Part III. AMPAC™ 10
User Reference
Table of Contents
 A. Keyword Reference

 0SCF — Read in data, then stop.
 1ELECTRON — Final oneelectron matrix will be printed.
 1SCF — Do 1 SCF calculation and then stop.
 ALLOWATOMS — Set maximum number of atoms allowed in calculation.
 ALLVEC — All atomic orbital contributions to the MOs will be printed.
 ALPHA — Specify alpha of the desired solvent.
 AM1 — The AM1 Hamiltonian will be used.
 AM1D3H4 — Use AM1 Hamiltonian plus D3H4 dispersion and hydorgenbond corrections.
 AM1FS2 — Use AM1 Hamiltonian plus AM1FS2 dispersion and hydorgenbond corrections.
 AMSPRNT — Set level of AMSOL printout.
 ANNEAL — Simulated annealing search for geometric minima
 APOLAR — Compute nonlinear optical properties using analytic gradient.
 AUTOLIMIT — Define default preliminary periodic boundaries.
 AVEPMO — Averaged density matrix in MO basis for the first
n
eigenstates.
 BETA — Specify beta of the desired solvent.
 BFGS — Use BFGS method in geometry optimization.
 BIRADICAL — System has two unpaired electrons.
 BONDS — Print only nonzero elements of final twocenter bond order matrix.
 BPFREF — Define central value of the bandpass filter.
 BPFSIG — Define halfwidth of the bandpass filter.
 BRUTEKPOLAR — Use Kurtz’s method for computing nonlinear optical properties in the genuine
Cartesian frame.
 CATCHTS — Define the neglect threshold for lowenergy extrema during FULLCHN jobs.
 CGDIIS — Use DIIS during conjugategradient steps.
 CHAIN — Find transition state using CHAIN method.
 CHARGE — Define the charge on the system (e.g.
NH_{4}^{+}, CHARGE=1).
 CHN — Locate limitant transition state along CHN path.
 CHECKCHN — Build trial path for CHN only.
 C.I. — configuration interaction
 CIDIP — Calculate charges and dipole moments for CI eigenstates.
 CIGAP — Specify energy gap used to determine microstate degeneracy.
 CIMAX — Specify the maximum number of microstates.
 CIOK — Override degeneracy check.
 CIOUT — Write details about the CI eigenstates to file.
 CISTATE — Specify the number of final CI eigenstates to be calculated and
printed.
 CITRANS — Calculate and write transition dipole data between all calculated CI eigenstates instead of just between the primary CI
eigenstate and the others.
 CODESSA —
Generate output options for CODESSA™
 CONNOLLY — Enable use of the Connolly surface for the ESP calculation.
 CONTRIB — Print list of external contributors.
 COSMO — Invoke the COSMO solvation model.
 COSMOWRT — Write out data for further COSMO processing.
 CRUDE — Use crude rejection scheme.
 CUOLDSAM1 — Use old parameters for element Cu with SAM1.
 DAVDBG — Write details about the CI matrix diagonalization to file.
 DDMAX — Define the maximum size of the trust radius.
 DDMIN — Define the minimum size of the trust radius.
 DECET — RHF decet state required.
 DELSC — Specify the effective molecular radius of the desired solvent.
 DEGEN — Print warnings if degenerices in HOMO.
 DEN — Specify a different point density for the Connolly surface.
 DENSITY — Final density matrix will be printed.
 DENMAT — Density matrix will be written to disk in ASCII format.
 DENOUT — Density matrix will be written to disk in binary format.
 DERINU — Derivatives will be computed numerically.
 DFP — Use DavidonFletcherPowell in geometry optimization.
 DIELECSpecify the dielectric constant for desired solvent. (Equivalent to EPS)
