Index

Symbols

.visfile

control of, NOVIS, VIS=MIN

A

abbreviations, Abbreviations

active site, Use of Partial Charge Sparkles

acubegen , acubegen

afreqgen , afreqgen

AM1, NDDO Theory, AM1

AM1 elemental parameter sets, Defined Parameters

AM1-D3H4, AM1-D3H4

AM1-FS2, AM1-FS2

ampac , ampac

ampac10.key , Package Administration

AMPAC_DIR , Package Administration

AMSOL, AMSOL Model Module

example, AMSOL
keywords, AMSOL Dedicated Keywords
output, AMSOL Output

analytically computed gradients, Calculation of Gradient Norms

annealing, Non-local Optimization (ANNEAL, MANNEAL, GANNEAL, and TSANNEAL) (see simulated annealing)

APOLAR

example, APOLAR

arc2dat , arc2dat

ASCII density matrix, DENMAT, OLDMAT

atomic charges, Archive File (optimization/opt_gnorm.arc):

atomic masses, Archive File (optimization/opt_gnorm.arc):

atomic orbital electron populations, DENSITY

B

binary density matrix, DENOUT, OLDENS
bond angle, Geometry Specification, Internal Coordinates
bond length, Geometry Specification, Internal Coordinates
bond order, BONDS

C

canonically ordered MOs, PROTO

catcsm , catcsm

central finite difference, LTRD and NEWTON

characterization of stationary points, Characterization of Stationary Points

check_env.sh , check_env.sh

CHN, Finding Transition States (CHN and FULLCHN), CHN Methods

example, Finding a Specific Transition State (CHN)
keywords, CHN Dedicated Keywords
theory, CHN Theory

CI (see configuration interaction)

citation, Citation

col, Potential Energy Surfaces (PES), Characterization of Stationary Points

commands

acubegen , acubegen
afreqgen , afreqgen
ampac , ampac
arc2dat , arc2dat
catcsm , catcsm
dump_util , dump_util
haltampac , haltampac
keycleaner , keycleaner
mampac , mampac
rm_ampac_results , rm_ampac_results
visdump , visdump

comments, Title and Comments

complex points on potential surface, EF Strategies

Computational Methods, information from, Models and Results

config_ampac.sh, config_ampac.sh

configuration interaction, Configuration Interaction

example, A Simple Example of Using Configuration Interaction
excluded keywords, Keywords Incompatible With CI
extra input data, Reordering of MOs for CI
half-electron, Open-Shell RHF: The “Half-Electron” Method
input, CI Input
keywords, Configuration Interaction Dedicated Keywords
microstates, The Initial CI Microstate Space
theory, CI Theory

Connolly surface, CONNOLLY, SCALE

contour maps, GRAPH

contributors, Contributors

conventions, Conventions Used in This Manual

convergence, Fast SCF Convergence

CORE-CORE REPULSION ENERGY, Semiempirical Heats of Formation

COSMO, COSMO Solvation Model

example, COSMO
keywords, COSMO Dedicated Keywords

Coulson charges, Archive File ( properties/prop_esp_sto6g.arc ):

counterion, Sparkles, Use of Partial Charge Sparkles

crenel, MANNEAL

critical points, Potential Energy Surfaces (PES)

cyclohexane, Example I (“Floppy” system)

cyclooctatetraene, AMPAC™ Energy Minimizers Near Maxima

D

data files, Data Files

debugging, Debugging

density matrix

ASCII, DENMAT, OLDMAT
binary, DENOUT, OLDENS
final, DENSITY
in reaction pathway, Input File (rxnpath/rxnpath1.dat):

dihedral angle, Geometry Specification, Internal Coordinates

sign convention, Internal Coordinates

dipole moment, Archive File (optimization/opt_gnorm.arc):

dummy atoms, LTRD and NEWTON, Dummy Atoms

dump_util , dump_util

E

EF (see eigenvector following)

eigenvector following, Eigenvector Following

keywords, Dedicated EF Keywords
strategies, EF Strategies

eigenvectors, ALLVEC, VECTORS

electron spin resonance, ESR

ELECTRONIC ENERGY, Semiempirical Heats of Formation

electrostatic potential, Electrostatic Potential

background, ESP Notes and Background
charges, DIPOLE
example, Electrostatic Potential Charges (ESP)
integrals, ESP Integral Calculation
keywords, ESP Dedicated Keywords

entropy, Cartesian Frequencies and Thermodynamics (FORCE), THERMO

entropy of formation, Cartesian Frequencies and Thermodynamics (FORCE)

errors

reference, Error Messages

ESP (see electrostatic potential)

