Example: Restarting a geometry optimization¶
#!/bin/sh
# Step 1: Run the entire optimization in one go to get the reference result.
AMS_JOBNAME=reference $AMSBIN/ams 2>&1 << EOF
Task GeometryOptimization
System
Atoms
Mg 0.00000000 0.00000000 0.00000000
H -1.27917000 4.11016000 4.72389000
O 2.16655000 -0.38813000 -7.10271000
H -1.42939000 1.48933000 -2.39439000
H 1.09521000 1.50513000 -11.11199000
C -1.73924000 -3.56815000 -7.25491000
O 1.13468000 2.30574000 -6.31297000
H -1.00635000 -3.89600000 0.57440000
C 2.39949000 1.96079000 -8.76280000
H -0.50312000 -2.26723000 5.55260000
H 0.50312000 2.26723000 -5.55260000
C -1.58070000 0.43033000 8.37317000
C 1.68553000 0.69328000 -9.20655000
H 3.10514000 2.27128000 -9.54815000
C -2.12273000 1.75783000 3.90134000
C -1.41195000 -3.08564000 8.52014000
C -0.80701000 1.55547000 8.71125000
H 2.96787000 1.75892000 -7.84715000
H -3.10514000 -2.27128000 9.54815000
H 1.41484000 -2.74396000 -7.00335000
H 1.12426000 -3.20203000 2.78552000
C -0.17468000 1.56294000 9.95926000
C -0.72719000 -2.63659000 -6.99325000
C -1.09765000 -3.99973000 9.52904000
H -0.25814000 -8.23193000 -3.30969000
C 1.14520000 -2.61556000 -3.22986000
O 0.72583000 -0.95806000 -1.56717000
H -2.36816000 -5.34341000 -4.50996000
H -2.96787000 -1.75892000 7.84715000
H -2.25336000 0.75053000 3.46787000
N 2.80755000 -2.14965000 -4.91471000
C -0.30154000 0.48014000 10.82965000
C 0.54101000 -2.17341000 -2.01004000
C 2.39908000 0.51189000 4.29012000
H -1.63623000 -3.94265000 10.47839000
H 0.19490000 0.50042000 11.80153000
N 0.47889000 1.91215000 -0.81627000
C -0.66060000 -2.05093000 2.26021000
H -0.20633000 -7.24015000 -5.59602000
H 1.49008000 0.40226000 3.68367000
H -0.39995000 4.15871000 -4.93170000
H -1.12426000 3.20203000 -2.78552000
C -1.03828000 -0.64018000 10.44800000
H 1.56169000 4.33269000 8.01583000
C -0.11223000 -4.97150000 9.34588000
C -0.03554000 7.26375000 2.87602000
H -1.09521000 -1.50513000 11.11199000
H 3.22983000 0.79151000 3.62424000
C 3.45382000 -1.03521000 -6.98441000
O -0.72583000 0.95806000 1.56717000
H 2.36816000 5.34341000 4.50996000
C -1.68553000 -0.69328000 9.20655000
H 4.21952000 -0.40168000 -7.46345000
H -1.28611000 -2.92413000 2.51305000
C 1.07673000 -4.19100000 5.79908000
C 0.46002000 6.10723000 3.76764000
H 0.19942000 5.47949000 5.84797000
H -0.11989000 5.68080000 -10.14146000
N -2.80755000 2.14965000 4.91471000
H 1.23144000 -6.29513000 -5.15638000
C 3.74078000 -1.20712000 -5.50076000
N -0.47889000 -1.91215000 0.81627000
C -0.57607000 5.02038000 -8.13428000
H 1.60192000 -5.15615000 5.75895000
H -1.13094000 -1.13799000 2.64965000
C -0.23845000 -3.15299000 -1.28978000
C -0.05550000 -4.76579000 -3.14405000
H -1.35753000 5.76910000 -7.98196000
H 3.72395000 -0.21480000 -5.00525000
H -1.13142000 7.24453000 2.78458000
H -4.76310000 1.61527000 5.41439000
H 4.76310000 -1.61527000 -5.41439000
C 2.12273000 -1.75783000 -3.90134000
C -0.28104000 4.13616000 -7.08959000
C 0.73514000 3.17615000 -7.28394000
C 0.81335000 -3.86199000 -3.77035000
C -2.39908000 -0.51189000 -4.29012000
H 2.25336000 -0.75053000 -3.46787000
C 1.41195000 3.08564000 -8.52014000
C -0.52384000 -4.40125000 -1.88411000
C -1.84973000 1.90289000 -4.97333000
H 0.20633000 7.24015000 5.59602000
C 1.09765000 3.99973000 -9.52904000
H 0.11989000 -5.68080000 10.14146000
H 0.25814000 8.23193000 3.30969000
H -1.49008000 -0.40226000 -3.68367000
H 1.63623000 3.94265000 -10.47839000
C -2.10065000 3.07251000 -5.70877000
C 0.57607000 -5.02038000 8.13428000
H -1.56169000 -4.33269000 -8.01583000
C 0.11223000 4.97150000 -9.34588000
H -1.13449000 -5.10187000 -1.30711000
H 0.39995000 -4.15871000 4.93170000
H 1.35753000 -5.76910000 7.98196000
C -3.29750000 3.15241000 -6.42939000
C 0.23845000 3.15299000 1.28978000
H -3.22983000 -0.79151000 -3.62424000
C -0.59486000 2.70197000 7.73655000
C 0.28104000 -4.13616000 7.08959000
C 0.52384000 4.40125000 1.88411000
H 0.43755000 2.42353000 10.23864000
H -3.50575000 4.04950000 -7.01656000
