Sections of the Jaguar Input File Describing the Molecule and Calculation

The rest of the input file is composed of named sections. The sections may appear in any order. Character case (upper or lower) is ignored; therefore, either case, or a combination of the two, may be used. Equals signs (=), commas (,), blank spaces ( ), and tabs are all considered spacing characters; however, if you plan to use the GUI, we suggest that you use equals signs between a keyword and its value, and avoid using them anywhere else. Blank lines, or multiple spacing characters in a row, are equivalent to a single spacing character and thus may be used to improve readability.

The gen section contains a list of the general keywords which control the calculation. Defaults are provided for all unspecified keywords. The other sections contain lists, such as atomic coordinates. The sections are listed in Table 1, and link to pages that describe their distinct format in detail. Keywords in the gen section can have integer, real, or character string values. Generally, valid integer values are limited to a small set which differs for each keyword. Real values can optionally include a “d” or “e” floating point power of ten. Character string keyword values may be limited to a small set, as for a basis set description, or may allow a general string like a file name. Comments in the gen section are preceded by a "!" character.

Each section is delineated by a pair of “&” or “$” characters. The section name follows immediately after the first “&” or “$.” Thus, for example, the general keyword section may begin with “&gen” or “$gen” and ends with “&” or “$.” Within the gen section, allowed keywords are followed by numerical arguments giving their values, whose meanings are explained in The gen Section of the Jaguar Input File. At least one spacing character must precede and follow each keyword or keyword/value pair.

Table 1. Sections for Jaguar input files
Section	Description
zmat	Contains list of atomic coordinates describing molecular geometry, in Cartesian or Z‑matrix format.
zvar	Sets values for zmat section variables.
coord	Specify particular internal coordinates to be used for optimization.
connect	Specify particular internal coordinates to be used when generating coordinates for optimization.
tvec	Specify reaction coordinate at transition state for IRC calculations.
gen	Sets general control keywords, including those describing the calculation performed, the grids, dealiasing functions, and cutoff parameters used, the electrostatic, geometry, and solvation properties calculated and the parameters used, and the output generated.
xcfunc	Specify custom density functionals
lmp2	Sets LMP2 pairs for local local MP2 calculations and delocalization of LMP2 pairs.
relativity	Sets keywords for relativistic Hamiltonians.
atomic	Sets atom-specific properties, including atomic masses (for isotopes), van der Waals radii for PBF solvation calculations, and basis functions for individual atoms.
hess	Allows input of initial nuclear Hessian.
guess	Allows input of initial wave function.
guess_basis	Specification of the basis set for the initial guess in the guess section.
pointch	Adds independent point charges.
efields	Adds electric field or fields.
egridpt	Grid points for calculation of electrostatic potential and electric field.
ham	Allows user input of Hamiltonian.
orbman	Allows orbitals to be reordered or linearly combined.
cdft	Specifies constraints for charge or spin density in a DFT calculation.
ctf	Specifies fragments for calculation of charge transfer numbers.
loc_ib	Specifies the bond from which an electron is removed from the neutral system in a B3LYP-LOC calculation.
echo	One-word section indicating that the input file should be echoed in the output file.
path	Specifies execution path, listing order of Jaguar programs to be run.
nbo	Specifies NBO directives for NBO calculation.
core	Specifies $CORE keylist for NBO calculation.
choose	Specifies $CHOOSE keylist for NBO calculation.
nrtstr	Specifies $NRTSTR keylist for NBO calculation.

For example,

&gen iguess=0 molchg=1 &

sets the iguess and molchg keywords of the gen section to 0 and 1, respectively. Sections may span multiple lines, and more than one section may appear in a line. However, a gen section keyword and its value must be on the same line. The following example is interpreted in the same way as the gen section example given above:

This is a comment.
&gen iguess=0
   molchg=1 &
This is also a comment.