AFIRサンプル

List of Options

List of Options

 

Note: All options read from the input file will be listed in xxx_PARAM.rrm. The user is encouraged in every calculation to check whether or not a desired calculation is running by checking this file.

To be given above the root (#) section:

%infile = yyy

Sets the file name of a previous job which provides structural inputs for the current job. If used with ADDF, all structures in yyy_EQ_list.log, yyy_TS_list.log, and yyy_DC_list.log are copied to the current list files, to continue the automated search. If used with ReStruct, structures in yyy_EQ_list.log, yyy_TS_list.log, yyy_DC_list.log, and yyy_PT_list.log are re-optimized. If used with ReEnergy, single-point calculations are done at structures in yyy_EQ_list.log, yyy_TS_list.log, yyy_DC_list.log, and yyy_PT_list.log. If used with MC-AFIR, AFIR paths are computed starting from structures in yyy_EQ_list.log file. If used with LUP, a path in yyy.log is optimized. If used with RePath, paths in yyy_EQi.log, yyy_TSj.log, yyy_DCk.log, and yyy_PTl.log are optimized. If used with SC-AFIR, all structures in yyy_EQ_list.log, yyy_TS_list.log, yyy_DC_list.log, and yyy_PT_list.log are copied to the current list files, to continue the automated search.

Specifies the external electronic structure calculation code.

To be given in the coordinate section:

External Atoms

Atoms shown below this keyword (and above the Frozen Atoms keyword) are optimized before every displacement of the reaction-center atoms (microiteration). In Reactant’s coordinate section of 2PSHS, SCW, or DS-AFIR, coordinates for both the reaction-center and external atoms should be given without the External Atoms keyword.

Frozen Atoms

Atoms shown below this keyword are fixed at given initial positions. In inputs of 2PSHS, SCW, and DS-AFIR, the Frozen Atoms keyword as well as coordinates of frozen atoms should be given only once below the Reactant’s coordinates.

Product

In SC-AFIR, the search is terminated if the structure given below the Product keyword is obtained. In FREQ, the geometrical difference between the initial structure and the structure given below the Product keyword is decomposed by the normal modes and the energy-weighted (harmonic frequency-weighted) normal modes.

Reactant

In 2PSHS, SCW, or DS-AFIR, a path between the initial structure and the structure given below the Reactant keyword is computed.

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To be given below the Options keyword:

ATOM MASS

Arbitrary atomic mass values (in atomic mass unit) can be given to all atoms. Following this keyword, mass values are given (single value per line) for all natom atoms (atoms given above the External Atoms and Frozen Atoms keywords). The program expects that there are natom lines below this keyword.

Add Interaction … END

Between the keywords Add Interaction and END, various options that control the way of applying the artificial force are given. This keyword is required in MC-AFIR and SC-AFIR.

Bond Condition … END

In ADDF and SC-AFIR, ADDF or SC-AFIR is applied only to local minima that fulfill given bond conditions. In ReStruct and ReEnergy, local minima that fulfill given bond conditions and TSs which have a connection to them are optimized. In MC-AFIR with the Read Part-n = yyy_EQ_list.log option, structures in yyy_EQ_list.log that fulfill given bond conditions are selected.

BondConTarget = i,j,k-l

When used with NoBondRearrange, the difference in bond connectivity from the initial structure is checked looking only the arrangement of atoms i, j, k, k+1, k+2, …, l.

DCDecTarget = i,j,k-l

The judgement whether the structure is dissociated or not is done looking only the arrangement of atoms i, j, k, k+1, k+2, …, l.

Derivative = Energy

Force and Hessian are computed by energy differentiations.

Derivative = Force

Hessian is computed by force differentiations.

Detect Error

A search stops when an external program (such as G09) gave an error (link-error). This is default for FREQ, MIN, SADDLE, IRC, 2PSHS, SCW, ReEnergy, LUP, and DS-AFIR. For the other jobs, in default, a geometry (or path) which encountered a link-error is omitted to proceed the search.

DownDC = n

Definition of dissociation channel (DC). A structure which has two or more blocks that are distant to each other more than 0.1×n×2×(Ri+Rj) is regarded to be dissociated, where Ri and Rj are the covalent radii of atom i in one block and atom j in the other block, respectively. In default, n = 8. Also see Definition of dissociation channel.

DownFC = n

Exact Hessian is computed in every n steps in IRC calculations (default is n = 10, and if n = −1 Hessian is not calculated and a model Hessian is updated with force).

DownInitSize = n

Size of the initial step in IRC calculation is set n×0.01 Å (in default, the value of DownSize is applied).

