AFIRサンプル

Geometry refinement calculation (ReStruct)

Geometry refinement calculation (ReStruct)

The ReStruct calculation automatically apply geometry optimizations to all structures that are read from previous results. IRC calculations are also done starting from all obtained TSs and DCs. An input file for formaldehyde is:

%infile=yyy
ReStruct/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 = C2v
C         -0.000000000006          0.000000000039         -0.534656356092
O          0.000000000003         -0.000000000004          0.677825423735
H          0.000000000002          0.946918882193         -1.123179033811
H          0.000000000002         -0.946918882228         -1.123179033833
Energy    = -114.411104864438
Spin(**2) =    0.000000000000
ZPVE      =    0.026610552464
Normal mode eigenvalues : nmode = 6
  0.053632974   0.059321405   0.087390141   0.120044413   0.325206009
  0.341971262
 
# Geometry of EQ 1, SYMMETRY = Cs
C         -0.014464331935         -0.146282396113         -0.937385734968

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

List of Transition Structures
 
# Geometry of TS 0, SYMMETRY = Cs
C         -0.014438717020         -0.114141816271         -0.908210809051
O          0.033311271596          0.258262704934          0.352879022852
H         -0.032997409557          1.078901467851         -0.486082506137
H          0.014124854982         -1.223022356510         -1.061774707666
Energy    = -114.273925684508
Spin(**2) =    0.000000000000
ZPVE      =    0.020463091300
Normal mode eigenvalues : nmode = 6
 -0.163261240   0.021771822   0.063485937   0.073016129   0.258007097
  0.324535644
CONNECTION : 1 - 0
 
# Geometry of TS 1, SYMMETRY = Cs
C         -0.025314919219         -0.376948691957         -0.229636874620
O         -0.003401661385          0.070377234148          0.855757777084
H          0.055283877687          0.802578510711         -1.401311002190
H         -0.026567297074         -0.496007052917         -1.327998900275
Energy    = -114.272371551111
Spin(**2) =    0.000000000000
ZPVE      =    0.018462205512
Normal mode eigenvalues : nmode = 6
 -0.140193388   0.024810706   0.030095627   0.069143329   0.131568672
  0.384188098
CONNECTION : 0 - DC
 
# Geometry of TS 2, SYMMETRY = C1
C          0.118182388283         -0.213250205550         -1.035903244986

Here, CONNECTION : 1 - 0 indicates that this TS is a transition state between EQ1 and EQ0, and CONNECTION : 0 - DC indicates that this TS is a transition state for a dissociation channel (DC) from EQ0. 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          0.021926761829         -0.292868830946         -0.303240708128
O          0.040843955560         -0.297766423101          0.874810857878
H         -0.133759222034          1.819976096633         -1.749887546929
H          0.070988504643         -1.229340842590         -0.924871602821
Energy    = -114.256666258259
Spin(**2) =    0.000000000000
ZPVE      =    0.015452598399
Normal mode eigenvalues : nmode = 5
  0.002898679   0.017120532   0.044447956   0.133451015   0.312129949
CONNECTION : 0 - DC
 
# Geometry of DC 1, SYMMETRY = C2v
C          0.032121160171          0.002878768811         -0.772176196725

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 : 0 - DC indicates that the meta-IRC (mass-weighted steepest descent path starting from a non-stationary point) starting from this DC structure reaches EQ0. Results of meta-IRC calculations starting from DCn are printed in xxx_DCn.log file.

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

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