#!/bin/bash

export NSCM=1

# Here we show the role played by the  (ForceField.Type) atom attribute

# on purpose we specify a strange type for the carbon atoms "C_2" (nonsensical for any of the regions)

# we also show that capitalization does not matter for the keys ForceField.Charge and Type.
# For the values, such as C_R the case matters


# In the first run we specify in the input ForceField.Type
# The result is that for all regions this will be used, and the type for C is always C-2
# -------------------
# region mol.  C-type
# -------------------
#  MM    CH3   C_2
#  *     C2H6  C_2
#  QM    CH4   C_2 
#--------------------


export AMS_JOBNAME=type=inp.cap=none

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task GeometryOptimization

Properties Gradients=yes

System
    Atoms
        C -1.559601 -1.234340  0.000641 region=QM forcefield.charge=-0.27  forcefield.type=C_2
        H -1.898371 -0.303860  0.503021 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        H -2.034545 -2.108050  0.494609 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        H -1.869847 -1.205955 -1.065139 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        C -0.047661 -1.348892  0.094039 region=MM ForceField.Charge=-0.27  ForceField.Type=C_2
        H  0.427282 -0.475182 -0.399929 region=MM ForceField.Charge=0.09   ForceField.Type=H_
        H  0.291107 -2.279373 -0.408341 region=MM ForceField.Charge=0.09   ForceField.Type=H_
        H  0.262583 -1.377277  1.159819 region=MM ForceField.Charge=0.09   ForceField.Type=H_
    End
    GuessBonds True
End


Engine Hybrid
    QMMM qmRegion=QM qmEngineID=DFTB mmEngineID=ForceField
    
    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

EndEngine

eor

#  Not specifying the types, they will be guessed independently for all regions

# -------------------
# region mol.  C-type
# -------------------
#  MM    CH3   C_R
#  *     C2H6  C_3
#  QM    CH4   C_3 
#--------------------

export AMS_JOBNAME=type=none.cap=none

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task GeometryOptimization

Properties Gradients=yes

System
    Atoms
        C -1.559601 -1.234340  0.000641 region=QM forcefield.charge=-0.27
        H -1.898371 -0.303860  0.503021 region=QM ForceField.Charge=0.09 
        H -2.034545 -2.108050  0.494609 region=QM ForceField.Charge=0.09 
        H -1.869847 -1.205955 -1.065139 region=QM ForceField.Charge=0.09 
        C -0.047661 -1.348892  0.094039 region=MM ForceField.Charge=-0.27
        H  0.427282 -0.475182 -0.399929 region=MM ForceField.Charge=0.09 
        H  0.291107 -2.279373 -0.408341 region=MM ForceField.Charge=0.09 
        H  0.262583 -1.377277  1.159819 region=MM ForceField.Charge=0.09 
    End
    GuessBonds True
End


Engine Hybrid
    QMMM qmRegion=QM qmEngineID=DFTB mmEngineID=ForceField
    
    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

    GuessAttributesOnce False

EndEngine

eor


# The last two runs are mostly a technical test
# We change the capping setup, but that influences only the capping atom

export AMS_JOBNAME=type=inp.cap=inp

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task GeometryOptimization

Properties Gradients=yes

System
    Atoms
        C -1.559601 -1.234340  0.000641 region=QM forcefield.charge=-0.27  forcefield.type=C_2
        H -1.898371 -0.303860  0.503021 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        H -2.034545 -2.108050  0.494609 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        H -1.869847 -1.205955 -1.065139 region=QM ForceField.Charge=0.09   ForceField.Type=H_
        C -0.047661 -1.348892  0.094039 region=MM ForceField.Charge=-0.27  ForceField.Type=C_2
        H  0.427282 -0.475182 -0.399929 region=MM ForceField.Charge=0.09   ForceField.Type=H_
        H  0.291107 -2.279373 -0.408341 region=MM ForceField.Charge=0.09   ForceField.Type=H_
        H  0.262583 -1.377277  1.159819 region=MM ForceField.Charge=0.09   ForceField.Type=H_
    End
    GuessBonds True
End


Engine Hybrid
    QMMM qmRegion=QM qmEngineID=DFTB mmEngineID=ForceField
    
    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

    Capping
        CappingElement Li
        AtomicInfoForCappingAtom ForceField.Type=Li
    End

EndEngine

eor

export AMS_JOBNAME=type=none.cap=inp

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams <<eor

Task GeometryOptimization

Properties Gradients=yes

System
    Atoms
        C -1.559601 -1.234340  0.000641 region=QM forcefield.charge=-0.27 
        H -1.898371 -0.303860  0.503021 region=QM ForceField.Charge=0.09  
        H -2.034545 -2.108050  0.494609 region=QM ForceField.Charge=0.09  
        H -1.869847 -1.205955 -1.065139 region=QM ForceField.Charge=0.09  
        C -0.047661 -1.348892  0.094039 region=MM ForceField.Charge=-0.27 
        H  0.427282 -0.475182 -0.399929 region=MM ForceField.Charge=0.09  
        H  0.291107 -2.279373 -0.408341 region=MM ForceField.Charge=0.09  
        H  0.262583 -1.377277  1.159819 region=MM ForceField.Charge=0.09  
    End
    GuessBonds True
End


Engine Hybrid
    QMMM qmRegion=QM qmEngineID=DFTB mmEngineID=ForceField
    
    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

    Capping
        CappingElement Li
        AtomicInfoForCappingAtom ForceField.Type=Li
    End

    GuessAttributesOnce False

EndEngine

eor