 DIPOLE — Constrain the ESP dipole moment as predicted by AMPAC’s
Coulson analysis.
 DIPX — Specify the x component of the dipole moment.
 DIPY — Specify the y component of the dipole moment.
 DIPZ — Specify the z component of the dipole moment.
 DIRECTSCF — Don’t store two electron integrals.
 DISEX — Distance threshold for using twopoint interaction approximation.
 DISSOC — Define the dissociation threshold for CHN methods.
 DMAX — Define the initial trust radius.
 DOUBLET — RHF doublet state required.
 DYNPOL — Dynamic Polarizability
 EF — Use the eigenvector following method to locate a minimum.
 EIGS — Print out HF eigenvalues at every step of the SCF procedure.
 ENHANCE — Increase the matrix form used in sparse PSOLVE.
 ENPART — Energy will be partitioned into components.
 EPSSpecify the dielectric constant for desired solvent. (Equivalent to
DIELEC)
 ESP — Invokes the electrostatic potential method for charge calculation.
 ESR — Unpaired spin density on atoms will be calculated.
 EXCITED — First excited singlet state will be optimized.
 FACARB — Specify the fraction of nonhydrogenic solvent atoms that are carbon atoms contained
in an aromatic ring.
 FCTOR3Determine balance between energy and gnorm (
MANNEAL only)
 FEHALO — Specify the fraction of nonhydrogenic solvent atoms that are electronegative
halogen atoms.
 FILL — Require use of defined set of prototype MOs.
 FILTER — Determine equivalency of configurations during the clustering sort.
 FLETCHER — Use FletcherReeves version of conjugate gradient.
 FOCK — Final Fock matrix will be printed.
 FORCE — Force calculation for a Cartesian frequency analysis requested.
 FREF — Define central value of the energy range.
 FULLCHN — Locate transition state(s) and intermediate point(s) along CHN path.
 FULLCNV — Fully converge conjugate gradient at each SCF cycle.
 GAMMA — Specify the macroscopic surface tension of the desired solvent.
 GANNEAL — Simulated annealing search for extrema within an energy range.
 GAUSSIAN — Use a Gaussian, rather than uniform, random number generator for geometry
displacement.
 GEOOK — Override interatomic distance check.
 GERSH — Use Gershgorin method to compute bounds on the Fock matrix eigenvalues.
 GNMIN — Activate gradient test for accepting geometry steps.
 GNORM — Exit geometry optimizations when RMS gradient norm falls below a specified
value.
 GRADIENTS — All gradient components and the gnorm will be printed.
 GRAPH — Write out data for graphics in binary format.
 GRID — Specify dimensions for a 2D reaction grid calculation.
 HESS — Specify the source of the Hessian matrix.
 HESSEI — Compute a few lowest Hessian eigenvalues.
 HESSIAN2 — Force 2point formula to compute Hessian.
 HESSIAN4 — Force 4point formula to compute Hessian.
 HGAS — Specify the heat of formation (kcal/mol) of the solute in the gas
phase.
 HMIN — Minimum allowed step length for IRC/Path.
 HYPERFINE — Computes hyperfine coupling constants for a UHF calculation.
 IADM — Interatomic Distance Matrix will be printed.
 INCI — Read final microstates from an ASCII file.
 INERTIAL — Cartesian force constants are output in the inertial frame.
 IOFRSpecify the index of refraction of the desired solvent. (Equivalent to
REFRACT)
 IRC — Follow the intrinsic reaction coordinate.
 ISOTOPE — Final force matrix written to disk (channel 9).