DownSize = n

Step size of IRC and DS-AFIR calculations is determined so that the Euler step of the differential equation integration is n×0.01 Å (default is n = 10).

DS = OrientOFF

In DS-AFIR, reactant’s structure which is given in the input is used (in default, its orientation is optimized to minimize the distance from product’s structure).

DS = SingleSTEP

In DS-AFIR, LUP calculation is skipped and the highest energy point along the AFIR path is optimized to TS.

DS-BETA = x

The strength of the artificial force in DS-AFIR. Default is x = 0.03.

EigenCheck

Perform normal-mode analysis after minimum or saddle-point optimization (default in SADDLE, IRC, 2PSHS, SCW, ADDF, ReStruct, LUP, RePATH, SC-AFIR, and DS-AFIR). See also NoEigenCheck.

EQ-Selection = n,m,k-l

In ADDF and SC-AFIR, these methods are applied only to EQn, EQm, EQk, EQk+1, …, EQl.

EQOnly

Optimize only local minima in ADDF, ReStruct, SC-AFIR, DS-AFIR, LUP, and RePATH. In SC-AFIR, DS-AFIR, and RePATH, either LUP or AFIR path is obtained when KeepLUPPath or KeepSCPath option is specified together with EQOnly.

FirstOnly

In ADDF and SC-AFIR, ADDF or SC-AFIR is applied only to a given initial structure.

Guess = HighSpin

(Works only with GAUSSIAN) MO-guess is prepared by a single-point calculation for the higher spin-state at some geometries.

Guess = HighSpin = AllPoint

(Works only with GAUSSIAN) MO-guess is prepared by a single-point calculation for the higher spin-state at every geometry.

Guess = Mix

(Works only with GAUSSIAN or GAMESS) Guess = Mix option is used at some geometries.

Guess = Mix = AllPoint

(Works only with GAUSSIAN or GAMESS) Guess=Mix option is used at every geometry.

H2 = DC

Structures that have an H—H bond shorter than 0.8 Å will be regarded to be dissociated.

HESLOW = [Level of theory]/[Basis set]

(Works only with GAUSSIAN) Initial Hessian for MIN or SADDLE is estimated by a low-level method [Level of theory]/[Basis set] (e.g., HF/3-21G), and this Hessian is updated using forces.

HESSIAN GUESS = yyy.zzz

Initial Hessian for MIN or SADDLE is read from yyy.zzz (it must be an output of the GRRM17 program showing Hessian).

Hessian Update = Conventional

Hessian updates are made using only the gradient vector at the last step (gradient vectors in previous several steps are used in default).

InitSize = n

Sets the smallest sphere size for the initial ADD detection in ADDF (default is n = 3).

KeepIntFiles

Forbids elimination of intermediate files, xxx_Pi.log and xxx_Pi_* (these files are deleted in default when the job is finished normally).

KeepLUPPath

In SC-AFIR with EQOnly, AFIR/LUP-paths and their peak structures are saved in xxx_PTn.log and xxx_PT_list.log files, respectively.

KeepSCPath

In SC-AFIR with EQOnly, AFIR-paths and their peak structures are saved in xxx_PTn.log and xxx_PT_list.log files, respectively.

LADD = n

Perform the large-ADD-following in ADDF.

LUP = OrientOFF

Forbid reorientation of node structures in LUP.

LUP = SingleSTEP

Only the highest point along the LUP-path is optimized to TS. In default, all maximum energy points are optimized to TSs.

LUPSize = n

Interval of optimization points in the second stage of LUP optimization is set n×0.1 Å (default is n = 5).

MatchAxes

Match orientations of structures to their principle axes in ReStruct before optimization starts.

MatchDecScale = x

A clustering of EQs is done with the thresholds x times larger than those used in the judgement whether two structures are identical or not (the threshold can be changed with StructCheckThreshold). Structures judged to be similar with these criteria are regarded to belong to the same group. Among EQs belonging to the same group, the most stable ones in terms of electronic energy or free-energy at T = k×Temperature/10 (0≤k≤10) are chosen as representatives, and SC-AFIR is applied only to these representatives. Default is x = 1.0 (the clustering is not made).

MatchDecTarget = i,j,k-l

The similarity judgement in the EQ clustering is done looking only the arrangement of atoms i, j, k, k+1, k+2, …, l.

MaxEnergy = x

This option is used in combination with Read Part-n = yyy_EQ_list.log option, and only EQs that are lower in energy than x relative to the lowest EQ in the EQ list are read.

MaxIRCSTEP = n

IRC calculation is terminated at the n-th step (default is n = 10000/DownSize).

