The path Section of the Jaguar Input File

The path section allows you to specify the execution path, which determines the order of the Jaguar (or other) programs to be run. If no path section exists, Jaguar will use the default path resulting from the settings in other sections of the input file.

The items listed in a path can be either Jaguar programs, UNIX commands, or other programs accessible from the executable directory. If a program or command is not accessible from the executable directory, you must specify the full path for that program, with a “/” character at the beginning of the path.

Table 1 gives a brief description of each Jaguar program.

Table 1. Individual programs included in Jaguar
Program	Description
jexec	Driver program for all Jaguar executables (note: inclusion of jexec in path will cause recursive Jaguar calculations)
pre	Reads and checks input (including path, if any), performs symmetry analysis, and calculates terms dependent on geometry (e.g., nuclear repulsion energy)
onee	Calculates one-electron integrals and effective core potential (ECP) contribution to one-electron Hamiltonian, when relevant
hfig	Calculates Hartree-Fock initial guess
probe	Ensures orthogonalization
grid	Generates grids
rwr	Generates Q operators
scf	Performs self-consistent field calculation
ch	Evaluates electrostatic properties (multipole moments, electrostatic potential fitting, Mulliken populations)
lmp2dip	Calculates dipole moments for LMP2 wave functions
cpolar	Finds polarizabilities and hyperpolarizabilities using coupled perturbed HF method
polar	Finds polarizabilities and hyperpolarizabilities using finite field method
elden	Calculates electron density on set of grid points
local	Performs localization of orbitals
lmp2	Performs local second-order Møller-Plesset perturbation theory calculation
cis	Performs CI singles and TDDFT calculation
der1a, der1b	Calculate analytic one- and two-electron first derivatives
lmp2der, lmp2gda, lmp2gdb	Calculate analytic one- and two-electron first derivative terms for LMP2 wave functions
nude	Calculates numerical second derivatives of energy (as numerical derivatives of the analytical gradient)
freq	Calculates vibrational frequencies and related properties
ira, irb	Calculate dipole derivative terms needed for calculation of IR intensities
geopt	Performs geometry optimization
pbf	Solves Poisson-Boltzmann equations for solvation calculation
solv	Performs solvation calculation with Poisson-Boltzmann solver
sm6	Performs solvation calculation with SM6 model
sm8	Performs solvation calculation with SM8 model
sole	Checks solvation energy convergence
dsolv	Computes solvation-related gradient terms for solvated geometry optimizations
post	Processes files, output, etc. at end of run
timex	Checks CPU time for entire run
machid	Utility program; returns machine information (not used in Jaguar calculations)

The simplest form available for the path section is a list of the programs to be run, as in the following example:

&path pre hfig grid rwr &

It is not actually necessary to list pre in paths, since the pre program will always be run.

If you want to run additional programs after a standard Jaguar calculation, you can use the word path to indicate the default path, as below:

&path path executable-list &

More complicated paths involve looping over programs until the last Jaguar program in the loop indicates that convergence is reached. The first program in the section of the path to be looped over is preceded by a loop label, and the last is followed by a goto label, where each of these labels is followed by the same character string. Nested loops are also allowed. The following path illustrates a loop which will cause the programs pre, onee, grid, and ig to run once, the series of programs rwr, scf, der1a, rwr, der1b, and geopt to run until the convergence criteria for geometry optimization are satisfied, and the program post to run once.

&path pre onee grid hfig loopa1 rwr scf der1a rwr der1b geopt gotoa1 post &

If you put a jump label between a loop label and a goto label, where jump is followed by the same character string that follows loop and goto (jumpa1 for the above path, for instance), the path will jump to the end of the loop after the goto label, and will exit the loop, when the jump label indicates that the convergence criterion for that program is reached.

Note that since loops only exit when convergence is reached, the program before a goto or jump label must have such a criterion. The three programs that can precede a goto or jump label are scf (when it is being used for solvation runs), geopt, and nude.

Sometimes you might want a path to include a command of more than one word—for instance, you might want to use the UNIX command mv old-filename new-filename to rename a file. In that case, you can enter the path section in such a way that each line contains a single command. To enter the path this way, you must include the word line after the &path (or $path) label at the beginning of the path section.