 IUPD — Choice of update method for the Hessian matrix.
 JKPRINT —
All unique two electron integrals over CIactive MOs written to output file.
 KPOLAR — Use Kurtz’s method for computing nonlinear optical properties in the inertial
frame.
 LETDo not reduce gradients in FORCE.
 LEWIS — Generate initial guess based on Lewis dot structure analysis.
 LFORCE — Compute the IR spectrum for a few lowest frequencies.
 LICENSE — Output information on your AMPAC™
license.
 LIMIT — Define periodic boundaries.
 LINDH — Use Lindh’s method for initial guess for Hessian matrix.
 LOCALIZE — Localized orbitals will be printed.
 LTRD — Minimize gradient using full Hessian.
 MANNEAL — Simulated annealing search for minima within an energy range
 MARK — All points of the Markov chains are written to channel 8.
 MATCI — Energies and AO coefficients of CIactive MOs printed to output file.
 MAXNOD — Maximum number of nodes in a CHAIN/CHN calculation.
 MAXQUE — Size of queue to store candidates in simulated annealing calculation.
 MECI — Print information about CI microstates and transitions.
 MICROS — Generates only microstates with spin =
n
.
 MINDO3 — The MINDO3 Hamiltonian will be used.
 MNDO — The MNDO Hamiltonian will be used.
 MNDOC — The MNDOC Hamiltonian will be used.
 MNDOD — The MNDO/d Hamiltonian will be used.
 MODE — Specify eigenvector to follow during optimization.
 MPG — Find molecular point groups and list tolerances.
 MPGCRT — Use specified value as tolerance to compute molecular point group.
 MSCHARG — specify spin of microstates
 MULLIKEN — Perform a pseudoMulliken population analysis.
 NBO — Perform natural bond orbital (NBO) analysis.
 NCPM6 — No special correction terms will be used with the PM6 Hamiltonian.
 NCHECK — Define interval for producing quenching candidates at each temperature.
 NEWDEN — Always start SCF with a new guess density.
 NEWTON — Minimize energy using full Hessian.
n
ET — Constrains the spin multiplicity of the primary CI eigenstate to be n.
 NMAX — Define maximum value of criterion calls at a given temperature.
 NOARC — Suppress output of the
.arc
file.
 NOHL — Avoid computation of the HOMOLUMO orbitals and gap.
 NONET — RHF nonet state required.
 NONR — Specify PRFO method for geometry projection.
 NOOUT — Suppress output of the
.out
file (Win32
only).
 NOPOL — Polarization energy computed with gas phase solvent wavefunction.
 NOPRECON — Do not use preconditioning during conjugate gradient.
 NOQUENCH — Skip quenching.
 NOREF — Elemental parameter set references will not be printed.
 NOUPDSuppress updating of the trust radius at Stage 3.
 NOVIS — Suppress output of the
.vis
file.
 NOXYZ — Suppress output of Cartesian coordinates.
 NPROC — Set number of processors to use during the calculation (if supported).
 NRAND — Define random number seed value.
 NSPA — Specify the number of segments per atom.
 NSURF — Change the number of surfaces used in the Connolly algorithm.
 OCI — Expand space of single excitations in a CI calculation.
 OCTET — RHF octet state required.
 OLDCMMINDO — Use old MINDO3 parameters with COSMO.
 OLDENS — Initial density matrix read from binary file.
 OLDMAT — Initial density matrix read from ASCII file.
 OMIN — Specify minimum overlap between successive TS search vectors.
 OPEN — Configuration Interaction
 OPTIL — Optimize left (reactant) starting geometry.