MaxLUPITR = n

Sets the number of LUP iterations as n (default is n = 5). In default, 2×n LUP iterations with a coarse path points interval and n LUP iterations with a fine path points interval are performed, where the initial 2×n LUP iterations with a coarse path points interval is skipped when the SkipLUPInitialStage option is provided.

MaxOPTCYCL = n

Sets the maximum number of iterations in geometry optimizations to [64+n×3×N], where N is the number of (reaction-center) atoms (in default, n = 2). The value of n is scaled by 2 when NOFC is specified.

MaxPATH = n

In SC-AFIR, the calculation is terminated after calculation of n AFIR paths.

MaxStepSize = x

Every geometrical displacement is restricted to be smaller than x Å (default is x = 0.5).

MaxStepSize-S = x

Geometrical displacement in saddle-point optimization, IRC calculation, the second stage of LUP optimization, is restricted to be smaller than x Å (default is x = 0.1).

MC = ReactivePathOnly

If the value of the force term in the AFIR function increased in the last 10 iterations in MC-AFIR, then the path is regarded to be non-reactive and omitted.

Meta-IRC

In IRC calculation, the backward IRC calculation is not computed.

MicroIt [= (MMOnly, NoCoupling/CoupleDist=n)]

This option is used together with the External Atoms keyword and works only with Gaussian 03/09/16. If MMOnly is specified, instead of ONIOM the MM method (UFF, AMBER, or DREIDING) used for the ONIOM low-layer is used in the optimization of the surrounding part (positions of atoms given below the External Atoms keyword). If NoCoupling is specified, coupling between the reaction center part and the surrounding part is not taken into account in the effective Hessian for the reaction center part. If CoupleDist=n is specified, coupling between the reaction center part and the surrounding part distant more than n/10 Å from the reaction center part is not taken into account in the effective Hessian for the reaction center part (default is n = 100). NoCoupling and CoupleDist=n are not used simultaneously.

MinFC = n

Exact Hessian is computed in every n steps in energy minimum point optimization including energy minimization in the hyperplane in LUP (default is n = 50, and if n = −1 Hessian is not calculated and a model Hessian is updated with force).

MO GUESS = yyy.zzz

Initial MO is read from yyy.zzz (e.g., .chk file of GAUSSIAN).

ModelF [= (Smooth/ModelParam=x, Guess=Same, SearchPath)]

In default, the seam model function (SMF) is used with its parameter x = 30 kJ/mol. If Smooth is specified, the avoiding model function (AMF) is used with its parameter x = 30 kJ/mol. The parameter of SMF or AMF can be changed by ModelParam=x. In default, the program assumes that the two states have different reference orbitals or densities; Guess=Same is added in case where the two states have common reference orbital or density. When SMF is used in automated structure searches either by ADDF or AFIR, EQOnly is applied in default; EQOnly can be disabled by adding SearchPath.

NFault = n

A stopping criterion of MC-AFIR (default is n = 10); if the last n AFIR paths didn’t find any new product, then stop.

NLowest = n

In ADDF and SC-AFIR, ADDF or SC-AFIR is applied only to the lowest n local minima; In ReStruct and ReEnergy, only the lowest n local minima and TSs which have a connection to them are optimized.

NoBondRearrange = x

In ADDF and SC-AFIR, ADDF or SC-AFIR is applied only to local minima that have the same bond connectivity which a given initial geometry has, where atoms i and j of covalent radii Ri and Rj are considered to have a bond when their distance is shorter than x×(Ri+Rj). If x is not specified, x = 1.25 is applied. In ReStruct and ReEnergy, local minima that have the same bond connectivity which a given initial geometry has and TSs which have a connection to them are optimized. In MC-AFIR with the Read Part-n = yyy_EQ_list.log option, structures in yyy_EQ_list.log that have the same bond connectivity which a given initial geometry has are selected.

Node = n

In 2PSHS, n hyperspheres are considered between reactant and product structures (default is n = 20).

NOFC

Exact Hessian will never be computed and always a model Hessian is updated with forces (NOT available in 2PSHS, SCW, and ADDF calculations). Same as the combination of MinFC=−1, SaddleFC=−1, DownFC=−1, and NoEigenCheck.

NoEigenCheck

Forbid normal-mode analysis after minimum or saddle-point optimization (default in MIN and MC-AFIR). See also EigenCheck.

NoGuess

MO files in the previous calculation are not used in ReStruct and ReEnergy.

NonScaled

Use the normal coordinates instead of the scaled normal coordinates in SCW.

NoPTSelection

In RePATH, all paths in the PT (path-top) list are read in. In default, only paths with missing connections in the TS list and paths with lower energy than TSs in the TS list of the corresponding connection are read in.

