A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z

Index

, 1

.atomig file 1, 2, 3, 4, 5, 6

specified in input file 1, 2

.basis file 1, 2, 3, 4, 5

specified in input file 1, 2

.cutoff file 1, 2, 3, 4, 5, 6, 7

description and format 1, 2

specified in input file 1, 2

.daf file 1, 2, 3, 4, 5

description and format 1, 2

neighbor ranges 1, 2, 3, 4

references to content in input file 1

specified in input file 1, 2

.grid file 1, 2, 3, 4, 5, 6, 7

description and format 1, 2

references to contents in input file 1

specified in input file 1, 2

.in file-see Input file1

.lewis file 1, 2, 3, 4

description and format 1, 2

specified in input file 1, 2

.trn file-see GVB2P5

.trn file1

A

About button 1, 2

Accuracy level 1, 2, 3

input keyword for 1, 2

AIMPAC .wfn file, input keyword for 1

All-analytic calculation 1, 2

output from 1

Analytic corrections 1, 2, 3

.cutoff file determination of 1

input keyword for 1

Analytic frequencies 1

Analytic gradient of energy 1, 2, 3, 4

convergence criteria based on 1

input keywords for 1

der1a and der1b programs 1

input keyword for 1

lmp2der, lmp2gda, and lmp2gdb programs 1

output of maximum and RMS elements for geometry optimization 1

Anions 1, 2

Atom labels 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

Atom numbers 1, 2, 3

Atomic charges-see ESP fitting, Mulliken population analysis Molecular charge1

atomic input file section 1

Atomic mass keyword 1

Atomic masses

for frequency calculations 1

input keyword for 1, 2

setting in atomic section 1, 2

Atomic orbital space

printing Fock matrix in 1

input keyword for 1

printing orbitals in (each SCF iteration) 1

input keyword for 1

Atomic properties, setting in atomic section 1, 2, 3

atomic section

format 1

input types 1

Atomic units 1, 2, 3, 4

Atomic units in output

for geometry 1

for multipole moments 1

B

Babel

using to generate output 1, 2

using to read input files 1, 2

basgss basis set label 1, 2

Basis functions 1, 2, 3, 4

contracted 1, 2

counterpoise calculations 1

derivatives of

Gaussian function list in output 1, 2

evaluating contributions on grid points 1

file containing 1, 2, 3

for individual atoms 1, 2

Gaussian function list in output 1, 2, 3

input keyword for 1

number of 1

type, as listed in output 1, 2, 3

uncontracted 1, 2

basis input type 1, 2

Basis set 1, 2, 3, 4, 5, 6

diffuse functions 1, 2, 3, 4

for individual atoms 1, 2

Gaussian function list in output 1, 2, 3

input keyword for 1

included in generated GAUSSIAN 92 input file 1

input keyword for 1, 2

keywords 1

minimal, with GVB 1

output from 1

polarization functions 1, 2, 3, 4, 5, 6

specifying for GAUSSIAN 92 input 1, 2

specifying for initial guess 1, 2, 3, 4

Basis set superposition error 1, 2, 3, 4

Basis Set window 1, 2

output from 1

Basis sets

file containing 1, 2, 3

Batch input file

example 1

format 1

Batch jobs

jaguar batch command for 1, 2, 3

running from Jaguar interface 1, 2

Benzene 1

BFGS method for Hessian updating

input keyword for 1

BIOGRAF

.bgf files 1

reading from Jaguar interface 1

.hes files 1

reading from Jaguar interface 1

reading files from Jaguar interface 1, 2

Bohr units for geometry input 1, 2, 3, 4

Bond dissociation 1, 2, 3

Bond lengths and angles output option 1, 2

input keyword for 1

Bond lengths, bond angles, or torsions

freezing 1

Bonding types, describing in lewis files 1

Boys localization 1, 2

Fock matrix output in Boys orbital space

input keyword for 1

input keywords for 1, 2, 3, 4

orbital printing 1

input keyword for 1, 2

order 1

output from 1

C

Calculating molecular properties 1

Calculation host 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

Calculation options, output file changes for 1

Canonical orbital space

printing Fock matrix in 1

input keyword for 1

printing orbitals in (each SCF iteration) 1, 2

input keyword for 1

Carbon tetrachloride 1

Cartesian format 1, 2, 3, 4, 5, 6

Cations 1, 2

ch program 1

output from 1, 2, 3

for solvation 1, 2

Charge fitting-see ESP fitting, Mulliken population analysis1

charge input type 1

Charge keywords 1

chdens electron density output file 1, 2, 3

Check Job button 1

Check option 1, 2, 3, 4

Chlorobenzene 1

CI-see Configuration interaction1

Cleanup button 1

Comment line 1, 2, 3

Configuration interaction (CI)