 OPTILR — Optimize both the left (reactant) and right (product) starting
geometries.
 OPTIR — Optimize right (product) starting geometry.
 OPTIRL — Optimize both the left (reactant) and right (product) starting
geometries.
 OPTMAX — Set the maximum number of geometry optimization cycles.
 OPTPRT — Monitor convergence of geometry optimization.
 ORIENT=ORIGINAL — Don't reorient the input geomtry.
 OVERLAP — Overlap matrix will be printed.
 PATH — Follow the descending reaction path.
 PCONV — Set the convergence criterion for PSOLVE=CGDMS or QNDMS.
 PEN1 — Activate close contact penalty function.
 PEN2 — Activate conformational penalty function.
 PEN2GRP — Activate conformational penalty function within distinct groups.
 PENA — Activate penalty function on the molecule’s moments of inertia.
 PERTU — Override the default perturbative selection of microstates.
 PI — Resolve density matrix into sigma and pi bonds.
 PM3 — The PM3 Hamiltonian will be used.
 PM3D3H4 — Use PM3 Hamiltonian plus D3H4 dispersion and hydorgenbond corrections.
 PM6 — The PM6 Hamiltonian will be used.
 PM6D3H4 — Use PM6 Hamiltonian plus D3H4 dispersion and hydorgenbond corrections.
 POTWRT — Dump out the surface points and electrostatic potential values.
 PREF — Define the energy window penalty coefficient.
 PRINT — Set verbosity of output.
 PRINTHESSIAN — Final Hessian matrix will be printed.
 PROTO — Define prototype MOs.
 PRTLWS — Set level of output during LEWIS.
 PSOLVE — Set the sparse matrix solver method.
 PSPRT — Set level of output during PSOLVE and other sparse matrix operations.
 QCSCF — Explicitly invoke quadratically convergent SCF procedure.
 QUARTET — RHF quartet state required.
 QUINTET — RHF quintet state required.
 RECALC — Specify interval (in number of steps) for Hessian recalculation.
 RECLAS — Reorder MOs.
 REFRACTSpecify the index of refraction of the desired solvent. (Equivalent to IOFR)
 RESTART — Calculation will be restarted using results from disk.
 RHF — Spinrestricted HartreeFock calculation.
 RIGIDCI — Propagate initial selection of microstates throughout a geometry
optimization.
 RM1 — The RM1 Hamiltonian will be used.
 RM1D3H4 — Use RM1 Hamiltonian plus D3H4 dispersion and hydorgenbond corrections.
 RMAX — Adjust maximum criterion for accepting geometry steps.
 RMIN — Adjust minimum criterion for accepting geometry steps.
 ROHF — Restricted openshell Hartree–Fock calculation.
 ROOT — Specify spin state to follow.
 ROT — Defines rotational symmetry.
 RSCAL — Scale the PRFO step.
 RSOLV — Specify the molecular radius of the desired solvent.
 SAM1 — The SAM1 Hamiltonian will be used.
 SAM1D — The SAM1 Hamiltonian, with dorbitals on I and Cl, will be
used.
 SCALE — Change the base scaling factor in the Connolly treatment.
 SCFBOOST — Additional cycles for final convergence of wavefunction.
 SCFCI — Defines two sets of openshell MOs and their fractional occupancies to be used in a “HalfElectron” RHF
SCF calculation preceding a CI calculation.
 SCFCRT — SCF termination criteria computed based on specified value.
 SCFDIIS — Use DIIS to improve convergence of the SCF.
 SCFLOCAL — Localized MOs are produced by the SCF procedure.
 SCFMAX — Set limit on number of SCF iterations to specified value.
 SCFPRT — Monitor convergence in selfconsistent field procedure.
 SC.I. — Specify CIactive MOs in a SCI calculation.
