which is generated automatically and encompasses the van der Waals radii of all atoms in the molecule. The plot file can be used by Maestro and other programs to display surfaces for a particular value of the density, potential, or amplitude. The length units for the grid are set with the iunit keyword.

The possible values of the plotting keywords are given in Table 1. See Jaguar Surfaces for information on setting up plot data using the GUI.

Orbital amplitude data can only be generated for SCF wave functions: MP2 calculations do not generate natural orbitals that could be used for generating surfaces.

When the job is run, each type of output requested is written to a file whose name depends on jobname, the name for the job (for example, h2o), and the type of information being plotted. The file name stem is jobname_density for a density plot, jobname_spin for a spin density plot, and jobname_potential for a potential plot. Orbital plot information is written to separate files for each orbital. The orbital file name stems are of the form jobname_spin_HOMO# for occupied orbitals, and jobname_spin_LUMO# for unoccupied orbitals, where spin can be alpha or beta, and # is the orbital index number relative to the HOMO or LUMO (empty string instead of 0 for the HOMO or LUMO, −n for occupied orbitals, +n for unoccupied orbitals). For instance, the HOMO from the job h2o would be written to the file h2o_alpha_HOMO.vis.

Table 1. Keywords for generating plot data
Keyword	Value	Meaning
iplotden	0	Do not generate electron density data
	1	Generate electron density data
	2	Generate electron density data and electron density difference data between the final SCF density and the initial guess density.
iplotspn	0	Do not generate electron spin density data
	1	Generate electron spin density data
iplotesp	0	Do not generate electrostatic potential data
	1	Generate electrostatic potential data (also sets epn=1).
iorb1a	0	Do not generate any alpha orbital data
	>0	Index of first alpha orbital for which to generate data
	`homo-`n	Index of first alpha orbital for which to generate data, relative to highest occupied molecular orbital (HOMO). n can be any positive integer.
	`lumo+`n	Index of first alpha orbital for which to generate data, relative to lowest unoccupied molecular orbital (LUMO). n can be any positive integer.
iorb2a	>0	Index of last alpha orbital for which to generate data.
	`homo-`n	Index of last alpha orbital for which to generate data relative to highest occupied molecular orbital (HOMO). n can be any positive integer.
	`lumo+`n	Index of last alpha orbital for which to generate data relative to lowest unoccupied molecular orbital (LUMO). n can be any positive integer.
iorb1b	0	Do not generate any beta orbital data
	>0	Index of first beta orbital for which to generate data. Ignored for restricted wave functions.
	`homo-`n	Index of first beta orbital for which to generate data, relative to highest occupied molecular orbital (HOMO). Ignored for restricted wave functions. n can be any positive integer.
	`lumo+`n	Index of first beta orbital for which to generate data, relative to lowest unoccupied molecular orbital (LUMO). Ignored for restricted wave functions. n can be any positive integer.
iorb2b	>0	Index of last beta orbital for which to generate data.
	`homo-`n	Index of last beta orbital for which to generate data, relative to highest occupied molecular orbital (HOMO). n can be any positive integer.
	`lumo+`n	Index of last beta orbital for which to generate data, relative to lowest unoccupied molecular orbital (LUMO). n can be any positive integer.
tddft_nto	0	Do not calculate natural transition orbitals for TDDFT calculations.
	1	Calculate natural transition orbitals for TDDFT calculations.
iplotalie	0	Do not generate average local ionization energy data.
	1	Generate average local ionization energy data.
fukui_fn	0	Do not calculate Fukui functions.
	1	Calculate Fukui function for system with N+fukui_delta electrons. If `lowdin=1` is set, calculate Löwdin populations of the N+fukui_delta electron density.
	−1	Calculate Fukui function for system with N−fukui_delta electrons. If `lowdin=1` is set, calculate Löwdin populations of the N−fukui_delta electron density.
fukui_delta	0.01	Fraction of an electron to use in Fukui function calculations.
iplotnoncov	0	Do not calculate data for display of noncovalent interactions.
	1	Calculate the reduced density gradient, interaction strength, and density Laplacian for display of noncovalent interaction; identify bond critical points and include them as dummy atoms with zero-order bonds in the output structure file.
plotresnoncov	20.0	Number of points per unit length for noncovalent interaction plots. A higher density than for other plots is required for good visualization. The length units are defined by the iunit keyword. The default given here is in points/bohr.
ncicut_high	0.1	Maximum value of the density used to visualize the interactions. Values of the reduced gradient and Laplacian are not calculated at grid points where the density is greater than this value.
ncicut_low	0.0	Minimum value of the density used to visualize the interactions. Values of the reduced gradient and Laplacian are not calculated at grid points where the density is less than this value.
plotres	2.5	Number of points per unit length. The length units are defined by the iunit keyword. The default given here is in points/bohr.
xmaxadj	0.0	Amount to adjust the box boundary on the +x-axis. Can be positive or negative.
xminadj	0.0	Amount to adjust the box boundary on the -x-axis. Can be positive or negative.
xadj	0.0	Amount to adjust the x dimension of the box. Half the adjustment is added to each boundary. Can be positive or negative.
ymaxadj	0.0	Amount to adjust the box boundary on the +y-axis. Can be positive or negative.
yminadj	0.0	Amount to adjust the box boundary on the −y-axis. Can be positive or negative.
yadj	0.0	Amount to adjust the y dimension of the box. Half the adjustment is added to each boundary. Can be positive or negative.
zmaxadj	0.0	Amount to adjust the box boundary on the +z-axis. Can be positive or negative.
zminadj	0.0	Amount to adjust the box boundary on the -z-axis. Can be positive or negative.
zadj	0.0	Amount to adjust the z dimension of the box. Half the adjustment is added to each boundary. Can be positive or negative.

Plotting Keywords in the Jaguar Input File

Calculation of Molecular Properties Examples