Part III. AMPAC™ 10
User Reference
Table of Contents
- A. Keyword Reference
-
- 0SCF — Read in data, then stop.
- 1ELECTRON — Final one-electron 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.
- AM1-D3H4 — Use AM1 Hamiltonian plus D3H4 dispersion and hydorgen-bond corrections.
- AM1-FS2 — Use AM1 Hamiltonian plus AM1-FS2 dispersion and hydorgen-bond 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 non-zero elements of final two-center bond order matrix.
- BPFREF — Define central value of the band-pass filter.
- BPFSIG — Define half-width of the band-pass filter.
- BRUTEKPOLAR — Use Kurtz’s method for computing nonlinear optical properties in the genuine
Cartesian frame.
- CATCHTS — Define the neglect threshold for low-energy extrema during FULLCHN jobs.
- CGDIIS — Use DIIS during conjugate-gradient steps.
- CHAIN — Find transition state using CHAIN method.
- CHARGE — Define the charge on the system (e.g.
NH4+, 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.
- CI-OK — 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.
- CU-OLDSAM1 — 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 Davidon-Fletcher-Powell 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 two-point 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 non-hydrogenic solvent atoms that are carbon atoms contained
in an aromatic ring.
- FCTOR3Determine balance between energy and gnorm (
MANNEAL only)
- FEHALO — Specify the fraction of non-hydrogenic 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 Fletcher-Reeves 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.
- GEO-OK — 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 2-point formula to compute Hessian.
- HESSIAN4 — Force 4-point 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 CI-active 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 CI-active 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 pseudo-Mulliken population analysis.
- NBO — Perform natural bond orbital (NBO) analysis.
- NC-PM6 — 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 HOMO-LUMO orbitals and gap.
- NONET — RHF nonet state required.
- NONR — Specify P-RFO 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.
- PM3-D3H4 — Use PM3 Hamiltonian plus D3H4 dispersion and hydorgen-bond corrections.
- PM6 — The PM6 Hamiltonian will be used.
- PM6-D3H4 — Use PM6 Hamiltonian plus D3H4 dispersion and hydorgen-bond 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 — Spin-restricted Hartree-Fock calculation.
- RIGIDCI — Propagate initial selection of microstates throughout a geometry
optimization.
- RM1 — The RM1 Hamiltonian will be used.
- RM1-D3H4 — Use RM1 Hamiltonian plus D3H4 dispersion and hydorgen-bond corrections.
- RMAX — Adjust maximum criterion for accepting geometry steps.
- RMIN — Adjust minimum criterion for accepting geometry steps.
- ROHF — Restricted open-shell Hartree–Fock calculation.
- ROOT — Specify spin state to follow.
- ROT — Defines rotational symmetry.
- RSCAL — Scale the P-RFO step.
- RSOLV — Specify the molecular radius of the desired solvent.
- SAM1 — The SAM1 Hamiltonian will be used.
- SAM1D — The SAM1 Hamiltonian, with d-orbitals 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 open-shell MOs and their fractional occupancies to be used in a “Half-Electron” 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 self-consistent field procedure.
- SC.I. — Specify CI-active MOs in a S-CI calculation.
- SCINCR — Specify the increment between multipliers for the Connolly surface.
- SDC.I. — Specify CI-active MOs in a SD-CI calculation.
- SDTC.I. — Specify CI-active MOs in a SDT-CI calculation.
- SEPS — Specify energy gap used to determine eigenstate degeneracy.
- SEPTET — RHF septet state required.
- SEXTET — RHF sextet state required.
- SHOWPARAM — Show semi-empirical 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 half-width 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 Sz.
- 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 — Spin-unrestricted Hartree-Fock 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 system-specific 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 SELF-CONSISTENCY
- 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 semi-empirical 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 semi-emperical 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.
