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Add input and scripts for PFHub3 benchmark
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‎benchmarks/PFHub3/REAME

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#
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# Generate initial conditions (for phi)
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#
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python make_nuclei.py -x 1440 -y 1440 -z 1 -r 16 \
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--center0 "0, 0, 0" -w 1.4 1440.nc
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#
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# Run ampe
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#
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mpirun -np 32 ampe2d dendrite.input
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#
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# Analyze results
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#
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#extract solid fraction out of output
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python volfracvstime.py dendrite.log > solid_fraction.csv
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#plot it
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gnuplot solid_fraction.plt
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display SolidFraction.png
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#extract tip position out of VisIt dumps
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visit -cli -verbose -nowin -s tipPosition.py
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#plot tip position vs time
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gnuplot tip_position.plt
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display TipPosition.png
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#extract phi=0.5 contour out of last VisIt frame
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#into .xyz file
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visit -cli -verbose -nowin -s phase_field_1500.py
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#convert data to .csv format
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python xyz2csv.py phase_contour.xyz > phase_field_1500.csv
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#plot contour
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gnuplot phase_contour.plt
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display phase_field_1500.png
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#extract energy vs. tim
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python energy.py dendrite.log > free_energy.csv
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gnuplot energy.plt
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display Energy.png
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‎benchmarks/PFHub3/dendrite.input

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model_type = "KWCcomplex"
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end_time = 1500. // required
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max_timesteps = 1600 // optional, default is INT_MAX
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Verbosity { // optional, block
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level = 1 // optional, default=1
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}
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Visit {
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interval = 15.
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interval_type = "time"
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}
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TimerManager {
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timer_list = "solv::*::*","xfer::*::*","AMPE::*::*"
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print_threshold = 0.0
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}
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ModelParameters {
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epsilon_anisotropy = 0.05
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H_parameter = 0.0 // we need quaternions to define anisotropy
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epsilon_phi = 2.
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phi_mobility = 0.25
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orient_mobility = 1.
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epsilon_orient = 1.
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Temperature{
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type = "heat"
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equation_type = "unsteady"
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meltingT = 1.
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cp{
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SpeciesA{
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a = 17.020371256848037 // to get L/cp =1.
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}
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}
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thermal_diffusivity = 10.e-8 // cm^2/s
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latent_heat = 17.020371256848037 // 32*lambda/30.
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}
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// free energy parameters:
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// f(phi) = scale_energy_well*g(phi)
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// where g is a double well potential
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phi_well_scale = 0.25
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phi_well_func_type = "double"
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phi_interp_func_type ="p"
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FreeEnergyModel{
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type = "linear"
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}
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molar_volume = 1.e-6 // used to convert cp and latent heat into (pJ/(mu m)^3*K)
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BoundaryConditions {
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Phase{
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boundary_0 = "slope", "0"
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boundary_1 = "slope", "0"
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boundary_2 = "slope", "0"
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boundary_3 = "slope", "0"
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}
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Temperature{
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boundary_0 = "slope", "0"
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boundary_1 = "slope", "0"
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boundary_2 = "slope", "0"
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boundary_3 = "slope", "0"
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}
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Quat{
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boundary_0 = "slope", "0"
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boundary_1 = "slope", "0"
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boundary_2 = "slope", "0"
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boundary_3 = "slope", "0"
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}
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}
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}
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ScalarDiagnostics {
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interval = 15.
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interval_type = "time"
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}
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Integrator {
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atol = 1.e-4
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}
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InitialConditions { // required block
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filename = "1440.nc"
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init_t = 0.7 // initial temperature
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init_q = 1., 0.
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}
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Geometry{
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periodic_dimension = 0, 0
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coarsest_level_resolution = 1440, 1440
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x_lo = 0., 0. // lower end of computational domain.
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x_up = 960., 960. // upper end of computational domain.
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}

‎benchmarks/PFHub3/energy.plt

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set terminal png
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set size 0.7,0.7
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set datafile separator ","
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set output "Energy.png"
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set xlabel "Time"
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set ylabel "Free Energy"
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set xtics 500
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set ytics 0.5e6
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set xrange [0:1500]
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set key off
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plot 'free_energy.csv' u 1:2 w lines
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‎benchmarks/PFHub3/energy.py

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import sys, string
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input_ =open(sys.argv[1],'r')
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lines = input_.readlines()
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shift=-960.*960.*0.25
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time=-1.
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for line in lines:
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if line.count('cycle'):
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words=line.split()
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time = words[6]
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if line.count('Total') and line.count('energy'):
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words=line.split()
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energy=eval(words[4])+shift
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print( "{}, {}".format(time, energy))
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‎benchmarks/PFHub3/phase_contour.plt