coefficients

for GVB pair natural orbitals, in output 1

energy lowering

for GVB pair natural orbitals, in output 1

connect input file section 1

Connectivity 1

connectivity table output option 1

input keyword for 1

input keyword for bonding 1, 2

Consecutive Jaguar jobs

running from Jaguar interface 1, 2

running with jaguar batch 1, 2

Constraints for geometry optimization 1, 2, 3, 4, 5, 6, 7, 8

input keyword for applying 1

input keywords for 1

output from 1

Contracted basis functions 1, 2, 3

Convergence criteria

geometry optimization 1, 2, 3

analytic gradient criteria 1, 2

displacement criteria 1, 2

energy change criterion 1

gradient-related only 1

input keywords for 1, 2, 3

SCF energy criterion 1

SCF energy criterion 1, 2

input keyword for 1

solvation energy 1

input keyword for 1

Convergence problems, troubleshooting 1

Convergence schemes 1

DIIS 1, 2

input keywords for 1, 2

OCBSE 1

output from 1

coord input file section 1

Coordinates

constraining 1

freezing 1

Coulomb and exchange matrices output option 1, 2

input keyword for 1

Coulomb corrections 1

Coulomb energy contribution 1, 2, 3, 4

Coulomb field, charge fitting to 1

Coulomb operator (J) 1, 2

input keyword for output 1

obtaining i/o information for 1

Per Iteration matrix output option 1, 2

pseudospectral assembly of 1, 2

Counterpoise calculations 1, 2, 3, 4

Coupled perturbed Hartree-Fock (CPHF) terms

for LMP2 dipole moments 1, 2

for LMP2 ESP fitted charges 1, 2

for polarizability and hyperpolarizability calculations 1

Coupled perturbed Hartree-Fock-see CPHF calculations1

cov input type 1

CPHF calculations

grid used for 1

of hyperpolarizability 1, 2

of polarizability 1, 2

cpolar program 1

cpu time 1, 2

Culot-Fletcher method for trust radius adjustment

input keyword for 1

cut10 1

cut20 1

Cutoff methods 1, 2, 3, 4, 5

Cutoffs 1, 2, 3, 4

.cutoff file 1, 2, 3, 4

as shown in output 1, 2

Cyclohexane 1

D

daf input type 1

Data directory 1

Dealiasing function keywords 1

Dealiasing functions 1, 2, 3, 4, 5, 6

contracted 1, 2, 3

dealiasing function choices for calculation 1, 2, 3, 4, 5, 6

Gaussian function list in output

input keyword for 1

long-range 1, 2, 3

neighbor ranges for 1, 2, 3, 4

short-range 1, 2, 3

uncontracted 1, 2, 3

default.atomig file 1

default.basis file 1

Delocalization of LMP2 pairs 1, 2, 3

Density

plotting with plot section 1, 2

Density functional theory (DFT) 1, 2, 3, 4

customized functional combinations for 1, 2

hybrid methods 1, 2

input keywords for 1, 2, 3

optimization output 1, 2

output from 1

standard functional combinations for 1, 2

Density matrix 1, 2

convergence criterion for elements 1, 2

input keyword for 1

in DIIS error vector 1, 2

input keyword for output 1

Per Iteration output option 1

Density matrix output option 1

input keyword for 1

der1a program 1

output from 1, 2, 3

der1b program 1

output from 1, 2, 3

Derivatives of basis set functions 1

Gaussian function list in output 1

input keyword for 1

Derivatives of energy 1

Detailed timing information output option 1

input keyword for 1

DFT keywords 1

DFT window 1, 2

output from 1

DFT-see Density functional theory1

Dichloroethane 1

Dielectric constant 1

input keywords for 1

Dielectric continuum method-see pbf program1

Differential density matrix 1, 2

input keyword for output 1

Per Iteration output option 1

RMS of elements in output 1, 2

Differential density matrix output option 1

input keyword for 1

DIIS coefficients output option

input keyword for 1

DIIS convergence scheme 1, 2, 3, 4

coefficients, listing in output

input keyword for 1

input keywords for 1, 2

DIIS error vector

maximum elements, listed in output 1, 2

Dimming of menu items 1

Dipole moment-see Multipole moments1

Direct Inversion in the Iterative Subspace method-see DIIS convergence scheme1

Displacement 1

convergence criteria based on 1

input keywords for 1

Display host 1, 2, 3, 4

Display window 1

Displaying geometry input 1, 2

Dissociation 1, 2, 3

Driver for geometry scan 1, 2

dsolv program 1

Dummy atoms 1, 2

E

Echo input file and parameter list output option 1

echo input file section 1

ECPs-see Effective core potentials1

Edit window 1, 2, 3

counterpoise calculations, setting up 1

fixing bond lengths or angles 1

fixing Cartesian coordinates 1, 2

freezing bond lengths or angles 1, 2, 3, 4

freezing Cartesian coordinates 1, 2

Editing a geometry 1, 2

Editing input files from interface 1, 2

Effective core potentials (ECPs) 1, 2, 3, 4, 5, 6

efields input file section 1

Eigenvector following in transition state optimizations 1

input keywords for 1

Eigenvectors and eigenvalues of overlap matrix output option

input keyword for 1

elden program 1

Electric field for polarizability calculations 1

input file section for 1, 2, 3

Electron density 1, 2

input keywords for 1, 2, 3

output from calculation 1

Electron-nuclear energy from solvation calculations 1

Electrons, information in output 1, 2, 3

