AFIR-web Support Site

Multi-component algorithm (MC-AFIR)

A stochastic search for AFIR paths starting from random mutual orientations and positions is performed when the MC-AFIR keyword is designated. An example for the Aldol reaction is shown below:

MC-AFIR/B3LYP/6-31G
 
0 1
C        0.000000    0.000000   -0.542432   1
O        0.000000    0.000000    0.689131   1
H        0.000000    0.933503   -1.129226   1
H        0.000000   -0.933503   -1.129226   1
C        0.000000    0.449088    0.000000   2
C        1.229479   -0.074689    0.000000   2
O       -1.202903   -0.246241    0.000000   2
H       -0.199138    1.513645    0.000000   2
H        1.411363   -1.146198    0.000000   2
H        2.098519    0.571041    0.000000   2
H       -1.064389   -1.214959    0.000000   2
Options
NFault = 50
Add Interaction
Fragm.1 = 1,2
Fragm.2 = 5-7,11
1 2
GAMMA = 200
END
 

The last integer in each Cartesian coordinate is for random distribution of each molecule; in this case, HCHO is part #1 and H2C=CHOH is part #2 (see Part designation for random structure generation).

The NFault = 50 keyword provides a stopping criterion, where the stochastic search will be terminated when the last 50 AFIR paths give no new product. In a MC-AFIR calculation, you need to specify a stopping criterion by using NFault = n or NSample = n keyword.

There are four lines between the Add Interaction … END keywords:
(1) Fragm.1 = 1,2 specifies that atoms 1 and 2 belong to fragment #1 (atoms belonging to the fragment A of the AFIR function),
(2) Fragm.2 = 5-7,11 specifies that atoms 5–7 and 11 belong to fragment #2 (atoms belonging to the fragment B of the AFIR function),
(3) the artificial force is applied between the fragments #1 and #2,
(4) the initial γ value is set to 200s kJ/mol and is gradually increased to 200 kJ/mol, where s is the random number between 0 and 1.

The history of AFIR minimizations and corresponding AFIR path profiles appear in xxx_EQn.log files. For example, this AFIR minimization gives the aldol addition product (3-hydroxypropanal, CHOCH2CH2OH) from HCHO and H2C=CHOH.

# Geometry optimization starting from a random structure
 
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
 
# ITR. 0
C         -0.540936514510          0.642893723683          0.666366212385
O          0.026751246314          0.125252441047          1.628928174905
H         -0.105004419262          1.492775128740          0.115530615210
H         -1.517832851012          0.286285985996          0.299951804105
C          0.568973384233         -0.053494217478         -0.791852842498
C         -0.262880591377          0.673833504707         -1.543500569145
O          0.268899839016         -1.228357438722         -0.113538516775
H          1.607310832988          0.204482332750         -0.623802280651
H         -1.302735396999          0.400164089027         -1.701678825180
H          0.086155801452          1.577613934590         -2.026773044611
H         -0.663847278893         -1.495343702957         -0.241217177722
           Item                    Value                Threshold
           ENERGY       -268.019793471042
           Spin(**2)       0.000000000000
           LAMDA          -0.352906091272
           TRUST RADII     0.100000000000
           STEP RADII      0.099999989666
  Maximum  Force           0.210290244955          0.000060000000
  RMS      Force           0.060599825781          0.000040000000
  Maximum  Displacement    0.020532281193          0.000300000000
  RMS      Displacement    0.009137884037          0.000200000000
NORMAL MODE EIGENVALUE : N_MODE = 27
 -0.014681504  -0.008511168  -0.000178336   0.011266906   0.017799578
  0.027561925   0.032817954   0.049674405   0.059800244   0.095898853
  0.122765847   0.129883647   0.137069574   0.162066311   0.173561445
  0.189233172   0.205047624   0.261867122   0.323541243   0.396700830
  0.593958115   0.790149481   0.819969212   0.961279874   1.069551765
  1.449123479   1.536917879
 
# ITR. 1
 

 
# ITR. 121
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
           Item nbsp;                   Value                Threshold
           ENERGY       -268.147165081138
           Spin(**2)       0.000000000000
           LAMDA           0.000000047011
           TRUST RADII     0.010000000000
           STEP RADII      0.000038327528
  Maximum  Force           0.000007800063          0.000060000000
  RMS      Force           0.000002700314          0.000040000000
  Maximum  Displacement    0.000016894323          0.002307673758
  RMS      Displacement    0.000006184179          0.001538449172
NORMAL MODE EIGENVALUE : N_MODE = 27
  0.002948307   0.003514348   0.011132064   0.017382588   0.028646131
  0.042045668   0.047591209   0.056494074   0.070584220   0.077213762
  0.099431003   0.105421624   0.144396599   0.178250796   0.195439892
  0.230543169   0.266132098   0.277794184   0.432649094   0.562201985
  0.693605925   0.783379895   0.814074876   0.883169566   0.916859801
  1.018291727   1.504266977
 
=========================================================================
Optimized structure, SYMMETRY = C1  
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
ENERGY    = -268.147165081138 (-268.266268520120 :    0.000000000000)
Spin(**2) =    0.000000000000
GRADIENT VECTOR
   0.000001792320
  -0.000000951514

  -0.000004418902
 
Stationary point was found
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
 
---Profile of AFIR path
   Itr.       Length (ang)          Energy (real)            Energy (fit)
      0     0.000000000000       -268.091781022859       -268.091843039207         -0.79
      1     0.052493147309       -268.106691683549       -268.106635647314         -0.82
      2     0.153933590264       -268.130250034996       -268.130176731684         -0.84
      ︙
    121     7.376087521129       -268.266268520120       -268.266221739599         -1.00
 
---Approximate TS geometry (between 53 and 54)
C         -0.769043350099          0.836174754828          0.553666033676
O         -0.946931216613         -0.363105624661          1.069183231473
H          0.081022489940          1.436287874035          0.914124669930
H         -1.652266963961          1.448484153975          0.333105701673
C          0.797124542080         -0.256455727715         -1.107244840230
C         -0.326367647985          0.553591793619         -1.306893151361
O          0.713078562496         -1.378208111551         -0.412787655918
H          1.808089199114          0.082216129416         -1.330941548075
H         -1.278879764100          0.062283179364         -1.488712985732
H         -0.184297425384          1.470276554491         -1.875647339676
H         -0.076674373533         -1.265439194417          0.320561434271
ENERGY    = -268.211573137597
 
---Approximate EQ geometry (121)
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
ENERGY    = -268.266221739599

The approximate product and TS structures will be listed in xxx_EQ_list.log and xxx_TS_list.log files, respectively. These approximate structures may be optimized either manually one by one (by using MIN, SADDLE or LUP keyword), or automatically using the RePATH keyword.

Frequently used options

Manual