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set terminal png
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set size 0.7,0.7
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#set datafile separator ","
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set output "phase_field_1500.png"
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set xlabel "x"
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set ylabel "y"
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set xtics 100
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set ytics 100
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set key off
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plot 'phase_field_1500.csv' u 1:2 w points
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‎benchmarks/PFHub3/phase_field_1500.py

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#usage:
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# visit -cli -verbose -nowin -s phase_field_1500.py
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#in main visit data directory
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import sys, string, os
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visitdir =os.getcwd()
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filename=visitdir+"/dumps.visit"
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myfile=open(filename,'r')
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lines=myfile.readlines()
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for line in lines:
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words=line.split()
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frame=words[0]
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#load data
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DB=visitdir+"/"+frame
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print( "#{}".format(DB))
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Var="phase"
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OpenDatabase(DB)
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DeleteAllPlots()
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AddPlot("Contour", "phase", 1, 1)
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# change Contour plot attributes
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c=ContourAttributes()
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c.contourNLevels=1
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#c.contourMethod=Value
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c.contourValue=(0.5)
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SetPlotOptions(c)
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DrawPlots()
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e=ExportDBAttributes()
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e.db_type = "XYZ"
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e.variables = ("x", "y")
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e.filename = "phase_contour"
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ExportDatabase(e)
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sys.exit()
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‎benchmarks/PFHub3/solid_fraction.plt

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set terminal png
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set size 0.7,0.7
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set datafile separator ","
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set output "SolidFraction.png"
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set xlabel "Time"
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set ylabel "Solid Fraction"
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set xtics 500
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set ytics 0.005
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set xrange [0:1500]
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set key off
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plot 'solid_fraction.csv' u 1:2 w lines
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‎benchmarks/PFHub3/tipPosition.py

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#usage:
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# visit -cli -verbose -nowin -s tipPosition.py
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#in main visit data directory
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import sys, string, os
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visitdir =os.getcwd()
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filename=visitdir+"/dumps.visit"
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myfile=open(filename,'r')
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lines=myfile.readlines()
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frames=[]
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counter=0
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for line in lines:
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words=line.split()
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if counter%5 == 0:
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frames.append(words[0])
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counter=counter+1
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print( "#{}".format(frames))
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#load data
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DB=[]
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for frame in frames:
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DB.append(visitdir+"/"+frame)
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Var="phase"
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#extract coordinates of end points in x direction
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OpenDatabase(DB[0])
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ierr = AddPlot("Pseudocolor", Var)
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if ierr==1:
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DrawPlots()
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Query("SpatialExtents")
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pxy = GetQueryOutputValue()
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p0 = ( pxy[0], 0. )
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p1 = ( pxy[1], 0. )
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for db in DB:
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OpenDatabase(db)
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ierr = AddPlot("Pseudocolor", Var)
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if ierr==1:
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DrawPlots()
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# Do a lineout on variable to produce curve.
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Lineout(p0, p1, ("default"))
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# extract data into CSV format
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SetActiveWindow(2)
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output = open("tip_position.csv",'w')
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for k in range(len(DB)):
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SetActivePlots(k)
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vals = GetPlotInformation()["Curve"]
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Query("Time")
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t0 = GetQueryOutputValue()
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print "# time: %g" % (t0)
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xm=0.
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xp=0.
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ym=0.
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yp=0.
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for i in range(len(vals) / 2):
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if vals[2*i+1]>0.5:
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xm=p0[0]+vals[2*i]
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ym=vals[2*i+1]
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if vals[2*i+1]<0.5:
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xp=p0[0]+vals[2*i]
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yp=vals[2*i+1]
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slope=(yp-ym)/(xp-xm)
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x0=(0.5-ym)/slope+xm
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output.write("%g, %g\n" % (t0,x0))
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break
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sys.exit()

‎benchmarks/PFHub3/tip_position.plt

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set terminal png
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set pointsize 2
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set size 0.7,0.7
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set datafile separator ","
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set output "TipPosition.png"
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set xlabel "Time"
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set ylabel "Tip position"
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set xtics 500
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set ytics 100
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set xrange [0:1500]
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set key off
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plot 'tip_position.csv' u 1:2 w lines lw 2
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‎benchmarks/PFHub3/xyz2csv.py

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import sys, string
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input_ =open(sys.argv[1],'r')
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lines = input_.readlines()
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count=0
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for line in lines:
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count=count+1
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if count<3:
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continue
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words=line.split()
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print( "{}, {}".format(words[1], words[2]))
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‎utils/volfracvstime.py

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# POSSIBILITY OF SUCH DAMAGE.
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#
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#usage:
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# python volfracvstime.py ampe.log > volfraction.dat
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# python volfracvstime.py ampe.log > solid_fraction.csv
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#
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import sys, string
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from math import pi
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break
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words=L[line].split()
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vol=eval(words[6])
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print("{} {}".format(time,vol))
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print("{}, {}".format(time,vol))

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