A
- abbreviations, Abbreviations
- active site,
- acubegen, Description
- AM1, NDDO Theory, AM1
- AM1 elemental parameter sets, Defined Parameters
- ampac, Description
- ampac.key, Package Administration
- AMPAC_DIR, Package Administration
- AMSOL, AMSOL Model Module
- activation of, The Amsol Solvation Model Module
- example, Example Calculation
- keywords, AMSOL Dedicated Keywords
- license, The Amsol Solvation Model Module
- output, AMSOL Output
- analytically computed gradients, Calculation of Gradient Norms
- annealing, Non-local Optimization (ANNEAL, MANNEAL, GANNEAL, and TSANNEAL) (see simulated annealing)
- APOLAR
- example, Example Calculation: APOLAR
- arc2dat, Description
- 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
C
- canonically ordered MOs, PROTO
- Capabilities of , Summary of AMPAC 8 Capabilities
- catcsm, Description
- central finite difference, LTRD and NEWTON
- characterization of stationary points, Characterization of Stationary Points
- check_env.csh, Description
- CHN, Finding Transition States (CHN and FULLCHN), CHN Methods
- example, Example Calculation
- keywords, CHN Dedicated Keywords
- theory, CHN Theory
- CI (see configuration interaction)
- citation, Citation
- col, Potential Energy Surfaces (PES), Characterization of Stationary Points
- commands
- acubegen, Description
- ampac, Description
- arc2dat, Description
- catcsm, Description
- haltampac, Description
- keycleaner.exe, Description
- mampac, Description
- rm_ampac_results, Description
- visdump, Description
- comments, Title and Comments
- complex points on potential surface, EF Strategies
- Computational Methods, information from, Models and Results
- configuration interaction, Configuration Interaction
- example, CI Output
- excluded keywords, Keywords Incompatible With CI
- extra input data, Reordering of MOs for CI
- half-electron, The Half-Electron Method
- input, CI Input
- keywords, Configuration Interaction Dedicated Keywords
- microstates, The Initial CI Microstate Space
- theory, CI Theory
- config_ampac.csh, Description
- 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, Example Calculation
- keywords, COSMO Dedicated Keywords
- Coulson charges, Archive File (properties/prop_esp_sto6g.arc) :
- counterion, Sparkles,
- crenel, MANNEAL
- critical points, Potential Energy Surfaces (PES)
- cyclohexane, Example I ("Floppy" system)
- cyclooctatetraene, 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
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, Example Calculation
- integrals, ESP Integral Calculation
- keywords, ESP Dedicated Keywords
- entropy, Ouput File (properties/prop_thermo_trans.out) :, THERMO
- entropy of formation, Ouput File (properties/prop_thermo_trans.out) :
- errors
- reference, Error Messages
- ESP (see electrostatic potential)
- excited state, EXCITED
F
- fast SCF convergence, Fast SCF Convergence
- files
- ampac.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, , GRID, STEP1, STEP2
- grid search,
H
- half-electron, The Half-Electron Method
- haltampac, Description
- 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
- limits (annealing), Limits for Simulated Annealing
- old format, Extra Input Data Using Old Format
- PEN2 groupings (annealing), PEN2 Groupings for Simulated Annealing
- 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
- intallation, Package Administration
- internal coordinates, LTRD and NEWTON, Geometry Specification
- internal energy, THERMO
- intrinsic reaction coordinate, , IRC
- ionization potential, Archive File (optimization/opt_gnorm.arc) :
- IR (infrared) spectra, Computational Chemistry in Context
K
- keycleaner, Dealing with Corrupted Keyfiles
- keycleaner.exe, Description
- 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
- compatibility, Compatibility
- Configuration Interaction, Configuration Interaction / Spin State
- COSMO, COSMO
- EF, Eigenvector Following
- eigenvector following, Eigenvector Following
- electrostatic potential, Electrostatic Potential
- esp, Electrostatic Potential
- general controls, General Controls
- 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
- 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, Example Calculation: KPOLAR
M
- mampac, Description
- methyl rotations, Internal Coordinates
- microstates, The Initial CI Microstate Space
- microwave spectral bands, Ouput File (properties/prop_thermo_trans.out) :
- 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, MULLIK
- multiple minima, Simulated Annealing
N
- NDDO, NDDO Theory
- negative eigenvalue,
- neglect of diatomic differential overlap, NDDO Theory
- 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
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
- penalty functionsx, Example I ("Floppy" system)
- pi bonds, PI
- PM3, NDDO Theory, PM3
- PM3 elemental parameter sets, Defined Parameters
- polarizability, Polarizability Methods, APOLAR, KPOLAR
- Polarizability
- keywords, Polarizability Keywords
- polarization functions, Sparkles
- potential energy surface, Potential Energy Surfaces (PES)
- principal moments of inertia, Ouput File (properties/prop_thermo_trans.out) :
- program
- set up, Package Administration
R
- Raman spectra, Computational Chemistry in Context
- reaction coordinate, Characterization of Stationary Points, Internal Coordinates, Reaction Coordinate Values,
- 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, The Half-Electron Method
- references, References
- ridge, Potential Energy Surfaces (PES), Characterization of Stationary Points
- rm_ampac_results, Description
- 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.csh, Description
- 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,
- descriptors in AMSOL, AMSOL Output, SOLVNT
- integration in COSMO, Solvation Integration
- parameters in COSMO, Solvent Parameters
- solvent-accessable surface, Solvation Integration
- solvent-accessable surface area, AMSOL Output
- sparkles, Dummy Atoms, Sparkles, Polarizability Methods,
- 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), , , PATH (see approximate)
- transition state location
- by CHN, CHN
- by LTRD, LTRD
- by reaction coordinate,
- by simulated annealing, MANNEAL
- methyl rotations, Internal Coordinates
- transition states, Finding Transition States (CHN and FULLCHN)
- transition vector,
- extra input data, Transition Vector Weights, Transition Vector Information
- troubleshooting, Troubleshooting
U
- unpaired spin density, ESR
- utilities
- acubegen, Description
- ampac, Description
- arc2dat, Description
- catcsm, Description
- check_env.csh, Description
- config_ampac.csh, Description
- haltampac, Description
- keycleaner.exe, Description
- mampac, Description
- reference, Utilities
- rm_ampac_results, Description
- Set_File_Protection.csh, Description
- visdump, Description
- xglinfo.exe, Description
- UV/visible spectra, Introduction, CI Theory
