Example*: Mechanical embedding (QUILD)¶

#!/bin/sh

hybridenginename=hybrid     # this is a temporary hack
report=report.txt

echo "Start of the report" > $report


echo "------------------------------" >> $report
echo "Start of the region names test" >> $report
echo "------------------------------" >> $report

export AMS_JOBNAME=regionnamestest

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task SinglePoint

Properties Gradients=yes

System
  Atoms
     C 0.0  0.0 0.0  region=a
     O 1.13 0.0 0.0  region=A
     O -1.13 0.0 0.0 region=B
  End
  BondOrders
       1 2 2.0
       1 3 2.0
  End
End

Engine Hybrid
   Energy
      Term factor=1.0   region=*     engineID=ForceField
      Term factor=1.0   region=A       engineID=dftB-2
      Term factor=-1.0  region=a       engineID=ForceField
   End

   Capping
      AllowHighBondOrders True # Because we cut through double bonds here ...
      AtomicInfoForCappingAtom ForceField.Type=H_   # Remove ForceField.Charge because we do not specify charges for other atoms
   End

   Engine ForceField
   EndEngine
   Engine dftb dftb-1
     Model GFN1-xTB
   EndEngine
   Engine dftb dFtb-2
     Model SCC-DFTB
     ResourcesDir QUASINANO2015
   EndEngine
   Engine mopac
   EndEngine

EndEngine
eor

echo "Energy for region names test" >> $report
$AMSBIN/amsreport $AMS_JOBNAME.results/$hybridenginename.rkf -k "AMSResults%Energy"   >> $report

echo "----------------------------" >> $report
echo "End of the region names test" >> $report
echo "----------------------------" >> $report



echo "--------------------------" >> $report
echo "Start of the gradient test" >> $report
echo "--------------------------" >> $report

# strange capitalization is on purpose

for capping in fractionAl fiXed
do

for num in true false
do

export AMS_JOBNAME=gradtest.capping=$capping.num=$num

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task SinglePoint


Properties Gradients=yes

EngineDebugging IgnoreGradientsRequest=$num NeverQuiet=false

NumericalDifferentiation NuclearStepSize=1.0e-4

System
  Atoms
     C 0.0  0.0 0.0  region=a
     O 1.13 0.0 0.0  region=a
     O -1.13 0.0 0.0 region=b
  End
  BondOrders
       1 2 2.0
       1 3 2.0
  End
End

Engine Hybrid
   Capping
      Option $capping
      AllowHighBondOrders True # Because we cut through double bonds here ...
      AtomicInfoForCappingAtom ForceField.Type=H_   # Remove ForceField.Charge because we do not specify charges for other atoms
   End
   Energy
      Term factor=1.0   region=*     engineID=ForceField
      Term factor=1.0   region=a       engineID=dftb-2
      Term factor=-1.0  region=a       engineID=ForceField
   End

   Engine ForceField
   EndEngine
   Engine dftb dftb-1
     Model GFN1-xTB
   EndEngine
   Engine dftb dftb-2
     Model SCC-DFTB
     ResourcesDir QUASINANO2015
   EndEngine
   Engine mopac
   EndEngine

EndEngine


eor

echo "gradients for capping=$capping num=$num:" >> $report
$AMSBIN/amsreport $AMS_JOBNAME.results/$hybridenginename.rkf -k "AMSResults%Gradients##3"   >> $report

done
done

echo "------------------------" >> $report
echo "End of the gradient test" >> $report
echo "------------------------" >> $report



echo "---------------------------" >> $report
echo "Start of the singleton test" >> $report
echo "---------------------------" >> $report

echo "Calculate the same system twice with the same engine but with different settings. The energy should be non-zero" >> $report

for engine in dftb band adf mopac
do
export AMS_JOBNAME=testsingleton.engine.$engine

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams << eor

Task SinglePoint

System
   GeometryFile $AMSHOME/atomicdata/Molecules/TestMols/Acetamide.xyz
End

Engine Hybrid
   AllowSanityCheckWarnings true
   Energy
      Term factor=1.0   region=*       engineID=$engine-1
      Term factor=-1.0  region=*       engineID=$engine-2
   End

   Engine band band-1
      xc gga=pbe
   EndEngine
   Engine band band-2
      basis type=SZ
   EndEngine
   Engine adf adf-1
      xc gga=pbe
   EndEngine
   Engine adf adf-2
      basis type=SZ
   EndEngine
   Engine mopac mopac-1
      Model PM6
   EndEngine
   Engine mopac mopac-2
      Model PM7
   EndEngine
   Engine DFTB dftb-1
      Model GFN1-xTB
   EndEngine
   Engine DFTB dftb-2
      Model SCC-DFTB
      ResourcesDIR QUASINANO2015
   EndEngine

EndEngine

eor


echo "Hopfully nonzero energy for engine=$engine" >> $report
$AMSBIN/amsreport $AMS_JOBNAME.results/$hybridenginename.rkf -k "AMSResults%Energy"   >> $report

done

echo "-------------------------" >> $report
echo "End of the singleton test" >> $report
echo "-------------------------" >> $report


cat $report