#!/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 "$AMSBIN/ams" <<EOR
# Set the random number seed to ensure reproducible results for testing. Omit this in normal runs.
RNGSeed -2056449389 -1942239902 -422783941 -563204803 439708673 85320298 1328648683 -688288369
Task MolecularDynamics
MolecularDynamics
nSteps 1000
TimeStep 0.25
CalcPressure True
InitialVelocities Type=Zero
Trajectory SamplingFreq=10
Deformation
StopStep 500
Type Cosine
TargetLength 20 12
Period 125
End
Deformation
StartStep 500
Type Linear
TargetLattice
5 0 0
0 5 0
End
End
End
System
Atoms
Ar 0.5 0.6 0.7
Ar 3.0 3.2 3.4
End
Lattice
10.0 2.0 0.0
1.0 10.0 0.0
End
End
Engine LennardJones
Rmin 3.753962043231411
Eps 3.98e-4
Cutoff 12.0
EndEngine
EOR
# Print the evolution of the lattice parameters in the "fort.59" format
# of old standalone reaxff for testing purposes.
echo "BEGIN fort59 nobarostat"
"$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"