NRUN = n

In ADDF and SC-AFIR, the search starts from n random geometries. In MIN with NRUN=1, the initial structure of geometry optimization is done starting from a random structure.

NSample = n

A stopping criterion of MC-AFIR (in default, NFault=10 is applied); the stochastic search will stop after calculations of n AFIR paths.

NumDiffE = x

Step size of energy differentiations is set x Å (default is x = 0.005).

NumDiffF = x

Step size of force differentiations is set x Å (default is x = 0.005).

Opt = Cartesian

Optimization is performed using the Cartesian coordinates (mixed internal and cartesian coordinates are used in default).

Opt = Fragment

Minimum point optimization is performed with fixing the centers of given parts.

Opt = Fragment = Independent

Minimum point optimization is performed with fixing the centers and orientations of given parts.

Opt = Loose

Loose optimization criteria are adopted. See also StructCheckThreshold.

Opt = Tight

Tight optimization criteria are adopted. See also StructCheckThreshold.

Opt = VeryLoose

Very loose optimization criteria are adopted. See also StructCheckThreshold.

OptCheck = n

Controls the frequency of reconstruction of MOs. This option can be used together with Stable=Opt, Guess=Mix, or Guess=HighSpin.

OptX [=(Seam/Conical, ModelParam=x, MaxGap=y, Guess=Same)]

In default, the minimum energy seam of crossing (MESX) or conical intersection (MECI) point is optimized by the SMF based algorithm in which the parameter of SMF x is gradually minimized until the energy gap between the two states becomes smaller than y kJ/mol, where the initial value of x and the threshold value y can be changed by ModelParam=x and MaxGap=y (in default, x = 30 kJ/mol and y = 1 kJ/mol). If Seam is specified, the MESX point is optimized by the gradient projection (GP) method. If Conical is specified, the MECI point is optimized by the GP method combined with the branching plane updating method. Seam and Conical are not used simultaneously. In default, the program assumes that the two states have different reference orbitals or densities; Guess=Same is added in case where the two states have common reference orbitals or densities.

PerturbSize = n

Decrease or increase the atom-atom distance by n% or n+30%, respectively, to generate the perturbed structure in SC-AFIR (default is n = 20).

Pressure = x

Gibbs free energy is evaluated with pressure x atm (default is x = 1.0).

PriorityPath … END

Paths given between the PriorityPath and END keywords will be calculated prior to the other paths. Multiple paths can be given between these keywords as, 1 2 plus or 1 2 minus. The path 1 2 plus pushes fragments defined around atom 1 and atom 2 together, and the path 1 2 minus pulls fragments defined around atom 1 and atom 2 apart.

Project

Projection of the force vector is eliminated in normal-mode analysis.

PTOnly

In RePATH, only paths of the PT (path-top) list are read in. (With this option, previous lists of EQ, TS, and DC are just copied.)

RandBox-X = x0 x1

Random structure is generated within the range x0xx1.

RandBox-Y = y0 y1

Random structure is generated within the range y0yy1.

RandBox-Z = z0 z1

Random structure is generated within the range z0zz1.

RandDC = n

How far [Ri+Rj+0.1×n Å] given parts will be pulled apart in initial random structure generation (default is n = 5), where Ri and Rj are the covalent radii.

Read Part-n = yyy_EQ_list.log

In MC-AFIR, initial geometry of part-n are read from yyy_EQ_list.log.

ReadBareEnergy

In selecting the lowest n local minima, the first energy value in parenthesis of the EQ list (actual energy value without artificial force) are used.

ReadMultipleInFile … END

If used in SC-AFIR with the %InFile option, all structures in zzz_EQ_list.log, zzz_TS_list.log, zzz_DC_list.log, and zzz_PT_list.log are copied to the current list files, to continue the automated search, where zzz is replaced by lines given between ReadMultipleInFile and END.

ReDefinePath

When the %InFile keyword is used together with SC-AFIR, paths starting from each EQ are redefined and recalculated. In default, paths defined in the previous calculation are read in and those calculated in the previous job are not calculated again.

RTemperature = x

Temperature used for the Monte Carlo path sampling in SC-AFIR. This temperature determines how frequently paths starting from high energy minima are considered in the stochastic search and does not necessarily related to experimental temperature. Usually this value is set to a very large value such as 10×Temperature (x = 2981.5 K in default).

Saddle+IRC

Perform IRC calculation after SADDLE.

SaddleFC = n

Exact Hessian is computed in every n steps in saddle point optimizations (default is n = 5, and if n = −1 Hessian is not calculated and a model Hessian is updated with force).