excited state, EXCITED

F

fast SCF convergence, Fast SCF Convergence

files

ampac10.key , Package Administration
data, Data Files
initialization, Package Administration
jobname.arc , Presenting Input to the Program, CHN Theory
jobname.dat , Presenting Input to the Program, EF Strategies, OLDENS, OLDMAT
jobname.den , EF Strategies, DENOUT, OLDENS, RESTART
jobname.dmt , DENMAT, OLDMAT
jobname.esp , ESP Integral Calculation, POTWRT
jobname.gpt , GRAPH
jobname.mrk , MARK
jobname.out , Presenting Input to the Program, CHN Theory
jobname.res , EF Strategies, HESS, RESTART
jobname.vis , CHN Theory
solvent data, solvent.data

force constant matrix, LTRD and NEWTON

non-stationary point, LET

force constants, FORCE

force matrix, FORCE

free energy of solvation, AMSOL Model Module

frequencies

Cartesian coordinates, FORCE
internal coordinates, LTRD
vibrational, LTRD and NEWTON, FORCE, LTRD

FULLCHN, Finding Transition States (CHN and FULLCHN)

G

geometry, Geometry Specification
geometry optimization, Geometry Optimization
gnorm, Characterization of Stationary Points, GNORM, GRADIENTS
gradient components, Calculation of Gradient Norms, GRADIENTS
gradient minimization, LTRD
gradient norm, GRADIENTS, LTRD
grid calculation, Two-Dimensional Grid Search, GRID, STEP1, STEP2
grid search, Two-Dimensional Grid Search

H

half-electron, Open-Shell RHF: The “Half-Electron” Method

haltampac , haltampac

heat capacity, THERMO

heat of formation, Semiempirical Heats of Formation, AMSOL Output, Archive File (optimization/opt_gnorm.arc):

Hessian matrix, LTRD and NEWTON, Potential Energy Surfaces (PES), Eigenvector Following, FORCE, HESS, LTRD, THERMO

2-point finite difference, HESSIAN2
4-point finite difference, HESSIAN4
initial guess, LINDH
lowest eigenvalues, HESSEI

hilltop, Potential Energy Surfaces (PES), Characterization of Stationary Points

HUMAN FACTOR, A General Philosophy for Semiempirical Parameterization

hybridization, PI

hyperpolarizability, Polarizability Methods

I

index of refraction, COSMO Solvation Model, AMSOL Model Module

init_ampac.csh , Package Administration

init_ampac.sh , Package Administration

input, Presenting Input to the Program

dummy atoms, Dummy Atoms

extra data, Extra Input Data

connectivity, Input Connectivity Data
limits (annealing), Limits for Simulated Annealing
old format, Extra Input Data Using Old Format
PEN2 groupings (annealing), PEN2 Groupings for Simulated Annealing
properties, External Property Data
reaction coordinate, Reaction Coordinate Values
RECLAS (C.I.), Reordering of MOs for CI
symmetry, Symmetry Definition
T.V. weights, Transition Vector Weights
transition vector, Transition Vector Information

geometry, Geometry Specification

keywords, Keywords

sparkles, Dummy Atoms

z-matrix, Internal Coordinates

installation, Package Administration

internal coordinates, LTRD and NEWTON, Geometry Specification

internal energy, THERMO

intrinsic reaction coordinate, IRC

example, Intrinsic Reaction Coordinate (IRC) Calculation

ionization potential, Archive File (optimization/opt_gnorm.arc):

IR (infrared) spectra, Computational Chemistry in Context

J

Jacobian matrix, LTRD and NEWTON

K

keycleaner , Dealing with Corrupted Keyfiles, keycleaner

keyword reference, Keyword Reference

keywords, Keywords

debugging, Debugging

in input file, Keywords

listed by topic, Topical List of Major Keywords Used in AMPAC™

AMSOL, AMSOL
annealing, Annealing
CHN methods, CHN Methods
CODESSA™ , CODESSA™
compatibility, Compatibility
Configuration Interaction, Configuration Interaction / Spin State
COSMO, COSMO
dispersion, Dispersion and Hydrogen Bonding Corrections
EF, Eigenvector Following
eigenvector following, Eigenvector Following
electrostatic potential, Electrostatic Potential
esp, Electrostatic Potential
general controls, General Controls
hydrogen bonding, Dispersion and Hydrogen Bonding Corrections
methods, Methods
optimization, Geometry Optimization, Transition State Location, CHN Methods
output controls, Output Controls
population analysis, Population Analysis
properties, Properties
restart, Restart
SCF convergence, SCF Convergence
simulated annealing, Annealing
solvation, Solvation
Sparse matrix keywords, Sparse Matrix Keywords
spin state, Configuration Interaction / Spin State
SYBYL® , SYBYL®
transition state, Transition State Location, CHN Methods

obsolete, Obsolete Keywords

reference, Keyword Reference

specification, Specification of Keywords

kinetic isotope effect, ISOTOPE

Koopman’s theorem, Archive File (optimization/opt_gnorm.arc):