 SCINCR — Specify the increment between multipliers for the Connolly surface.
 SDC.I. — Specify CIactive MOs in a SDCI calculation.
 SDTC.I. — Specify CIactive MOs in a SDTCI calculation.
 SEPS — Specify energy gap used to determine eigenstate degeneracy.
 SEPTET — RHF septet state required.
 SEXTET — RHF sextet state required.
 SHOWPARAM — Show semiempirical method parameters for each element.
 SINGLET — RHF singlet state required.
 SLOPE — Change the scaling factor when using MNDO ESP charges.
 SM5.2 — Request a calculation using the SM5.2 model.
 SM5.2R — Request a calculation using the SM5.2R model.
 SM5C — Request a calculation using the SM5C model.
 SM5CR — Request a calculation using the SM5CR model.
 SOLVNT — Indicate which parameter set will be used in the SM5 calculation.
 SPARSE — Perform sparse matrix calculation using the specified neglect threshold.
 SPIN — Final UHF spin matrix will be printed.
 SREF — Specify halfwidth of the searched energy range.
 STD — Define thermalization criterion.
 STEP — Define maximum step size in the annealing search.
 STEP1 — Specify step size for first coordinate in reaction grid calculation.
 STEP2 — Specify step size for second coordinate in reaction grid calculation.
 STEPCV — Define a lower bound for the step size (% of initial step).
 STEPHESS — Specify step size in numerical differentiation of Hessian.
 STO3G — Specify basis set to “deorthogonalize” the semiempirical density
matrix.
 STO6G — Specify basis set to “deorthogonalize” the semiempirical density
matrix.
 SYBYL — Output information for input into SYBYL®.
 SYMAVG — Average charges which should have the same value by symmetry.
 SYMMETRY — Symmetry conditions will be imposed.
 SZ — Specify value of S_{z}.
 T — Define time limit for calculation.
 TEMP — Starting “temperature” for the annealing procedure.
 TEST — Print extra debugging output.
 TEXPN — Solvation trapezoidal integration shell growth factor.
 THERMO — Set the temperature range for calculating thermodynamic properties.
 TIMES — Print timings at various stages of the calculation.
 TLAW — Specify the decay constant in the temperature.
 TOL — Permitted relative variation of a bond length from its initial value.
 TONE — Solvation trapezoidal integration shell thickness.
 TRANS — Deletes the n lowest vibrations in a THERMO calculation.
 TRIPLET — Triplet state required.
 TRUES — Calculate the true solvation free energy.
 TRUSTE — Default method for geometry optimization using trust radii.
 TRUSTG — Default method for gradient minimization using trust radii.
 TS — Use the eigenvector following method to locate a transition state.
 TSANNEAL — Simulated annealing search for extrema within an energy range.
 T.V. — A transition vector is provided for IRC or PATH.
 UHF — Spinunrestricted HartreeFock calculation.
 VALIDCI — Indicate that the microstates to be read in are fully consistent.
 VDW — Specify an element’s van der Waals radius.
 VECTORS — Selected atomic orbital contributions to the MOs will be printed.
 VSHIFT — Set level shift during CGDMS or QNDMS.
 VIS=MIN — Reduce the output in the
.vis
file.
 WEIGHT — Weights for T.V. components will be provided for PATH.
 WHOLE — End the quenching steps will full optimizations.
 WILLIAMS — Specify surface generation procedure of Donald Williams.
 XYZ — Optimization to proceed in Cartesian space.
 B. Utilities


