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	tAdded python script for uniaxial compression experiment - sphere - GPU-based 3…
	git clone git://src.adamsgaard.dk/sphere
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	commit c6de88dc953fd288dbc1556b2b6b1427263a3aa0
	parent fd4911c71e33e2676faec3512d6fea2fba47a120
	Author: Anders Damsgaard <[email protected]>
	Date: Wed, 29 Aug 2012 14:16:05 +0200

	Added python script for uniaxial compression experiment

	Diffstat:
	A python/1e4-largesize-uniaxial.py \| 136 +++++++++++++++++++++++++++++…

	1 file changed, 136 insertions(+), 0 deletions(-)
	---
	diff --git a/python/1e4-largesize-uniaxial.py b/python/1e4-largesize-uniaxial.py
	t@@ -0,0 +1,136 @@
	+#!/usr/bin/env python
	+
	+# Import sphere functionality
	+from sphere import *
	+import subprocess
	+
	+# Determine system hostname
	+import os;
	+hostname = os.uname()[1]
	+
	+# Simulation ID
	+sid = "1e4-largesize-uniaxial"
	+
	+# Delete previous output
	+subprocess.call("rm ../{img_out,output}/" + sid + "*", shell=True);
	+
	+
	+#### GRAVITATIONAL CONSOLIDATION
	+
	+# New class
	+init = Spherebin(np = 1e4)
	+
	+# Generate random radii
	+init.generateRadii(psd = 'logn', histogram = 1, radius_mean = 0.02)
	+
	+# Initialize particle parameters
	+# Values from Yohannes et al. 2012
	+init.defaultParams(ang_s = 28,
	+ ang_d = 28,
	+ ang_r = 0,
	+ rho = 2600,
	+ k_n = 1.16e9,
	+ k_t = 1.16e9,
	+ gamma_n = 0.0,
	+ gamma_t = 0.0,
	+ gamma_r = 0.0)
	+
	+# Place particles in grid-like arrangement
	+# periodic: 0 = frictional x- and y-walls
	+# periodic: 1 = periodic x- and y-boundaries
	+# periodic: 2 = periodic x boundaries, frictional y-walls
	+# shearmodel: 1 = viscous, frictional shear force model
	+# shearmodel: 2 = elastic, frictional shear force model
	+init.initRandomGridPos(gridnum = numpy.array([20,10,600]), periodic = 1, shear…
	+
	+# Initialize temporal parameters
	+init.initTemporal(total = 5.0, file_dt = 0.10)
	+
	+# Write output binary for sphere
	+init.writebin("../input/" + sid + "-initgrid.bin".format(sid))
	+
	+# Render start configuration
	+render("../input/" + sid + "-initgrid.bin", out = sid + "-initgrid")
	+
	+# Run simulation
	+subprocess.call("cd ..; ./sphere_*_X86_64 " + sid + "-initgrid", shell=True)
	+
	+# Plot energy
	+visualize(sid + "-initgrid", "energy", savefig=True, outformat='png')
	+
	+
	+#### CONSOLIDATION UNDER DEVIATORIC STRESS
	+
	+# New class
	+cons = Spherebin(np = init.np, nd = init.nd)
	+
	+# Find out which output file was the last generated during gravitational conso…
	+lastfile = status(sid + "-initgrid", verbose = False)
	+filename = "../output" + sid + "-initgrid.output{0}.bin".format(lastfile)
	+
	+
	+## Uniaxial compression loop:
	+# 1. Read last experiment binary
	+# 2. Set new devs and zero current time
	+# 3. Run sphere
	+# 4. Visualize wall data and find void ratio (e)
	+# 5. Save name of last binary written
	+
	+# Define deviatoric stresses to test
	+stresses = numpy.array([10e3, 20e3, 40e3])
	+voidratio = numpy.zeros(1, length(stresses))
	+
	+i = 0
	+for devs in stresses:
	+
	+ # Simulation ID for consolidation run
	+ cid = sid + "-uniaxial-{0}Pa".format(devs)
	+
	+ # Read the last output file of from the gravitational consolidation experime…
	+ cons.readbin(filename)
	+
	+ # Setup consolidation experiment
	+ cons.consolidate(deviatoric_stress = devs, periodic = init.periodic)
	+
	+ # Zero time variables and set new total time
	+ cons.initTemporal(total = 3.0, file_dt = 0.03)
	+
	+ # Write output binary for sphere
	+ cons.writebin("../input/" + cid + ".bin")
	+
	+ # Run simulation
	+ subprocess.call("cd ..; ./sphere_*_X86_64 " + cid, shell=True)
	+
	+ # Plot energy and wall data
	+ visualize(cid, "energy", savefig=True, outformat='png')
	+ visualize(cid, "walls", savefig=True, outformat='png')
	+
	+ # Find void ratio
	+ lastfile = status(cid, verbose = False)
	+ cons.readbin(cid)
	+ voidratio[i] = voidRatio()
	+ i = i+1
	+
	+ # Name of last output file
	+ filename = "../output" + cid + ".output{0}.bin".format(lastfile)
	+
	+
	+# Save plot of measured compression curve
	+fig = plt.figure(figsize(15,10),dpi=300)
	+figtitle = "{0}, measured compression curve".format(sid)
	+fig.text(0.5,0.95,figtitle,horizontalalignment='center',fontproperties=FontPro…
	+ax1 = plt.subplot2grid((1,1),(0,0))
	+ax1.set_xlabel('Stress [kPa]')
	+ax1.set_ylabel('Void ratio')
	+ax1.semilogx(stresses, voidratio, '+-')
	+
	+# Save values to text file
	+fh = None
	+try:
	+ fh = open(sid + "-uniaxial.txt", "w")
	+ for i in range(length(stresses)):
	+ fh.write("{0}\t{1}\n".format(stresses[i], voidratio[i]))
	+ finally:
	+ if fh is not None:
	+ fh.close()
	+