KPOLAR

example, KPOLAR

L

large molecules, Large Molecule Calculations (PSOLVE and SPARSE), Sparse Matrices, A Large Molecule using Sparse Matrices (SPARSE, PSOLVE)

lewis dot structure

example, Analyzing the Lewis Dot Structure of a Molecule (LEWIS)

license, License Administration

ampac10.key , Installing the ampac10.key Key File
determining status of, Getting License Information from AMPAC™
expiration date, Getting License Information from AMPAC™

literature references, References

local geometric minima, Simulated Annealing

local minimizers, Simulated Annealing

M

mampac , mampac

methyl rotations, Internal Coordinates

microstates, The Initial CI Microstate Space

microwave spectral bands, Cartesian Frequencies and Thermodynamics (FORCE)

MINDO3, MINDO3

MINDO3 atom pair parameters, Defined Parameters

MNDO, NDDO Theory, MNDO

electrostatic potential, SLOPE
MNDO elemental parameter sets, Defined Parameters

MNDO/d, MNDOD

MNDO/d elemental parameter sets, Defined Parameters

MNDO/ESP, SLOPE

MNDOC, MNDOC

MNDOC elemental parameter sets, Defined Parameters

molecular formula, Archive File (optimization/opt_gnorm.arc):

Mulliken-type population analysis, MULLIKEN

multiple minima, Simulated Annealing

N

Natural Bond Orbital (NBO) analysis, NBO

nbo

example, Natural Bond Orbital Analysis (NBO)

NC-PM6, NC-PM6

NDDO, NDDO Theory

negative eigenvalue, PATH Calculation with Transition Vector

neglect of diatomic differential overlap, NDDO Theory

new features, New Features in AMPAC 10

Newton algorithm, LTRD and NEWTON, NEWTON

non-linear optics, Polarizability Methods, KPOLAR

non-local optimization, Non-local Optimization (ANNEAL, MANNEAL, GANNEAL, and TSANNEAL)

numerical energy derivatives, DERINU

numerically computed gradients, Calculation of Gradient Norms

O

optimization flags, Internal Coordinates, Symmetry Definition, Reaction Coordinate Values
oscillator strengths, Transition Dipole Moments and Oscillator Strengths

P

parameter sets, Defined Parameters

parameterization, A General Philosophy for Semiempirical Parameterization

partial charges, Ouput File (optimization/opt_gnorm.out):

(see also atomic charges)

partition function, THERMO

penalty functions, Annealing Methods, Penalty Functions, Example I (“Floppy” system)

pi bonds, PI

PM3, NDDO Theory, PM3

PM3 elemental parameter sets, Defined Parameters

PM3-D3H4, PM3-D3H4

PM6, PM6, PM6

PM6 elemental parameter sets, Defined Parameters

PM6-D3H4, PM6-D3H4

polarizability, Polarizability Methods, APOLAR, KPOLAR

alpha, Polarizability Methods
beta, Polarizability Methods
first order, Polarizability Methods
gamma, Polarizability Methods
second order, Polarizability Methods
third order, Polarizability Methods

Polarizability

keywords, Polarizability Keywords

polarization functions, Sparkles

potential energy surface, Potential Energy Surfaces (PES)

principal moments of inertia, Cartesian Frequencies and Thermodynamics (FORCE)

program

set up, Package Administration

Q

quenching, Quenching, NOQUENCH

R

Raman spectra, Computational Chemistry in Context

reaction coordinate, Characterization of Stationary Points, Internal Coordinates, Reaction Coordinate Values, One-Dimensional Reaction Pathway

extra input data, Reaction Coordinate Values

reaction gradient, Archive File (rxnpath/rxnpath1.arc):

reaction path, Integration of a Reaction Path in PATH or IRC

reaction pathway (see reaction coordinate)

reduced masses, ISOTOPE

reference wavefunction, CI Theory, Open-Shell RHF: The “Half-Electron” Method

references, References

ridge, Potential Energy Surfaces (PES), Characterization of Stationary Points

RM1, RM1, RM1

RM1 elemental parameter sets, Defined Parameters

RM1-D3H4, RM1-D3H4

rm_ampac_results , rm_ampac_results

rotational contribution, ROT

rotational symmetry, ROT

S

saddle point, Potential Energy Surfaces (PES), Characterization of Stationary Points

SAM1, General Theoretical Basis of SAM1, SAM1

SAM1 elemental parameter sets, Defined Parameters

SAM1D, SAM1D

SAM1D elemental parameter sets, Defined Parameters

SCF convergence, Fast SCF Convergence, SCFMAX

criteria, Criteria and Accuracy in SCF Convergence

SCF convergence criteria, Criteria and Accuracy in SCF Convergence

second derivative matrix, ISOTOPE

(see also Hessian matrix)