electrostatic potential 1

Electrostatic potential fitting-see ESP fitting1

Electrostatic properties

ch program 1

Energy components output option 1

input keyword for 1

Energy convergence criterion 1, 2

input keyword for 1

Energy difference

geometry optimization convergence criterion based on 1, 2

input keyword for 1

Energy output 1, 2

nuclear repulsion 1, 2, 3, 4, 5

nuclear-point charge energy from solvation calculations 1

SCF 1, 2

components for each iteration 1

components, for each iteration 1

Coulomb contribution 1, 2, 3, 4

exchange contribution 1, 2, 3, 4

for each iteration 1, 2

one-electron 1, 2, 3, 4

orbital energies 1

total 1, 2

two-electron 1, 2

solvation 1, 2, 3

electron-nuclear energy 1

first shell correction factor 1

nuclear-solvent energy 1

reorganization energy 1

solute cavity energy 1, 2

solution phase energy 1, 2

solvation energy 1

total solvent energy 1

Enthalpy calculations-see Thermochemical properties1

Entropy calculations-see Thermochemical properties1

Environment variables, setting 1

ESP 1

ESP fitting 1, 2

ch program 1

constraining to reproduce multipole moments 1, 2, 3

output from 1, 2

error as reported in output 1

for LMP2 wavefunctions 1

for solvation calculations 1, 2

grid for 1, 2

input keywords for 1, 2

input keywords for 1

output from 1, 2

recalculating multipole moments from 1, 2

output from 1, 2

to atom centers 1

output from 1

to atom centers and bond midpoints 1

output from 1

esp input type 1

Exchange corrections 1

Exchange energy contribution 1, 2, 3, 4

Exchange operator (K) 1, 2

input keyword for output 1

obtaining i/o information for 1

Per Iteration matrix output option 1, 2

pseudospectral assembly of 1, 2

Executable directory 1, 2, 3, 4, 5

Execution path 1, 2, 3

F

Field, electric, input file section for 1, 2, 3

File names 1, 2

File viewer window 1, 2

Files output keywords 1

Files output options 1, 2

GAMESS input file (.gamess) generation 1

GAMESS input file (gamess.inp) generation 1

GAUSSIAN 92 basis set (.gbs file) output option 1, 2

GAUSSIAN 92 input deck (.g92 file) generation 1, 2

input keywords corresponding to 1, 2

Molden orbitals file (.molf file) output option 1

SPARTAN archive file (.arc file) generation 1

XYZ file (.xyz file) output option 1

First shell correction factor for solvation 1

input keyword for 1

Fixing bond lengths or angles for geometry optimization 1, 2

input keyword for applying 1

input keywords for 1

output from 1

Fixing Cartesian coordinates for geometry optimization 1, 2

Fock matrix 1, 2

in DIIS error vector 1, 2

input keywords for output 1

new estimate from DIIS scheme 1, 2, 3

output in Boys orbital space

input keyword for 1

Per Iteration output options 1

pseudospectral assembly of 1, 2

updating 1, 2, 3

input keyword for 1

Fock matrix output option

in AO (HF) or MO (GVB) space 1

input keyword for 1

in CO space 1

input keyword for 1

Forces 1, 2, 3

analytic calculation of 1

numerical calculation of 1

input keywords for 1, 2

output from 1, 2

numerical calculation of derivatives of 1

input keywords for 1, 2

output from 1, 2

table in output 1

formal input type 1

frag input type 1

Freezing bond lengths or angles for geometry optimization 1, 2, 3, 4

Freezing Cartesian coordinates for geometry optimization 1, 2

freq program 1

Frequencies 1

for a fragment of system 1, 2

freq program 1

input keywords for 1, 2

output 1, 2

scaling 1

input keywords for 1

Frequencies window 1, 2

output from 1, 2

Frequency-related keywords 1

Frequency-related properties 1, 2

output 1, 2

Functionals settings 1

G

GAMESS

generating input files with Jaguar 1

input files, generating with Jaguar

input keyword for 1

Gas phase optimizations 1

GAUSSIAN

input files

reading from Jaguar interface 1, 2

GAUSSIAN 92

basis set output (.gbs file) generating with Jaguar 1

basis set output (.gbs file), generating with Jaguar 1, 2

Hessian format 1

input files

generating with Jaguar 1, 2, 3, 4, 5

reading from Jaguar interface 1, 2

orbital output in format for 1, 2

GAUSSIAN 92 basis set (.gbs file) output option 1, 2

input keyword for 1

GAUSSIAN 92 input deck (.g92 file) generation 1, 2

input keyword for 1, 2, 3

Gaussian function list in output

for basis set 1, 2, 3

input keyword for 1

for dealiasing functions

input keyword for 1

for derivatives of basis functions 1

input keyword for 1

gen input file section 1

Generalized gradient approximation 1

Generalized Valence Bond method-see GVB calculations1

Geometries in atomic units also output option 1

Geometry buttons 1, 2, 3

Display option 1, 2

Symmetrize option 1, 2, 3

Geometry input 1, 2, 3, 4, 5, 6

Cartesian format 1, 2, 3, 4, 5

displaying 1, 2

editing 1, 2

file types for scanning 1, 2

format 1, 2, 3, 4

input file sections for 1, 2

keywords 1

obtaining from MOPAC 1

output file, echoed in 1

symmetrizing 1, 2, 3, 4

tolerance 1

translating and rotating during calculation 1

troubleshooting 1

units

input keyword 1, 2, 3, 4

