AFIRサンプル

Global reaction route mapping by single-component algorithm (SC-AFIR)

Global reaction route mapping by single-component algorithm (SC-AFIR)

If SC-AFIR is used, AFIR paths and related EQs, TSs, and DCs are explored automatically starting from local minima. An example for HCHO is shown below:

SC-AFIR2/B3LYP/D95V(d)
 
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
Options
Add Interaction
GAMMA = 1000
END
SC=FindUDC
 

In the SC-AFIR calculations, fragments are defined automatically in a given system, and let them react with each other by the AFIR method. There is a single line between the Add Interaction … END keywords, and it provides the γ value to be applied to the system. In this case, a very large value GAMMA = 1000 is adopted, in order to explore the entire PES of the given system and obtain the global reaction route map.

SC-AFIR2 applies up to two force functions simultaneously to the system; this keyword is used when to search not only low energy regions but also high energy regions of the PES. SC-AFIRn (10 ≥ n ≥ 2) which applies n force functions simultaneously to the system, are also available. When your interest is only low energy regions, SC-AFIR should be used instead of SC-AFIRn. SC-AFIRn generates many dummy EQs, where dummy EQs can be distinguished from the actual EQs when one draws the reaction path network because these dummy EQs do not have any connection with the other EQs. For further details of SC-AFIRn, see S. Maeda, et al., J. Comput. Chem., 2018, 39, 233–251 (this paper is Open Access).

In default, dissociation channels that do not have any peak along the corresponding dissociation path (e.g., radical-radical dissociation/association path) are discarded even if such paths are found. This is because, in general, such paths produce unstable species such as a radical pair. These paths are examined automatically and stored in xxx_DC_list.log and xxx_DCn.log files when the SC=FindUDC option is used.

Only five lowest energy EQs are printed in xxx.log file. Many other intermediate (.rrm) and output (.log) files are created. Structures and energies of obtained EQs and transition structures (TSs) are listed in xxx_EQ_list.log and xxx_TS_list.log files, respectively. 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         -0.000000000711          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
Energy    = -114.523864895551 (-114.523864895551 :    0.000000000000)
Spin(**2) =    0.000000000000
ZPVE      =    0.026781405457
Normal mode eigenvalues : nmode = 6
  0.054381882   0.061068479   0.089972737   0.125646043   0.324888966
  0.338899385
 
# Geometry of EQ 1, SYMMETRY = C2v
C         -0.000054615078          0.000101770730         -0.388100269398

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         -0.013929376714         -0.113628814870         -0.904273945128
O          0.033439783352          0.256223450929          0.353350645790
H         -0.033321748175          1.077578601983         -0.489832301447
H          0.013811341538         -1.220173238037         -1.062433399216
Energy    = -114.382131496277 (-114.382131496277 :    0.000000000000)
Spin(**2) =    0.000000000000
ZPVE      =    0.020550398599
Normal mode eigenvalues : nmode = 6
 -0.169514707   0.021336409   0.065437855   0.078875924   0.256573067
  0.319851666
CONNECTION : 0 - 2
 
# Geometry of TS 1, SYMMETRY = Cs
C         -0.025738746327         -0.383842986070         -0.230798533873
O         -0.003221966526          0.073111205144          0.854128407915
H          0.055183110811          0.800938483652         -1.401634981810
H         -0.026222397949         -0.490206702740         -1.324883892233
Energy    = -114.379676494086 (-114.379676494086 :    0.000000000000)
Spin(**2) =    0.000000000000
ZPVE      =    0.018560127095
Normal mode eigenvalues : nmode = 6
 -0.142573079   0.025289387   0.030238913   0.070045993   0.136813641
  0.381177579
CONNECTION : 0 - DC
 
# Geometry of TS 2, SYMMETRY = C1
C          0.113880206829         -0.219873259124         -1.044499136373

Here, CONNECTION : 0 - 2 indicates that this TS is a transition state between EQ0 and EQ2, 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 (without the SC=FindUDC option, this file is empty):

List of Dissociated Structures
 
# Geometry of DC 0, SYMMETRY = Cs
C          0.021376273838         -0.286120468290         -0.308965590088
O          0.040985632603         -0.300575286442          0.871319277483
H         -0.133759222034          1.819976096633         -1.749887546929
H          0.071397315590         -1.233280341904         -0.915655140467
Energy    = -114.362872246755 (-114.362872246755 :    0.000000000000)
Spin(**2) =    0.000000000000
ZPVE      =    0.015667083380
Normal mode eigenvalues : nmode = 5
  0.003276649   0.018657217   0.048593722   0.139832834   0.302067304
CONNECTION : 0 - DC
 
# Geometry of DC 1, SYMMETRY = C2v
C          0.032457086336          0.002924755381         -0.774654956854

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.

In addition to lists for EQs, TSs, and DCs, xxx_PT_list.log file will be created. 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 (when the EQOnly option is used without neither KeepSCPath nor KeepLUPPath, this file is empty):

List of Path Top (Approximate TS) Structures
 
# Geometry of TS 0, SYMMETRY = Cs
C         -0.013929376714         -0.113628814870         -0.904273945128
O          0.033439783352          0.256223450929          0.353350645790
H         -0.033321748175          1.077578601983         -0.489832301447
H          0.013811341538         -1.220173238037         -1.062433399216
Energy    = -114.382131496277 (-114.382131496277 :    0.000000000000)
Spin(**2) =    0.000000000000
ZPVE      =    0.020550398599
Normal mode eigenvalues : nmode = 6
 -0.169514707   0.021336409   0.065437855   0.078875924   0.256573067
  0.319851666
CONNECTION : 0 - 2
 
# Geometry of TS 1, SYMMETRY = Cs
C         -0.013929278485          0.113628777754         -0.904273961931

PTs corresponds to the highest energy point along the AFIR or LUP path. In default, PTs are the highest energy point along the LUP path. When KeepSCPath option is used together with EQOnly, PTs are the highest energy point along the AFIR path. When KeepLUPPath option is used together with EQOnly, PTs are the highest energy point along the LUP path. The corresponding AFIR or LUP path including PTn as the highest energy point is shown in xxx_PTn.log file. CONNECTION : 0 - 2 indicates that local minimum optimization starting from the two end points of the AFIR or LUP path converged to EQ0 and EQ2, respectively.

Frequently used options
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Updated At:April 3, 2018, 4:49 p.m.

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