AFIRサンプル

Path refinement calculation (RePath)

Path refinement calculation (RePATH)

The RePATH calculation automatically applies LUP path optimizations, EQ optimizations starting from local minima along LUP paths, TS optimizations starting from local maxima along LUP paths, and IRC calculations starting from obtained TSs, to all paths (AFIR path, LUP path, IRC path, and/or meta-IRC paths from DCs) that are read from previous results. This calculation is done for various purposes, and the previous calculation can be MC-AFIR, SC-AFIR, DS-AFIR, RePATH, ReStruct, or ADDF.

An example is given as follows:

%infile=yyy
RePATH/B2PLYPD/jun-cc-pVDZ
 
0 1
C         -0.000000000711          0.000000000452         -0.533622543616
O          0.000000000233          0.000000000201          0.679217381431
H          0.000000000239          0.942015259527         -1.124391918573
H          0.000000000239         -0.942015260180         -1.124391919242
 

All results for yyy.com should exist in the working directory. The initial geometry has no meaning (though necessary to read information of atoms), and all structures are read from the outputs of yyy.com.

Structures, energies, spin expectation values, ZPVE values, and normal mode eigenvalues of each EQ are listed in the xxx_EQ_list.log file as:

List of Equilibrium Structures
 
# Geometry of EQ 0, SYMMETRY = Cs
C         -0.014854698946         -0.146246385398         -0.938810994283
O          0.030790451464          0.274322658797          0.310659342355
H         -0.001145868521          1.246781240174          0.300168268345
H          0.027204056606         -1.260246125923         -0.811316654339
Energy    = -114.326507185415
Spin(**2) =    0.000000000000
ZPVE      =    0.026805899087
Normal mode eigenvalues : nmode = 6
  0.045570622   0.055899684   0.065813544   0.085704523   0.320739118
  0.523358805
 
# Geometry of EQ 1, SYMMETRY = C2v
C         -0.012982881166         -0.031848129324         -0.821343990509

Structures, energies, spin expectation values, ZPVE values, normal mode eigenvalues, and connections of each TS are listed in xxx_TS_list.log file as (when the EQOnly option is used, this file is empty):

List of Transition Structures
 
# Geometry of TS 0, SYMMETRY = Cs
C         -0.014441897787         -0.114161725616         -0.908239011859
O          0.033308589243          0.258379037743          0.352908202909
H         -0.032990380622          1.078764658960         -0.486055144261
H          0.014123689168         -1.222981971083         -1.061803046786
Energy    = -114.273925672238
Spin(**2) =    0.000000000000
ZPVE      =    0.020464285078
Normal mode eigenvalues : nmode = 6
 -0.163207131   0.021752056   0.063459475   0.072991023   0.258162467
  0.324666671
CONNECTION : 0 - 1
 
# Geometry of TS 1, SYMMETRY = Cs
C         -0.025327706585         -0.377172856577         -0.229865447304
O         -0.003457688053          0.069489577606          0.855822601693
H          0.055311207764          0.803065738021         -1.400726659129
H         -0.026525813118         -0.495382459068         -1.328419495261
Energy    = -114.272371548766
Spin(**2) =    0.000000000000
ZPVE      =    0.018460394614
Normal mode eigenvalues : nmode = 6
 -0.140210724   0.024813958   0.030098172   0.069158886   0.131553679
  0.383963504
CONNECTION : 1 - DC
 
# Geometry of TS 2, SYMMETRY = C1
C          0.097542768133         -0.213310287582         -1.050138647079

Here, CONNECTION : 0 - 1 indicates that this TS is a transition state between EQ0 and EQ1, and CONNECTION : 1 - DC indicates that this TS is a transition state for a dissociation channel (DC) from EQ1. Results of IRC calculation starting from TSn are printed in xxx_TSn.log file, and a product of DC can be identified from a structure of one end of the IRC path.

Structures, energies, spin expectation values, ZPVE values, normal mode eigenvalues, and connections of each DC are listed in xxx_DC_list.log file as:

List of Dissociated Structures
 
# Geometry of DC 0, SYMMETRY = Cs
C          0.021926761187         -0.292868804480         -0.303240722999
O          0.040843955480         -0.297766434462          0.874810852669
H         -0.133759222034          1.819976096633         -1.749887546929
H          0.070988505364         -1.229340857694         -0.924871582742
Energy    = -114.256666258259
Spin(**2) =    0.000000000000
ZPVE      =    0.015452598301
Normal mode eigenvalues : nmode = 5
  0.002898680   0.017120535   0.044447960   0.133451006   0.312129919
CONNECTION : 1 - DC
 
# Geometry of DC 1, SYMMETRY = Cs
C          0.261089488059          0.228184033158         -2.283670811027

The xxx_DC_list.log file shows structures obtained by a constrained geometry optimization in which the distance between centers of dissociated fragments (automatically defined) are kept fixed. Their ZPVE and normal mode eigenvalues are based on a normal mode analysis within the geometrical hyperspace active in the constraints. Here, CONNECTION : 1 - DC indicates that the meta-IRC (mass-weighted steepest descent path starting from a non-stationary point) starting from this DC structure reaches EQ1. Results of meta-IRC calculations starting from DCn are printed in xxx_DCn.log file.

Structures, energies, spin expectation values, ZPVE values, normal mode eigenvalues, and connections of each path top (PT) structure are listed in xxx_PT_list.log file as:

List of Path Top (Approximate TS) Structures
 
# Geometry of TS 0, SYMMETRY = Cs
C         -0.014441897787         -0.114161725616         -0.908239011859
O          0.033308589243          0.258379037743          0.352908202909
H         -0.032990380622          1.078764658960         -0.486055144261
H          0.014123689168         -1.222981971083         -1.061803046786
Energy    = -114.273925672238
Spin(**2) =    0.000000000000
ZPVE      =    0.020464285078
Normal mode eigenvalues : nmode = 6
 -0.163207131   0.021752056   0.063459475   0.072991023   0.258162467
  0.324666671
CONNECTION : 0 - 1
 
# Geometry of TS 1, SYMMETRY = Cs
C         -0.025246155778         -0.376131653929         -0.232720610362

PTs corresponds to the highest energy point along the LUP path. The corresponding LUP path including PTn as the highest energy point is shown in xxx_PTn.log file. CONNECTION : 0 - 1 indicates that local minimum optimization starting from the two end points of the LUP path converged to EQ0 and EQ1, respectively.

Frequently used options
Go back to INDEX
Updated At:Feb. 13, 2018, 6:18 p.m.

Attachment

Page list