Z-matrix format 1, 2, 3, 4, 5

Geometry optimization 1, 2

calculating forces only 1

der1a and der1b programs 1

input keyword for 1

constraining bond lengths or angles 1, 2, 3, 4, 5, 6

input keywords for 1

output from 1

constraining Cartesian coordinates 1, 2, 3, 4

convergence criteria 1, 2, 3

gradient-related only 1

input keywords for 1, 2, 3

convergence criterion for SCF 1

detailed output 1

fixed bond lengths or angles for 1, 2

input keywords for 1

output from 1

fixed Cartesian coordinates for 1, 2

frozen bond lengths or angles for 1, 2, 3, 4

frozen Cartesian coordinates for 1, 2

GDIIS method

input keyword for 1

generating input with new geometry 1

geopt program 1

in solution 1

output from 1

without gas phase calculation 1, 2

initial Hessians for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

input file section 1, 2, 3

input keyword for 1

input keywords for 1, 2

limiting step size for 1, 2

input keywords for 1, 2

maximum number of iterations for convergence 1, 2, 3

input keyword for 1

output from 1, 2, 3

bond lengths and angles 1, 2

forces table 1

refinement of initial Hessian for 1, 2, 3, 4, 5, 6, 7, 8, 9

tips 1, 2

troubleshooting 1

trust radius for 1, 2

input keywords for 1, 2

updating of Hessian during

input keyword for 1

Geometry optimization keywords 1

Geometry scans 1, 2

Geometry-only file

reading from interface 1

Geometry-see Geometry input, Geometry optimization1

geopt program 1

output from

for geometry optimization 1, 2

Ghost atoms

use in charge fitting to bond midpoints 1

Gibbs free energy calculations-see Thermochemical properties1

GPTSFILE 1

Gradient-see Analytic gradient of energy1

Grasp program 1

grid input type 1

Grid keywords 1

grid program 1

output from 1, 2, 3

Grid shell locations output option

input keyword for 1

Grids 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

dealiasing functions for fitting to 1, 2

evaluating basis function contributions on 1

for DFT calculations 1

for ESP fitting 1, 2

input keywords for 1, 2

grid choices for calculation 1, 2, 3, 4, 5

specifying your own grid 1, 2, 3

grid generation with program grid 1

output about grids 1

number of grid points 1

number of grid points for charge fitting 1

which used for iterations 1, 2

shells for 1, 2

ultrafine only 1

guess input file section 1, 2

GVB calculations 1, 2, 3, 4, 5

from HF converged wavefunction 1, 2

from HF initial guess 1

from input HF wavefunction 1

generating GAUSSIAN 92 input for 1

gvbig program for GVB initial guess 1

input keywords for SCF settings 1, 2

optimization output 1, 2

output from 1, 2, 3

pair selection tips 1

Per Iteration output option for data 1

printing orbitals 1, 2, 3

after initial guess is generated 1, 2

after SCF iterations 1, 2

at end of job 1

scf program 1

troubleshooting 1

GVB data output option 1

input keyword for 1

gvb input file section 1

GVB keywords 1

GVB pairs 1, 2

displaying 1, 2, 3

for GVB-LMP2 calculations 1

input file section for 1, 2, 3

output information 1, 2, 3

CI energy lowering 1

natural orbital assignment 1

natural orbital CI coefficients 1

orbital overlap 1

selection tips 1

setting from Lewis dot structure 1, 2

specifying for GAUSSIAN 92 input generation 1

troubleshooting 1

GVB window 1, 2

output from 1, 2

GVB2P5

.trn file

generating with Jaguar 1

convergence scheme (OCBSE) 1

generating MQM basis set (.bas file) for

input keyword for 1

orbital output in format for 1, 2

GVB2P5 trans matrix (.trn file) output option

input keyword for 1

gvbig program 1, 2

GVB-LMP2 calculations 1, 2

GVB-RCI calculations 1, 2, 3, 4

optimization output 1, 2

H

ham input file section 1

Hamiltonians

information in output 1, 2, 3

user input of 1, 2

Harmonic frequencies 1

Hartree-Fock (HF) calculations 1, 2, 3, 4, 5

input keywords for SCF settings 1, 2

printing orbitals

after initial guess is generated 1, 2, 3

after SCF iterations 1, 2

at end of job 1

scf program 1

used to get GVB initial guess 1

output from 1

Hartree-Fock calculations

optimization output 1, 2

output from standard 1

Heat capacity calculations-see Thermochemical properties1

Help window 1, 2

hess input file section 1

Hessian refinement, specifiying coordinates for 1

Hessians 1, 2, 3

effect of quality on geometry convergence 1, 2

from MOPAC 1, 2

input file section for input of 1, 2, 3

level shifting 1

input keyword for 1

reading BIOGRAF Hessians from Jaguar interface 1

refinement of initial Hessian 1, 2, 3, 4, 5, 6, 7, 8

input keywords for 1

selecting initial Hessian 1, 2

input keyword for 1

updating

input keyword for 1

Heteroatom pairs for local LMP2 calculations 1, 2

energy output for 1, 2

hfig program 1

output from 1, 2

How: Orbitals output options 1, 2, 3

input keywords for 1, 2

Hybrid methods 1

Hybridization types

describing in Lewis files 1

Hyperpolarizability 1, 2, 3, 4

input keywords for 1, 2, 3

output from 1

I

Icon for Jaguar interface 1

imw 1

Infrared intensities 1, 2

