#!/bin/sh

# This example consists of three MD runs exercising the Deformation feature in MD:
#   1. Simple deformations of a 2D slab
#   2. Complex sequence of deformations of a 3D box including multiple simultaneous deformations
#   3. Combination of a uniaxial strain with barostatting the remaining directions

# This run first oscillates the lengths of the lattice vectors of the original non-orthogonal
# lattice of an argon slab to 20 and 12 Angstrom respectively and back to the original values,
# with a period of 125 fs. Afterwards, it linearly morphs the lattice to a 5 by 5 Angstrom square.
AMS_JOBNAME=Ar-2D "$AMSBIN/ams" <<EOR
# Set the random number seed to ensure reproducible results for testing. Omit this in normal runs.
RNGSeed -2056449389 -1942239902 -422783941 -563204803 439708673 85320298 1328648683 -688288369

Task MolecularDynamics

MolecularDynamics
    nSteps 1000
    TimeStep 0.25
    CalcPressure True
    InitialVelocities Type=Zero
    Trajectory SamplingFreq=10
    Deformation
        StopStep 500
        Type Cosine
        TargetLength 20 12
        Period 125
    End
    Deformation
        StartStep 500
        Type Linear
        TargetLattice
            5 0 0
            0 5 0
        End
    End
    BinLog
        Step
        Time
        PressureTensor
        Pressure
        Volume
        Density
    End
End

System
    Atoms
        Ar 0.5 0.6 0.7
        Ar 3.0 3.2 3.4
    End
    Lattice
        10.0 2.0 0.0
        1.0 10.0 0.0
    End
End

Engine LennardJones
    Rmin 3.753962043231411
    Eps 3.98e-4
    Cutoff 12.0
EndEngine
EOR

# Print the evolution of the lattice parameters in the "fort.59" format
# of old standalone reaxff for testing purposes.
echo "BEGIN fort59 nobarostat"
"$AMSBIN/amspython" "$AMSHOME/scripting/standalone/reaxff-ams/fort59.py" Ar-2D.results
echo "END fort59"


# This run applies a sequence of deformations to a box of Lennard-Jones argon atoms.
AMS_JOBNAME=Ar-box "$AMSBIN/ams" <<EOR
# Set the random number seed to ensure reproducible results for testing. Omit this in normal runs.
RNGSeed 1450250278 2029462689 827312839 1518230169 1408825437 1769469410 -406759494 -1006638501

Task MolecularDynamics

MolecularDynamics
    nSteps 10000
    InitialVelocities Type=Random Temperature=300
    Thermostat Type=NHC Temperature=300 Tau=100
    Timestep 1
    Trajectory SamplingFreq=100
    CalcPressure True
    # Compress the a and b vectors to 20 Angstrom and stretch the c vector to 40 Angstrom over 2000 steps.
    Deformation
        StartStep 0
        StopStep 2000
        Type Linear
        TargetLength 20 20 40
    End
    # Oscillate the c vector (z axis) from 40 to 30 Angstroms and back again with a period of 1000 fs.
    Deformation
        StartStep 2000
        StopStep 3500
        Type Cosine
        TargetLattice
            20.0  0.0  0.0
            0.0  20.0  0.0
            0.0   0.0 30.0
        End
        Period 1000
    End
    # Shear the box by tilting the c vector 10 A away from the z axis in the xz plane.
    Deformation
        StartStep 3500
        StopStep 4000
        Type Linear
        TargetLattice
            20.0  0.0  0.0
            0.0  20.0  0.0
            10.0  0.0 30.0
        End
    End
    # The following two blocks apply simultaneous cosine and sine oscillations to the
    # x and y components of the c vector. The amplitude of both oscillations is the same,
    # indirectly defined by the maximum velocity (velocity at the inflection point).
    # The c vector thus traces out a cone around the z axis over 2000 fs.
    Deformation
        StartStep 4000
        StopStep 8000
        Type Cosine
        LatticeVelocity
            0.0  0.0  0.0
            0.0  0.0  0.0
           -3e-2 0.0  0.0
        End
        Period 2000
    End
    Deformation
        StartStep 4000
        StopStep 8000
        Type Sine
        LatticeVelocity
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0 3e-2  0.0
        End
        Period 2000
    End
    # This un-shears the box again, returning the c vector to the z axis.
    Deformation
        StartStep 8000
        StopStep 8500
        Type Linear
        TargetLattice
            20.0  0.0  0.0
            0.0  20.0  0.0
            0.0  0.0  30.0
        End
    End
    # Finally, apply an exponential ("true") strain by compressing the c vector by 1/1000th every step.
    Deformation
        StartStep 8500
        Type Exponential
        LengthRate 0.0 0.0 -1e-3
    End
End

