Example: Linear transit¶
#!/bin/sh
echo "================="
echo "HCN isomerization"
echo "================="
echo
AMS_JOBNAME=HCN_isomerization $AMSBIN/ams << EOF
Task PESScan
# (Linear transit is just a PES scan with 1 scan coordinate.)
System
Atoms
C 0.00000000 0.00000000 1.04219000
H 0.00000000 0.00000000 -0.03324000
N 0.00000000 0.00000000 2.20064000
End
End
PESScan
ScanCoordinate
nPoints 25
Angle 2 1 3 180.0 0.0
End
End
Engine DFTB
Model DFTB0
ResourcesDir DFTB.org/mio-1-1
EndEngine
EOF
echo
echo "==================="
echo "Water angle transit"
echo "==================="
echo
AMS_JOBNAME=water_angle $AMSBIN/ams << EOF
Task PESScan
System
Atoms
O 0.00000000 0.00000000 0.59372000
H 0.00000000 0.76544000 -0.00836000
H 0.00000000 -0.76544000 -0.00836000
End
End
PESScan
ScanCoordinate
nPoints 25
Angle 2 1 3 80.0 180.0
End
End
GeometryOptimization
! Delocalized coordinates currently have a problem with linear systems.
! So we will use cartesian coordinates here.
CoordinateType Cartesian
End
Engine DFTB
Model DFTB0
ResourcesDir DFTB.org/mio-1-1
EndEngine
EOF
echo
echo "===================="
echo "Hydrocarbon reaction"
echo "===================="
echo
AMS_JOBNAME=hydcarb $AMSBIN/ams << EOF
Task PESScan
System
Atoms
C 0.14667300 -0.21503500 0.40053800
C 1.45297400 -0.07836900 0.12424400
C 2.23119700 1.15868100 0.12912100
C 1.78331500 2.39701500 0.38779700
H -0.48348000 0.63110600 0.67664100
H -0.33261900 -1.19332100 0.35411600
H 2.01546300 -0.97840100 -0.14506700
H 3.29046200 1.03872500 -0.12139700
H 2.45728900 3.25301000 0.35150400
H 0.74193400 2.60120700 0.64028800
C -0.75086900 1.37782400 -2.43303700
C -0.05392100 2.51281000 -2.41769100
H -1.78964800 1.33942600 -2.09651100
H -0.30849400 0.43896500 -2.76734700
H -0.49177100 3.45043100 -2.06789100
H 0.98633900 2.54913500 -2.74329400
End
End
PESScan
ScanCoordinate
nPoints 25
Distance 1 11 3.36 1.538
Distance 4 12 3.36 1.538
End
End
Engine DFTB
Model DFTB0
ResourcesDir DFTB.org/mio-1-1
EndEngine
EOF
echo
echo "====================================="
echo "Retinal trans -> 11-cis isomerization"
echo "====================================="
echo
AMS_JOBNAME=retinal_transcis $AMSBIN/ams << EOF
Task PESScan
System
Atoms
H -2.10968473 -1.58238733 0.78224517
C -2.10306857 -0.54058322 0.46363503
C -0.89436995 0.04807217 0.25528247
H -0.85555481 1.05432693 -0.15803658
C 0.38987539 -0.58661182 0.49038464
C 1.53213446 0.09657801 0.14394773
H 1.40518949 1.08783970 -0.29205231
H 3.05232192 -1.34477492 0.72115301
C 2.88311454 -0.36358433 0.28105432
C 3.96024700 0.37378345 -0.12385974
H 3.77965758 1.35231793 -0.56821856
C 5.34627719 -0.04025647 -0.02249097
C 6.32191717 0.80135945 -0.49190463
H 6.00090638 1.74979100 -0.92101391
C -4.46825064 -0.90426552 -0.39585925
C -5.87277429 -0.25303564 -0.45007491
C -3.41139545 0.06493448 0.19516310
C -3.67932839 1.38221399 0.41656971
C -5.81598497 1.19032366 -0.92660753
C -5.00049358 2.01922634 0.05561242
C -4.58391145 -2.18782901 0.46346394
C -4.01729542 -1.30039402 -1.82272212
C -2.72429960 2.32303313 1.10290124
C 0.40919453 -1.96244629 1.09501374
C 5.64155973 -1.38034133 0.59419110
C 7.76996060 0.56699126 -0.48750226
O 8.57693167 1.36615612 -0.92976322
H -6.51997817 -0.84904979 -1.10100203
H -6.32039371 -0.28079023 0.54871092
H -5.36159995 1.23817633 -1.92112092
H -6.82595442 1.60207678 -1.01946858
H -5.58216571 2.18390764 0.97424181
H -4.81292271 3.01993001 -0.35246294
H -4.74166770 -1.94289144 1.51126095
H -5.43008715 -2.78247632 0.12572479
H -3.69644845 -2.81116549 0.38705593
H -3.02900804 -1.75403268 -1.79820003
H -4.71056940 -2.01489741 -2.26202914
H -3.97070839 -0.42860260 -2.47090348
H -2.16469005 2.92261100 0.38111736
H -3.27791517 3.02297911 1.72885233
H -2.00470188 1.79865198 1.72726573
H -0.13689001 -1.97717074 2.03825359
H -0.07664772 -2.68134154 0.43362393
H 1.41837401 -2.31391556 1.28591185
H 5.15278730 -2.17622743 0.03222328
H 6.70436647 -1.59729505 0.62729622
H 5.25700064 -1.42489613 1.61313095
H 8.12614442 -0.41441814 -0.04549414
End
End
PESScan
ScanCoordinate
nPoints 25
Dihedral 6 9 10 12 180 0
Dihedral 8 9 10 11 180 0
End
End
Engine DFTB
Model DFTB0
ResourcesDir DFTB.org/mio-1-1
EndEngine
EOF