Set_File_Protection.sh , Set_File_Protection.sh

sigma bonds, PI

simulated annealing, Non-local Optimization (ANNEAL, MANNEAL, GANNEAL, and TSANNEAL), Simulated Annealing

crenel, MANNEAL
examples, Example I (“Floppy” system), Example II (“Rigid” System)
extra input data, PEN2 Groupings for Simulated Annealing, Limits for Simulated Annealing
filtering, Filtering
keywords, Simulated Annealing Dedicated Keywords
methods, Annealing Methods
quenching, Quenching
strategies, Strategies for Annealing Searches
theory, Simulated Annealing Theory

solvation models

AMSOL, AMSOL Model Module
COSMO, COSMO Solvation Model

solvent, Use of Partial Charge Sparkles

descriptors in AMSOL, AMSOL Output, SOLVNT
integration in COSMO, Solvation Integration
parameters in COSMO, Solvent Parameters, Updated Parameters

solvent-accessable surface, Solvation Integration

solvent-accessable surface area, AMSOL Output

sparkles, Dummy Atoms, Sparkles, Polarizability Methods, Use of Partial Charge Sparkles

sparse matrix

description, Steps in a Sparse Matrix Calculation
keywords, Limitations/Restrictions for Sparse Matrix Calculations, Sparse Matrix Dedicated Keywords
theory, Large Molecule Calculations (PSOLVE and SPARSE), Sparse Matrices, Solving for the Density Matrix, Density Matrix Purification, Sparse Matrix Form (Fixed Form vs Let it Grow Strategies), Considerations for a Sparse Matrix Calculation, Optimization of Very Large Molecules

Sparse Matrix Methods, Sparse Matrix Methods

example, A Large Molecule using Sparse Matrices (SPARSE, PSOLVE)

Special PM6 Correction Terms, Special PM6 Correction Terms

spin density, SPIN

unpaired, ESR

spin matrix, SPIN

spin state, CI Theory, DOUBLET, n-ET, NONET, OCTET, QUARTET, QUINTET, ROOT, SEPTET, SEXTET, SINGLET, TRIPLET

stationary points, Potential Energy Surfaces (PES)

characterization of, Characterization of Stationary Points

summary section, Archive File (optimization/opt_gnorm.arc):

super saddle point, Potential Energy Surfaces (PES), Characterization of Stationary Points

symmetry, Symmetry Definition, SYMMETRY

extra input data, Symmetry Definition
functions, Symmetry Definition

T

thermodynamic quantities, ROT

thermodynamic values, THERMO

title, Title and Comments

topology of the potential surface, Integration of a Reaction Path in PATH or IRC

torsional angle, Internal Coordinates

tortional angle, Internal Coordinates

transition dipole moment, Transition Dipole Moments and Oscillator Strengths

transition metals, A General Philosophy for Semiempirical Parameterization, The Computational Challenges of Transition Metal Systems

transition state, Potential Energy Surfaces (PES), Transition States, Intrinsic Reaction Coordinate (IRC), One-Dimensional Reaction Pathway, Two-Dimensional Grid Search, PATH (see approximate)

transition state location

by CHN, CHN
by LTRD, LTRD
by reaction coordinate, One-Dimensional Reaction Pathway
by simulated annealing, MANNEAL
methyl rotations, Internal Coordinates

transition states, Finding Transition States (CHN and FULLCHN)

transition vector, PATH Calculation with Transition Vector

extra input data, Transition Vector Weights, Transition Vector Information

troubleshooting, Troubleshooting

U

unpaired spin density, ESR

utilities

acubegen , acubegen
afreqgen , afreqgen
ampac , ampac
arc2dat , arc2dat
catcsm , catcsm
check_env.sh , check_env.sh
config_ampac.sh , config_ampac.sh
dump_util , dump_util
haltampac , haltampac
keycleaner , keycleaner
mampac , mampac
reference, Utilities
rm_ampac_results , rm_ampac_results
Set_File_Protection.sh , Set_File_Protection.sh
visdump , visdump
xglinfo.exe , xglinfo.exe

UV/visible spectra, Introduction, CI Theory

V

valence-bond, LOCALIZE
valences, BONDS
vibrational frequencies, LTRD and NEWTON, FORCE, LTRD
vibrational spectra, Computational Chemistry in Context
visdump , visdump

W

Williams surface, SYMAVG

X

xglinfo.exe , xglinfo.exe

Z

z-matrix, Geometry Specification, Internal Coordinates
zero point energy, LTRD and NEWTON


VERBOSESMxx