SC = FindUDC

In SC-AFIR, dissociation channels that do not have TS are calculated and stored in xxx_DC_list.log. In default, such paths are just discarded. The DC structures are optimized with fixing the distance between the centers of dissociated fragments. The path presented in xxx_DCn.log correspond to the meta-IRC path computed starting from the corresponding DC structure.

SC = InterOnly

In SC-AFIR, paths in each part are omitted.

SC = IntraOnly

In SC-AFIR, paths between different parts are omitted.

SC = NegativeOFF

In SC-AFIR, paths of negative-force are omitted.

SC = PathPara–m/M

In SC-AFIR with FirstOnly, among P paths, only [1+{(m−1)P/M}]-th to [m P/M]-th paths are computed.

SC = StochasticON

In SC-AFIR, paths between atoms in a very long distance (paths that are omitted with the criteria of SC-MaxDist) are computed with low probability.

SC = UseSymmetry

The number of paths is reduced using the symmetry of EQs.

SC-HighLimit = x y z

SC-AFIR is applied only to EQs that have lower total electronic-energy than x hartree, lower total electronic-energy + zero-point-energy than y hartree, and/or lower total Gibbs free-energy than z hartree.

SC-MaxDist = x

The path between atom i and j is omitted if their distance is longer than x×(Ri+Rj), where Ri and Rj are covalent radii of these atoms, respectively. In default, x = 8.0.

ScaleStructCheckThreshold = x

The threshold values a, b, and c of StructCheckThreshold are scaled by x.

SCGO_mLatest = m

A stopping criterion of SC-AFIR used in combination with SCGO_nLowest=n. The search is terminated when the last (newest) m local minima do not update the lowest n local minima, where the n minima are the lowest in electronic energy or free-energy at T = k×Temperature/10 (0≤k≤10).

SCGO_nLowest = n

A stopping criterion of SC-AFIR used in combination with SCGO_pLatest or SCGO_mLatest.

SCGO_pLatest = m

A stopping criterion of SC-AFIR used in combination with SCGO_nLowest=n. The search is terminated when the last m AFIR paths do not update the lowest n local minima, where the n minima are the lowest in electronic energy or free-energy at T = k×Temperature/10 (0≤k≤10).

ShiftE = x

In calculations for two states such as ModelF and OptX, the potential energy surface of the first state is shifted by x kJ/mol.

SkipIRC

Skip IRC calculation in RePATH, LUP, and DS-AFIR.

SkipIRCMIN

With this option, the terminal points of the IRC path are not optimized.

SkipLUPInitialStage

In LUP-path optimization in LUP, RePATH, SC-AFIR, and DS-AFIR, the initial path relaxation with a coarse path points interval is skipped.

SkipPT

In RePATH, paths of the PT (path-top) list are omitted.

SPHIGH = [Level of theory]/[Basis set]

(Works only with GAUSSIAN) Perform a single-point calculation by a high-level method [Level of theory]/[Basis set] (e.g., CCSD(T)/cc-pVTZ) after MIN or SADDLE.

Stable = Opt

(Works only with GAUSSIAN) MO-stability check is performed at some geometries.

Stable = Opt = AllPoint

(Works only with GAUSSIAN) MO-stability check is performed at every geometry.

StructCheckThreshold = a b c

Change the criteria (thresholds) judging whether two structures are identical or not. Two structures are regarded to be identical when the difference in their electronic energies, the RMS error in interatomic distances, and the maximum error in interatomic distances are all smaller than a kJ/mol, 100b%, and 100c%. The default values are 2.0, 0.01, and 0.02 when Opt=Tight is adopted, 4.0, 0.02, and 0.04 when the default optimization threshold is adopted, 6.0, 0.03, and 0.06 when Opt=Loose is adopted, and 8.0, 0.04, and 0.08 when Opt=VeryLoose is adopted.

Symmetry number = n

Gibbs free energy is evaluated using the given symmetry number n (in default, automatically assigned depending on structures).

Temperature = x

Gibbs free energy is evaluated at temperature x K (default is x = 298.15).

UpDC = n

Definition of dissociation channel (DC) adopted only during sphere-expansion in ADDF and sphere-contraction in 2PSHS and SCW. In default, n = 10. See also Definition of dissociation channel.

UpFC = n

Exact Hessian is computed in every n steps in minimum point optimizations on scaled hypersphere surfaces in 2PSHS, SCW, and ADDF calculations (default is n = 50).

UpSize = n

Step size of sphere-expansion in ADDF and sphere-contraction in SCW (default is n = 10).

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Updated At:Feb. 13, 2018, 6:17 p.m.

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