input keyword for 1

output 1

Initial guess 1, 2, 3, 4, 5

file information for 1, 2, 3

for transition-metal-containing systems 1, 2, 3

GVB initial guess

from HF converged wavefunction 1

from input HF wavefunction 1

gvbig program 1

input keyword for output 1

Per Iteration output option 1

HF initial guess program hfig 1

input file section for 1, 2, 3

input keyword for 1, 2

orbital output in format for 1, 2

stopping after 1, 2

Initial guess keywords 1

Input file 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13

atomic section 1, 2, 3, 4, 5, 6

defining fragments with 1, 2

connect section 1, 2, 3

coord section 1, 2, 3

description and format 1, 2

description of sections 1, 2

echo section 1, 2

echoing in output 1, 2

echoing in output file 1

editing from interface 1, 2

efields section 1, 2, 3

gen section 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

generating with Save window 1, 2, 3

guess section 1, 2, 3, 4, 5, 6

gvb section 1, 2, 3

ham section 1, 2

hess section 1, 2, 3

keywords 1, 2

lmp2 section 1, 2, 3, 4, 5

nbo section 1, 2, 3, 4

new 1, 2, 3

orbman section 1, 2, 3

path section 1, 2, 3

plot section 1, 2, 3

pointch section 1, 2

reading from interface 1, 2, 3

section delineators 1

spacing characters 1

submitting by hand 1, 2

zmat section 1, 2, 3

zmat2 section 1, 2

zmat3 section 1, 2

zvar section 1, 2, 3, 4

zvar2 section 1, 2

zvar3 section 1, 2

Input file directory 1

Input of molecular structure (geometry)-see Geometry input1

Input type

basis 1

charge 1

cov 1

daf 1

esp 1

grid 1

isotope 1

mass 1

mulk 1

multip 1

vdw 1

vdw2 1

input type

formal 1

Integrals

one-electron 1

calculation with program onee 1

energy contribution listed in output 1

two-electron 1

energy contribution listed in output 1, 2

energy output breakdown into J and K parts 1, 2

Interface

customizing appearance with jaguar.style file 1

customizing settings with jaguar.hosts file 1, 2, 3, 4

problems starting 1, 2

Interface host 1, 2, 3, 4, 5

Internal coordinates 1

specifying in input with connect section 1, 2

specifying in input with coord section 1, 2

Ions 1, 2

ip172 1, 2

IR intensities 1, 2

input keyword for 1

output 1

ira program 1

irb program 1

isotope input type 1

Isotopes

choosing with atomic section 1, 2

input keyword for 1, 2

setting masses in atomic section 1, 2

Iterations, geometry convergence, maximum number for 1, 2, 3

input keyword for 1

Iterations, SCF, maximum number of 1, 2

input keyword for 1

J

jaguar command 1, 2, 3, 4

jaguar batch 1, 2, 3

jaguar help 1

jaguar hosts 1

jaguar jobs 1

jaguar kill 1, 2

jaguar run 1, 2

host option 1, 2

save temporary files option 1

time stamps to log file option 1

version option 1

jaguar run,

nice option 1

jaguar versions 1

Jaguar copyright information 1

Jaguar files

.atomig file-see .atomig file1

.basis file-see .basis file1

.cutoff file-see .cutoff file1

.daf file-see .daf file1

.grid file-see .grid file1

.lewis file-see .lewis file1

input file-see Input file1

log file-see log file1

output file-see Output file1

Jaguar programs

ch-see ch program1

cpolar-see cpolar program1

der1a-see der1a program1

der1b-see der1b program1

dsolv-see dsolv program1

elden-see elden program1

freq-see freq program1

geopt-see geopt program1

grid-see grid program1

gvbig-see gvbig program1

hfig-see hfig program1

ira-see ira program1

irb-see irb program1

jexec-see jexec program1

lmp2der-see lmp2der program1

lmp2dip-see lmp2dip program1

lmp2gda-see lmp2gda program1

lmp2gdb-see lmp2gdb program1

lmp2-see lmp2 program1

loclmp2-see loclmp2 program1

locpost-see locpost program1

machid-see machid program1

nude-see nude program1

onee-see onee program1

pbf-see pbf program1

polar-see polar program1

post-see post program1

pre-see pre program1

probe-see probe program1

rci-see rci program1

rwr-see rwr program1

scf-see scf program1

sole-see sole program1

solv-see solv program1

timex-see timex program1

jaguar results command 1, 2

jaguar.hosts file 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

jaguar.style file 1

jexec program 1

Job directory, local 1, 2

Job name 1, 2, 3, 4, 5

Job Status window 1, 2, 3

K

Keyword settings

input keyword for echoing in output 1

Keywords

atomic mass 1, 2

dealiasing function 1

DFT 1

files output 1

frequency-related 1

geometry optimization 1

grid 1

GVB 1

initial guess 1

lewis dot structure 1

LMP2 1

localization 1

memory usage 1

orbital output 1

properties 1

SCF iteration 1

SCF method 1

solvation 1

standard output 1

transition state 1

Killing jobs 1, 2

L

LDA (local density approximation) 1

Least-squares operator Q, description of 1

Level shifting 1, 2

input keyword for 1

to help SCF convergence 1

Lewis dot structure

.lewis file 1, 2, 3

input keywords for 1, 2

setting GVB pairs from 1, 2

setting van der Waals radii from 1, 2, 3, 4

Lewis dot structure keywords 1

Linear synchronous transit (LST) methods-see QST-guided transition state searches1