System
    Atoms
        Ar  22.97333  5.533091  19.78068
        Ar  5.255777  10.75370  3.164254
        Ar  8.594419  0.957110  14.00514
        Ar  8.407438  7.306515  2.762099
        Ar  5.335001  18.10475  11.25000
        Ar  13.84870  24.00523  1.485310
        Ar  18.65495  8.812906  24.08580
        Ar  23.50126  5.372569  24.77962
        Ar  20.32336  23.84153  3.669808
        Ar  7.692337  5.389691  10.57909
        Ar  2.407753  7.779618  0.755645
        Ar  1.520220  15.74803  13.75000
        Ar  2.921397  15.34413  20.41981
        Ar  1.660913  18.10666  3.895263
        Ar  19.54458  18.76246  20.66279
        Ar  3.853819  4.537228  14.15265
        Ar  17.57174  15.47554  17.14501
        Ar  8.601399  2.836638  1.872337
        Ar  2.786004  3.601185  22.17957
        Ar  0.047572  18.11282  24.78959
        Ar  0.172965  0.035326  0.223982
        Ar  6.604983  7.254174  21.83257
        Ar  16.63254  15.02432  7.992034
        Ar  7.941898  9.130224  17.89523
        Ar  18.26063  20.70600  5.643385
        Ar  22.63932  15.20789  23.33429
        Ar  1.138343  21.37810  13.97294
        Ar  0.461841  18.99572  6.401096
        Ar  22.67542  22.89935  9.344785
        Ar  7.215648  18.28717  3.411308
    End
    Lattice
        25.0  0.0  0.0
        0.0  25.0  0.0
        0.0   0.0 25.0
  end
end

Engine LennardJones
  Eps 3.67e-4
  RMin 3.4
  Cutoff 12.0
EndEngine
EOR

# Print the evolution of the lattice parameters in the "fort.59" format
# of old standalone reaxff for testing purposes.
echo "BEGIN fort59 nobarostat"
"$AMSBIN/amspython" "$AMSHOME/scripting/standalone/reaxff-ams/fort59.py" Ar-box.results | cut -c 1-86
echo "END fort59"


# This run simulates an experiment to measure the mechanical properties of an argon box
# by stretching the lattice in the z direction by 100 ppm per timestep (1 fs) while simultaneously
# keeping the x and y axes relaxed using a barostat.
AMS_JOBNAME=Ar-box-barostat "$AMSBIN/ams" <<EOR
# Set the random number seed to ensure reproducible results for testing. Omit this in normal runs.
RNGSeed 877404503 1621112889 -559440914 -1857103174 -1082101960 -1842609385 -845245172 -279655974

Task MolecularDynamics

MolecularDynamics
    nSteps 8000
    InitialVelocities Type=Random Temperature=300
    Thermostat Type=NHC Temperature=300 Tau=100
    Barostat Type=MTK Pressure=1e7 Tau=1000 Scale=XY Equal=XY
    Timestep 1
    Trajectory SamplingFreq=100
    Deformation
        Type Exponential
        StrainRate
            0.0 0.0 0.0
            0.0 0.0 0.0
            0.0 0.0 1e-4
        End
    End
End

System
    Atoms
        Ar  22.97333  5.533091  19.78068
        Ar  5.255777  10.75370  3.164254
        Ar  8.594419  0.957110  14.00514
        Ar  8.407438  7.306515  2.762099
        Ar  5.335001  18.10475  11.25000
        Ar  13.84870  24.00523  1.485310
        Ar  18.65495  8.812906  24.08580
        Ar  23.50126  5.372569  24.77962
        Ar  20.32336  23.84153  3.669808
        Ar  7.692337  5.389691  10.57909
        Ar  2.407753  7.779618  0.755645
        Ar  1.520220  15.74803  13.75000
        Ar  2.921397  15.34413  20.41981
        Ar  1.660913  18.10666  3.895263
        Ar  19.54458  18.76246  20.66279
        Ar  3.853819  4.537228  14.15265
        Ar  17.57174  15.47554  17.14501
        Ar  8.601399  2.836638  1.872337
        Ar  2.786004  3.601185  22.17957
        Ar  0.047572  18.11282  24.78959
        Ar  0.172965  0.035326  0.223982
        Ar  6.604983  7.254174  21.83257
        Ar  16.63254  15.02432  7.992034
        Ar  7.941898  9.130224  17.89523
        Ar  18.26063  20.70600  5.643385
        Ar  22.63932  15.20789  23.33429
        Ar  1.138343  21.37810  13.97294
        Ar  0.461841  18.99572  6.401096
        Ar  22.67542  22.89935  9.344785
        Ar  7.215648  18.28717  3.411308
    End
    Lattice
        25.0  0.0  0.0
        0.0  25.0  0.0
        0.0   0.0 25.0
  end
end

Engine LennardJones
  Eps 3.67e-4
  RMin 3.4
  Cutoff 12.0
EndEngine
EOR

# Print the evolution of the lattice parameters in the "fort.59" format
# of old standalone reaxff for testing purposes.
echo "BEGIN fort59 barostat"
"$AMSBIN/amspython" "$AMSHOME/scripting/standalone/reaxff-ams/fort59.py" Ar-box-barostat.results | cut -c 1-86
echo "END fort59"