acubegen
— Write a cube file from an AMPAC
.vis
file.

afreqgen
— Generate vibrational frequency information from an AMPAC
.vis
file.

ampac
— Execute AMPAC input files.

arc2dat
— Produce
.dat
file from .arc
file.

catcsm
— Convert
.csm
file to a plain text
format.

check_env.sh
— Diagnostic script to check if AMPAC is set
up correctly.

config_ampac.sh
— Set operating systemspecific configuration options.

dump_util
— Automatically convert AMPAC
binary files (
.vis
and
.csm
) to corresponding plain text files.

haltampac
— Bring AMPAC jobs to a controlled stop.

keycleaner
— Reformat AMPAC license key file or print license
information.

mampac
— Sequentially execute multiple input files.

rm_ampac_results
— Remove various result files produced by AMPAC.

Set_File_Protection.sh
— Set correct file permissions on all AMPAC
files.

visdump
— Convert
.vis
file to a plain text
format.

xglinfo.exe
— Dump extended information about GL properties.
 C. Error Messages

 ATOM NUMBER nn IS ILL DEFINED
 ATOMS mm AND nn ARE SEPARATED BY nn.nnnn ANGSTROMS
 C.I./SCFCI NOT ALLOWED WITH UHF
 CALCULATION ABANDONED AT THIS POINT
 CARTESIAN COORDINATES READ IN, AND CALCULATION...
 ELEMENT aa IS NOT VALID IN ...
 ELEMENT PAIR aa AND bb IS NOT VALID IN ...
 ERROR DURING READ AT ATOM NUMBER
 <<<<**** FAILED TO ACHIEVE SCF.
****>>>>
 GEOMETRY TOO UNSTABLE FOR EXTRAPOLATION...
 ILLEGAL ATOMIC NUMBER
 IMPOSSIBLE NUMBER OF OPEN SHELL ELECTRONS
 INCOMPATIBLE OPTION REQUESTED
 INTERNAL COORDINATES READ IN, AND SYMMETRY...
 THE LINE MINIMIZATION FAILED TWICE IN A ROW
 **** RMS GRADIENT IS TOO LARGE TO ALLOW...
 THERMO: TEMPERATURE RANGE STARTS TOO LOW...
 THERE HAVE BEEN 3 ATTEMPTS...
 THREE ATOMS BEING USED TO DEFINE...
        TIME UP       
 """"""""""""""UNABLE TO ACHIEVE SELFCONSISTENCY
 UNDEFINED SYMMETRY FUNCTION USED
 UNRECOGNISED ELEMENT NAME: (aa)
 WARNING: INTERNAL COORDINATES...
 **** WARNING **** RMS GRADIENT IS VERY LARGE...
 D. Data Files


solvent.data
— AMPAC Solvent Descriptor Data File
 E. Debugging

 CALPAR — Print additional debug information in subroutine CALPAR.
 COMPFG — Print additional debug information in subroutine COMPFG.
 DBGHESSE — Print additional debug information in subroutine HESSE1/HESSEI.
 DBGLOWDIN — Print additional debug information in subroutine LOWDIN.
 DCART — Print additional debug information in subroutine DCART.
 DEBUG — Turn on additional debug output.
 DEP — Print parameters for semiempirical methods.
 DERI2 — Print additional debug information in subroutine DERI2.
 DERIV — Print additional debug information in subroutine DERIV.
 DFORCE — Print additional debug information in subroutine FORCE.
 DHCORE — Print additional debug information in subroutine DHCORE.
 FLEPO — Print additional debug information in subroutine FLEPO.
 HCORE —
Print additional debug information in subroutine HCORE.
 ITER —
Print additional debug information in subroutine ITER.
 LINMIN —
Print additional debug information in subroutine FLEPO1.
 MOLDAT — Print additional debug information in subroutine MOLDAT.
 REPARAM — Recompute dependent parameters for current semiemperical method.
 TRUST21 — Print additional debug information in subroutine TRUST21.
 F. Obsolete Keywords

 BOOSTReplaced by SCFBOOST.
 CODSCF
Replaced by CODESSA.
 CODTHERMO
Replaced by CODESSA.
 CYCLESReplaced by OPTMAX.
 ESPRST — [obsolete]
 FAILSuperseded by
NEWDEN.
 ITRYReplaced by SCFMAX.
 LOG — [obsolete]
 MINVISReplaced by VIS=MIN.
 NLLSQReplaced automatically with TRUSTG.
 NOINTER — [obsolete]
 PL
Replaced by
SCFPRT.
 OLDCHAINSuperseded by CHN.
 OLDPOWELLSuperseded by TRUSTG.
 OLDSIGMASuperseded by TRUSTG.
 OLDNLLSQSuperseded by TRUSTG.
 POLARSuperseded by APOLAR and
KPOLAR.
 POWELLReplaced automatically with TRUSTG.
 PRECISE — [obsolete]
 PRNT — [obsolete]
 PULAY — [obsolete]
 SHIFT — [obsolete]
 SIGMAReplaced automatically with TRUSTG.
 SILENTSMxxSuperseded by AMSPRNT.
 SM1Superseded by SM5.2, SM5.2R, SM5C, and SM5CR.
 SM1ASuperseded by SM5.2, SM5.2R, SM5C, and SM5CR.
 SM2
Superseded by
SM5.2,
SM5.2R,
SM5C, and
SM5CR.
 SM2.1Superseded by SM5.2, SM5.2R, SM5C, and SM5CR.
 SM3
Superseded by
SM5.2,
SM5.2R,
SM5C, and
SM5CR.
 VERBOSESMxxSuperseded by AMSPRNT.