LMP2 calculations

setting up 1

lmp2 input file section 1

LMP2 keywords 1

LMP2 method 1, 2, 3, 4, 5

applying counterpoise corrections with 1

description of pseudospectral implementation 1, 2

grid used for 1

input keywords for 1

output from 1

LMP2 pairs

delocalization of 1, 2, 3

input file section for 1, 2, 3, 4, 5

input keywords for 1, 2

lmp2 program 1

output from 1

LMP2 window

output from 1

lmp2der program 1

lmp2dip program 1

lmp2gda program 1

lmp2gdb program 1

output from 1

Local density approximation (LDA) 1, 2

Local job directory 1, 2

Local local MP2 method 1, 2, 3

grid used for 1

input file section for 1, 2, 3

input keywords for 1, 2, 3

Local MP2 method 1, 2, 3, 4, 5

applying counterpoise corrections with 1

description of pseudospectral implementation 1, 2

grid used for 1

input keywords for 1

output from 1

Local MP2 settings 1

Local MP2 window 1, 2

Localization keywords 1

Localization of orbitals

at end of calculation 1, 2

for LMP2 1

with Boys method 1

input keywords for 1, 2, 3, 4

with Pipek-Mezey method 1, 2

input keywords for 1, 2, 3, 4

loclmp2 program 1

locpost program 1

log file 1, 2, 3, 4, 5

description and format 1, 2

M

machid program 1

MacroModel .dat files 1

reading from Jaguar interface 1

mass input type 1

Masses

for frequency calculations 1

input keyword for 1, 2

setting in atomic section 1, 2

Maximum number of iterations for geometry convergence 1, 2, 3

input keyword for 1

Maximum number of SCF iterations 1, 2

input keyword for 1

Memory

input keywords for 1, 2

troubleshooting related to 1

Memory usage keywords 1

Memory, disk and i/o information output option

input keyword for 1

Memory, disk, and i/o information output option 1

Methanol 1

Method options 1

Methods window 1, 2

accuracy level 1, 2

analytic corrections 1

convergence issues 1, 2

initial guess selection in 1, 2

input keywords for 1, 2

localization of orbitals 1

output from 1, 2

symmetry, use of in 1

wavefunction type selection in 1, 2

Molden orbitals file (.molf file) output option 1

input keyword for 1

Molecular charge 1

input keyword for 1

Molecular properties

calculating output from 1, 2

Molecular properties, calculating 1, 2

Molecular state keywords 1

Molecular structure-see Geometry input or Geometry optimization1

Møller-Plesset second-order perturbation theory-see MP21

MOPAC, interface from Jaguar to 1, 2

Mouse functions 1

MP2 (Møller-Plesset second-order perturbation theory) 1, 2, 3, 4, 5

input keywords for 1

optimization output for local MP2 1, 2

output from 1

MQM basis set (.bas file) output option

input keyword for 1

mulk input type 1

Mulliken population analysis 1, 2

ch program 1

for basis functions 1

output from 1

input keyword for 1

output from 1, 2

recalculating multipole moments from 1, 2

output from 1, 2

Mulliken spin populations 1

multip input type 1

Multiple Jaguar jobs

running from Jaguar interface 1, 2

running with jaguar batch 1, 2

Multiplicity 1

input keyword for 1

output from 1

Multiplicity keywords 1

Multipole moments 1, 2, 3

calculating 1, 2

ch program 1

ESP fitting

constraining to reproduce multipole moments 1, 2, 3, 4, 5

recalculating multipole moments from 1, 2, 3, 4

input keyword for 1

lmp2dip program 1

Mulliken population analysis, recalculating multipole moments from 1, 2, 3, 4

output from 1, 2

output in atomic units 1

tensors listed in output 1

units in output 1

Multipole moments in atomic units also output option 1

Murtagh-Sargent method

for Hessian refinement

input keyword for 1

for Hessian updating

input keyword for 1

N

Natural Bond Orbital calculations 1, 2, 3

NBO calculation, requesting 1

NBO calculations 1, 2, 3

output from 1

nbo inpu file section 1

Neighbor ranges 1, 2, 3, 4

New geometry, inputting 1, 2

Newton-Raphson step

output of maximum and RMS for geometry optimization

input keywords for 1

Nice option for "jaguar run" command 1

Nitrobenzene 1

NLDA (non-local density approximation) 1, 2

Non-local density approximation (NLDA) 1, 2, 3

Nuclear repulsion energy 1, 2, 3, 4, 5

Nuclear-point charge energy from solvation calculations 1

Nuclear-solvent energy from solvation calculations 1

nude program 1

Number of iterations for geometry convergence, maximum 1, 2, 3

input keyword for 1

Numeric updating of Hessian

input keyword for 1

Numerical gradient of energy 1

input keywords for 1, 2

output from 1, 2

Numerical Hessian, printing in output 1

Numerical methods 1, 2, 3

.cutoff file determination of 1

input keyword for 1

Numerical second derivative of energy 1

input keywords for 1, 2

nude program 1

output from 1, 2

updating

input keyword for 1

O

OCBSE convergence scheme 1

output from 1

onee program 1

output from 1, 2, 3

One-electron Hamiltonian output option 1

input keyword for 1

One-electron integrals 1

calculation with program onee 1

energy contribution listed in output 1, 2

for solvation 1, 2, 3

Open shell singlet 1

Open-shell systems 1, 2, 3

Optimization window 1, 2

output from 1, 2, 3

Optimizing

transition states 1

Optimizing geometry 1, 2

calculating forces only 1

der1a and der1b programs 1

input keyword for 1

constraining bond lengths or angles 1, 2, 3, 4, 5, 6

input keywords for 1

output from 1

constraining Cartesian coordinates 1, 2, 3, 4

convergence criteria 1, 2, 3

gradient-related only 1

input keywords for 1, 2, 3

convergence criterion for SCF 1

detailed output 1

fixed bond lengths or angles for 1, 2

input keywords for 1

output from 1

fixed Cartesian coordinates for 1, 2

frozen bond lengths or angles for 1, 2, 3, 4

frozen Cartesian coordinates for 1, 2

GDIIS method

input keyword for 1

generating input with new geometry 1

geopt program 1

in solution 1

output from 1

without gas phase calculation 1, 2

initial Hessians for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

input file section 1, 2, 3

input keyword for 1

input keywords for 1, 2

limiting step size for 1, 2

input keywords for 1, 2

maximum number of iterations for convergence 1, 2, 3

input keyword for 1

output from 1, 2, 3

bond lengths and angles 1, 2

forces table 1

refinement of initial Hessian for 1, 2, 3, 4, 5, 6, 7, 8, 9

tips 1, 2

troubleshooting 1

trust radius for 1, 2

input keywords for 1, 2

updating of Hessian during

input keyword for 1

Orbital energy 1

Orbital output keywords 1

Orbital reordering 1

Orbitals

combining using orbman section 1, 2

information in output 1, 2, 3, 4, 5, 6, 7, 8

GVB orbitals 1, 2, 3, 4, 5, 6

input keywords for printing 1, 2, 3

Orbitals output options

How: 1, 2, 3

What: 1

When: 1, 2

plotting with plot section 1, 2

reordering using orbman section 1, 2

Orbitals output options 1, 2

How 1

input keywords corresponding to 1, 2

printing orbitals-How: 1, 2, 3

input keywords for 1, 2

printing orbitals-What: 1

all orbitals 1, 2, 3

GVB orbitals 1, 2

input keywords for 1

occupied orbitals 1, 2, 3

printing orbitals-When: 1, 2

after final localization 1

after GVB initial guess is generated 1

after HF initial guess is generated 1, 2

after SCF iterations 1

at end of job 1

each iteration (in AO space) 1

each iteration (in CO space) 1, 2

input keywords for 1

What 1

When 1

orbman input file section 1

Order of Jaguar programs run, specifying 1, 2, 3

Organometallics

improving convergence 1, 2, 3

Output file 1, 2, 3, 4, 5, 6, 7

echoing input file in output 1

effect of calculation options on content 1, 2

Files output settings 1, 2

general description 1, 2

Orbitals output settings 1, 2

Per Iteration output settings 1, 2

Standard output settings 1, 2

summarizing 1, 2

viewing in interface window 1, 2

Output file changes

basis set calculations 1

DFT calculation options 1

frequency, IR, and thermochemistry calculations 1

geometry and transition state optimizations 1

geometry optimizations in solution 1

GVB calculations 1

GVB-RCI calculations 1

LMP2 calculation options 1

methods other than DIIS 1

non-default properties selections 1

optimizations with GVB-RCI wavefunctions 1

solvation calculations 1

Output options 1, 2

Files output options 1, 2

input keywords corresponding to 1, 2

Orbitals output options 1, 2

input keywords corresponding to 1, 2

Per Iteration output options 1, 2

input keywords corresponding to 1, 2

Standard output options 1, 2

bond lengths and angles 1

connectivity table 1

detailed timing information 1

echo input file and parameter list 1

Gaussian function list (basis set) 1

Gaussian function list (derivatives) 1

geometries in atomic units also 1

geometry optimization details 1

input keywords corresponding to 1, 2

memory, disk, and i/o information 1

multipole moments in atomic units also 1

one-electron Hamiltonian 1

overlap matrix 1

Output, summarizing 1, 2

Output-see Output file, Output options, Standard output options, Files output options, Per Iteration output options, Orbitals output, Babel1

