#!/bin/sh

export NSCM=1

#########################################################################################
# Phonons calculations
#########################################################################################

AMS_JOBNAME=reactant_phonons "$AMSBIN/ams" > reactant_phonons.out << EOF
    Task GeometryOptimization
    Properties Phonons=Yes
    System
        GeometryFile reactant.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=product_phonons "$AMSBIN/ams" > product_phonons.out << EOF
    Task SinglePoint
    Properties Phonons=Yes
    System
        GeometryFile product.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=transition_state_phonons "$AMSBIN/ams" > transition_state_phonons.out << EOF
    Task TransitionStateSearch
    Properties Phonons=Yes
    System
        GeometryFile transition_state.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=surface_phonons "$AMSBIN/ams" > surface_phonons.out << EOF
    Task GeometryOptimization
    Properties Phonons=Yes
    System
        GeometryFile surface.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

#########################################################################################
# Gamma Point Vibrational Analysis
#########################################################################################

AMS_JOBNAME=reactant "$AMSBIN/ams" > reactant.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes
    Thermo Temperatures=400.0
    System
        GeometryFile reactant.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=product "$AMSBIN/ams" > product.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes
    Thermo Temperatures=400.0
    System
        GeometryFile product.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=transition_state "$AMSBIN/ams" > transition_state.out << EOF
    Task TransitionStateSearch
    Properties NormalModes=Yes
    Thermo Temperatures=400.0
    System
        GeometryFile transition_state.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=surface "$AMSBIN/ams" > surface.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes
    Thermo Temperatures=400.0
    System
        GeometryFile surface.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=co2 "$AMSBIN/ams" > co2.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes
    Thermo Temperatures=400.0
    System
        GeometryFile co2.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

#########################################################################################
# Gamma Point Vibrational Analysis & Partial Hessian Approximation
#########################################################################################

AMS_JOBNAME=reactant_PH "$AMSBIN/ams" > reactant_PH.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes SelectedRegionForHessian=molecule
    Thermo Temperatures=400.0
    System
        GeometryFile reactant.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=product_PH "$AMSBIN/ams" > product_PH.out << EOF
    Task GeometryOptimization
    Properties NormalModes=Yes SelectedRegionForHessian=molecule
    Thermo Temperatures=400.0
    System
        GeometryFile product.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

AMS_JOBNAME=transition_state_PH "$AMSBIN/ams" > transition_state_PH.out << EOF
    Task TransitionStateSearch
    Properties NormalModes=Yes SelectedRegionForHessian=molecule
    Thermo Temperatures=400.0
    System
        GeometryFile transition_state.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

#########################################################################################
# Energy Landscape Refinement - Gamma Point Vibrational Analysis
#########################################################################################

AMS_JOBNAME=landscape "$AMSBIN/ams" > landscape.out << EOF
    Task PESExploration
    Thermo Temperatures=400.0
    PESExploration
        Job LandscapeRefinement
        LandscapeRefinement GenerateFragments=Yes
        StatesAlignment ReferenceRegion=surface DistanceDifference=0.5
    End
    System REACT
        GeometryFile reactant.xyz
    End
    System PROD
        GeometryFile product.xyz
    End
    System TS ts=Yes reactant=REACT product=PROD
        GeometryFile transition_state.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF

#########################################################################################
# Energy Landscape Refinement - Gamma Point Vibrational Analysis & Partial Hessian
#########################################################################################

AMS_JOBNAME=landscape_PH "$AMSBIN/ams" > landscape_PH.out << EOF
    Task PESExploration
    Properties SelectedRegionForHessian=molecule
    Thermo Temperatures=400.0
    PESExploration
        Job LandscapeRefinement
        LandscapeRefinement GenerateFragments=Yes
        StatesAlignment ReferenceRegion=surface DistanceDifference=0.5
    End
    System REACT
        GeometryFile reactant.xyz
    End
    System PROD
        GeometryFile product.xyz
    End
    System TS ts=Yes reactant=REACT product=PROD
        GeometryFile transition_state.xyz
    End
    Engine ReaxFF
        ForceField CHONSFPtClNi.ff
    EndEngine
EOF