H 0.38971000 7.20647000 1.86361000
H 1.13449000 5.10187000 1.30711000
C 1.84973000 -1.90289000 4.97333000
C -1.07673000 4.19100000 -5.79908000
H 0.62192000 -3.64814000 -8.29677000
C -4.20635000 2.09524000 -6.41695000
C 2.10065000 -3.07251000 5.70877000
O -0.62968000 1.82005000 -4.28278000
C 0.03554000 -7.26375000 -2.87602000
C 1.99778000 6.16492000 3.88117000
C 3.29750000 -3.15241000 6.42939000
H -1.41484000 2.74396000 7.00335000
O -0.07653000 -0.68618000 -5.67912000
H -5.13801000 2.17027000 -6.98038000
H 3.50575000 -4.04950000 7.01656000
C -3.45382000 1.03521000 6.98441000
C -1.14520000 2.61556000 3.22986000
H -2.30900000 -7.11968000 -4.33255000
C 4.20635000 -2.09524000 6.41695000
H 0.78141000 -0.75072000 -6.17605000
H 1.13142000 -7.24453000 -2.78458000
C -0.54101000 2.17341000 2.01004000
H 5.13801000 -2.17027000 6.98038000
C -3.91320000 0.93142000 -5.70744000
H -1.60192000 5.15615000 -5.75895000
H -0.43755000 -2.42353000 -10.23864000
C 3.91320000 -0.93142000 5.70744000
C 0.72575000 -2.17732000 2.89574000
H -4.21952000 0.40168000 7.46345000
H -4.60197000 0.08443000 -5.74068000
H 4.60197000 -0.08443000 5.74068000
H -0.62192000 3.64814000 8.29677000
H 2.30900000 7.11968000 4.33255000
H 1.27917000 -4.11016000 -4.72389000
C 2.72586000 -0.80591000 4.97465000
C -2.72586000 0.80591000 -4.97465000
H -0.19942000 -5.47949000 -5.84797000
H 1.42939000 -1.48933000 2.39439000
C 0.96682000 1.65125000 6.01252000
C -1.99778000 -6.16492000 -3.88117000
C 0.59486000 -2.70197000 -7.73655000
C -0.96682000 -1.65125000 -6.01252000
C 2.18562000 1.61836000 5.30149000
C 0.05550000 4.76579000 3.14405000
H 3.43079000 -2.01409000 -7.48984000
C 1.58070000 -0.43033000 -8.37317000
C 3.16089000 2.57613000 5.58075000
C -3.74078000 1.20712000 5.50076000
C -0.81335000 3.86199000 3.77035000
H -3.43079000 2.01409000 7.48984000
H 4.09911000 2.55793000 5.02051000
C -2.18562000 -1.61836000 -5.30149000
C 0.80701000 -1.55547000 -8.71125000
H -2.47896000 -6.08599000 -2.89560000
C 2.94890000 3.55128000 6.55908000
C -0.13167000 6.28247000 5.17426000
C 0.13167000 -6.28247000 -5.17426000
C 0.17468000 -1.56294000 -9.95926000
H 3.71667000 4.29632000 6.77231000
C -3.16089000 -2.57613000 -5.58075000
C -0.46002000 -6.10723000 -3.76764000
C -0.61444000 -2.98553000 0.08587000
C 1.73924000 3.56815000 7.25491000
O 0.62968000 -1.82005000 4.28278000
H -0.38971000 -7.20647000 -1.86361000
H 2.47896000 6.08599000 2.89560000
H -4.09911000 -2.55793000 -5.02051000
C -0.72575000 2.17732000 -2.89574000
O 0.07653000 0.68618000 5.67912000
C 0.61444000 2.98553000 -0.08587000
O -2.16655000 0.38813000 7.10271000
C 0.30154000 -0.48014000 -10.82965000
H -3.72395000 0.21480000 5.00525000
H 1.00635000 3.89600000 -0.57440000
H -0.78141000 0.75072000 6.17605000
C -2.94890000 -3.55128000 -6.55908000
C 0.72719000 2.63659000 6.99325000
C 0.66060000 2.05093000 -2.26021000
H -1.23144000 6.29513000 5.15638000
H -0.19490000 -0.50042000 -11.80153000
C -2.39949000 -1.96079000 8.76280000
H 1.28611000 2.92413000 -2.51305000
O -1.13468000 -2.30574000 6.31297000
H -3.71667000 -4.29632000 -6.77231000
C 1.03828000 0.64018000 -10.44800000
H 1.13094000 1.13799000 -2.64965000
C -0.73514000 -3.17615000 7.28394000
End
End
GeometryOptimization
CoordinateType Cartesian
End
Engine DFTB
ResourcesDir DFTB.org/3ob-3-1
Model DFTB3
DispersionCorrection D3-BJ
EndEngine
EOF
# Step 2: Start the optimization but abort after 5 steps.
AMS_JOBNAME=aborted $AMSBIN/ams 2>&1 << EOF
Task GeometryOptimization
GeometryOptimization
MaxIterations 5
CoordinateType Cartesian
End
LoadSystem
File reference.results/ams.rkf
Section InputMolecule
End
LoadEngine reference.results/dftb.rkf
EOF
# Step 3: Restart the aborted optimization and finish it.
AMS_JOBNAME=resume $AMSBIN/ams 2>&1 << EOF
Task GeometryOptimization
GeometryOptimization
CoordinateType Cartesian
End
LoadSystem
File aborted.results/ams.rkf
End
LoadEngine aborted.results/dftb.rkf
EngineRestart aborted.results/dftb.rkf
EOF