Overlap matrix

eigenvector and eigenvalue output option

input keyword for 1

in DIIS error vector 1, 2

smallest eigenvalue, listed in output 1

Overlap matrix output option 1

input keyword for 1

P

Parallel

jobs that can't be run in 1

running jobs in 1, 2

Parallel Jaguar module

about 1

installing 1

supported platforms 1

system requirements

HP 1

IBM 1

SGI 1

Sun 1

path input file section 1

Path specifying order of programs 1

input file section for 1, 2

pbf program 1, 2

output from geometry optimizations 1

Per Iteration output options 1, 2

All J and K matrices, AO space 1

Coulomb and exchange matrices output option 1, 2

density matrix 1

density matrix output option 1

energy components 1

energy components output option 1

Fock matrix in AO (HF) or MO (GVB) space 1

Fock matrix in CO space 1

Fock matrix output options 1

GVB data output option 1

GVB f, a, b, ci, and other coefficients 1

input keywords corresponding to 1, 2

perl 1, 2

Physical constants and conversion factors

input keyword for 1

Pipek-Mezey localization 1, 2

input keywords for 1, 2, 3, 4

orbital printing 1

pKa calculation

ab initio 1

conformational flexibility in 1

empirical corrections in 1

equivalent sites in 1, 2

geometry optimization in 1

initial geometry in 1

input files for 1

monitoring 1

multiple protonation sites in 1, 2

running 1

single point energies in 1

solvation free energy in 1

theory 1

pKa prediction module

installing 1

introduction 1

parameterization results 1

parameterized functional groups 1

results 1, 2, 3

Plot data, generating 1

plot input file section 1

Point charges, input file section for 1, 2

pointch input file section 1

Poisson-Boltzmann equations 1

Poisson-Boltzmann solver 1, 2

polar program 1

Polarizability 1, 2, 3, 4

input keywords for 1, 2, 3

output from 1

post program 1

output from 1

for solvation 1

Post-SCF DFT calculations 1

Potential

plotting with plot section 1, 2

Potential energy surface scan 1, 2

Powell method

for Hessian refinement

input keyword for 1

for Hessian updating

input keyword for 1

pre program 1, 2

output from 1

for geometry optimization 1

for solvation 1

Pressure for thermochemical calculations 1

input keyword for 1

output 1

P-RFO level shifting

input keyword for 1

probe program 1, 2

Probe radius of solvent 1, 2, 3

Program order, specifying 1, 2, 3

Programs in Jaguar-see relevant program name or Jaguar programs1

Properties keywords 1

Properties window 1, 2

electron density 1

ESP charge fitting 1, 2

Mulliken population analysis 1, 2

multipole moments 1

output from 1, 2

polarizability and hyperpolarizability 1, 2

Pseudospectral method, explanation of 1, 2

publications, citing Jaguar in 1

Q

QST-guided transition state searches 1, 2

additional structures for 1, 2

input keyword for 1

LMP2 delocalization for 1, 2

Quadratic energy error

input keyword for output 1

Quadratic synchronous transit-see QST-guided transition state searches1

Quit option 1, 2

R

Radian units for geometry input 1

RCI (restricted configuration interaction) calculations 1, 2, 3, 4, 5

optimization output 1, 2

output from 1, 2

rci program 1

rci program 1

Read window 1, 2

Reading input files 1, 2

file types 1, 2, 3

reading geometry input 1, 2

troubleshooting 1

Realigning and recentering geometry 1

Reorganization energy 1

Reset option 1

Resolution 1

RESP file output option

input keyword for 1

Restarting jobs 1, 2, 3, 4, 5, 6, 7, 8

Restricted configuration interaction-see RCI calculations1

Restricted open-shell wavefunctions 1, 2

input keyword for 1

Results, reporting

final 1

for each atom 1

intermediate 1

RFO level shifting

input keyword for 1

RODFT-see Restricted open-shell wavefunctions1

ROHF-see Restricted open-shell wavefunctions1

Run window 1, 2, 3, 4, 5, 6, 7

Running jobs 1, 2, 3, 4

by hand (outside the interface) 1, 2

by hand (outside the interface), 1

from the interface 1, 2, 3, 4

troubleshooting 1, 2

rwr program 1, 2

output from 1, 2, 3

S

Sample calculation 1, 2

Save window 1, 2, 3, 4, 5

Scaling frequencies 1

input keywords for 1

Scanning 1, 2, 3

SCF energy output 1, 2

SCF iteration keywords 1

SCF iterations maximum number of

input keyword for 1

SCF iterations, maximum number of 1, 2

SCF level shift 1

SCF method keywords 1

scf program 1

HF then GVB 1

output from 1

output from 1, 2, 3, 4, 5, 6, 7

for solvation 1, 2, 3, 4

use in solvation calculations 1

SCHRODINGER directory 1, 2

SCHRODINGER environmental variable 1, 2

SCRF method for solvation calculations 1, 2, 3

energy output 1

output from 1, 2

Search method, transition state 1

Searching

along paths and eigenvectors 1

Second derivative of energy

input keyword for updating numerical calculation of 1

input keywords for numerical calculation of 1, 2

nude program 1

numerical calculation of

output from 1, 2

Self-consistent reaction field method for solvation calculations 1, 2, 3

energy output 1

output from 1, 2

Shells

for grids 1, 2

information in output 1, 2, 3, 4, 5

Simons' method for trust radius adjustment

input keyword for 1

Singlet, open shell 1

sole program 1

output from 1

Solute cavity energy 1, 2

Solution phase energy from solvation calculations 1, 2

solv program 1

output from 1

Solvation 1, 2, 3, 4

choosing van der Waals radii for 1

from .lewis file 1, 2

input file sections for 1, 2, 3

input keyword for 1

convergence criterion for 1

input keyword for 1

dsolv program 1

energy output 1, 2, 3

electron-nuclear energy 1

first shell correction factor 1

nuclear-solvent energy 1

reorganization energy 1

solute cavity energy 1, 2

solution phase energy 1, 2

solvation energy 1, 2

total solvent energy 1

input keywords for 1, 2

molecular surface for 1

output from 1, 2, 3

restarting calculation with new input file 1

sole program 1

solv program 1

solvent choice for 1, 2

input keywords for 1, 2

Solvation energy 1, 2

Solvation energy convergence criterion

input keyword for 1

Solvation keywords 1

Solvation window 1, 2

output from 1, 2

Solvent choice for solvation calculations 1, 2

input keywords for 1, 2

Solvent parameters 1

SPARTAN

archive files, generating with Jaguar 1

input keyword for 1

Spectral information 1, 2

input keyword for 1

output 1

Spin multiplicity 1

input keyword for 1

output from 1

Spin populations, Mulliken 1

SQM frequency scaling method 1

Stage 1

Standard output keywords 1

Standard output options 1, 2, 3

bond lengths and angles output option 1

connectivity table output option 1

detailed timing information output option 1

echo input file and parameter list 1

Gaussian function list in output

for basis set 1, 2

for derivatives of basis functions 1

geometries in atomic units also output option 1

geometry optimization details output option 1

input keywords corresponding to 1, 2

memory, disk, and i/o information output option 1

multipole moments in atomic units also output option 1

one-electron Hamiltonian output option 1

overlap matrix output option 1

State window 1

Structure, input-see Geometry input1

Structure, optimizing-see Geometry optimization1

Submitting jobs-see Running jobs1

Summarizing results 1, 2

Superblocks 1

Symmetrizing geometry input 1, 2, 3, 4

finding point group 1

tolerance 1

Symmetry point group, reported in output 1

Symmetry, use of in calculation 1, 2, 3, 4, 5, 6

input keywords for 1, 2

specifying for GAUSSIAN 92 input 1

Symmetry-related keywords 1

Synchronous transit quasi-Newton methods-see QST-guided transition state searches1

System properties, calculating 1, 2

T

Technical support 1

Temp directory 1, 2, 3, 4, 5, 6

errors related to 1, 2

jaguar.hosts specification of 1, 2, 3

Temperatures for thermochemical calculations 1, 2

input keywords for 1

output 1

Temporary directory

saving at end of job 1

Temporary directory-see Temp directory1

Temporary files 1

saving at end of job 1

Thermochemical properties 1, 2

input keywords for 1, 2

output 1

Time stamps to log file option for "jaguar run" command 1

timex program 1

Timing 1

Total solvent energy from solvation calculations 1

Transition metals 1

improving convergence 1, 2, 3

initial guess for 1

Transition state keywords 1

Transition state optimization 1, 2

constraining bond lengths or angles 1, 2

input keywords for 1

convergence criteria 1

gradient-related only 1

input keywords for 1, 2, 3

convergence criterion for SCF 1

eigenvector following in 1

input keywords for 1

fixed bond lengths or angles for

input keywords for 1

frozen bond lengths or angles for 1, 2

in solution 1

without gas phase calculation 1, 2

initial Hessians for 1, 2, 3, 4, 5, 6, 7, 8, 9

input keyword for 1

input keywords for 1, 2

level shifting of Hessian

input keyword for 1

limiting step size for 1

input keywords for 1, 2

maximum number of iterations for convergence 1

input keyword for 1

output from 1, 2

refinement of initial Hessian for 1, 2, 3, 4, 5, 6, 7, 8, 9

trust radius for 1

input keywords for 1, 2

updating of Hessian during

input keyword for 1

Transition state search method 1

Trial wavefunction-see Initial guess1

Troubleshooting 1, 2

Trust radius for optimizations 1, 2

adjustment during optimization 1

input keywords for 1, 2

application of during optimization

input keyword for 1

input keywords for 1, 2

twm window manager 1

Two-electron integrals 1

energy contribution listed in output 1, 2, 3

breakdown into J and K parts 1, 2

U

UDFT-see Unrestricted wavefunctions1

UHF-see Unrestricted wavefunctions1

Uncontracted basis functions 1, 2

Unrestricted wavefunctions 1, 2

input keyword for 1

V

van der Waals radii 1

for solvation calculations 1

input file sections for 1, 2, 3

input keyword for 1

listed in output 1

setting from Lewis file data 1

van der Waals surface 1

Variables in geometry input 1, 2, 3, 4, 5, 6, 7, 8

vdw input type 1

vdw2 input type 1

Vibrational frequencies 1

freq program 1

input keywords for 1, 2

output 1, 2

scaling 1

input keywords for 1

View File button 1, 2, 3

virial ratio 1

Virtual orbitals

number in output 1

output 1, 2

W

Water 1

Wavefunction type 1

What: Orbitals output options 1

all orbitals 1, 2, 3

GVB orbitals 1, 2

input keywords for 1

occupied orbitals 1, 2, 3

When: Orbitals output options 1, 2

after Boys localization

input keyword for 1

after final localization 1

after GVB initial guess is generated 1

input keyword for 1

after HF initial guess is generated 1, 2

input keyword for 1

after SCF iterations 1

input keyword for 1

at end of job 1

each iteration (in AO space) 1

input keyword for 1

each iteration (in CO space) 1, 2

input keyword for 1

input keywords for 1

X

XYZ file (.xyz file) output option 1

Z

Zero point energies-see Thermochemical properties1

zmat input file section 1

zmat2 input file section 1

zmat3 input file section 1

Z-matrix format 1, 2, 3, 4, 5, 6

dummy atoms in 1

variables in 1, 2, 3, 4

zvar input file section 1

zvar2 input file section 1

zvar3 input file section 1

Schrödinger, Inc. http://www.schrodinger.com Voice: (503) 299-1150 Fax: (503) 299-4532 help@schrodinger.com Last updated: Thu Oct 11 19:11:27 2001