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	tadd function for total grain mass, add script for heavy wall sim - sphere - GP…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit e3eaa59ec862f4fc931a1ebc9be62b89f6ddf12a
	parent 5389122ce8220481fc757b59cb5ff598b308a985
	Author: Anders Damsgaard Christensen <[email protected]>
	Date: Fri, 10 Jun 2016 10:48:03 -0700

	add function for total grain mass, add script for heavy wall sim

	Diffstat:
	A python/jp-long-shear-soft-damping.… \| 163 +++++++++++++++++++++++++++…
	M python/sphere.py \| 11 +++++++++++

	2 files changed, 174 insertions(+), 0 deletions(-)
	---
	diff --git a/python/jp-long-shear-soft-damping.py b/python/jp-long-shear-soft-d…
	t@@ -0,0 +1,163 @@
	+#!/usr/bin/env python
	+
	+# Import sphere functionality
	+import sphere
	+
	+### EXPERIMENT SETUP ###
	+initialization = False
	+consolidation = False
	+shearing = True
	+rendering = False
	+plots = True
	+
	+# CUDA device to use
	+device = 0
	+
	+# Number of particles
	+np = 1e4
	+
	+# Common simulation id
	+sim_id = "jp-long-shear-soft"
	+
	+# Deviatoric stress [Pa]
	+devslist = [100e3]
	+
	+### INITIALIZATION ###
	+
	+# New class
	+init = sphere.sim(np=np, nd=3, nw=0, sid=sim_id + "-init")
	+
	+# Save radii
	+init.generateRadii(mean=0.01)
	+
	+# Use default params
	+init.defaultParams(k_n=1.16e7, k_t=1.16e7, gamma_n=100.0, mu_s=0.6, mu_d=0.6)
	+
	+# Add gravity
	+init.g[2] = -9.81
	+
	+# Periodic x and y boundaries
	+init.periodicBoundariesXY()
	+
	+# Initialize positions in random grid (also sets world size)
	+hcells = np**(1.0/3.0)
	+init.initRandomGridPos(gridnum=[hcells, hcells, 1e9])
	+
	+# Set duration of simulation
	+init.initTemporal(total=10.0, epsilon=0.07)
	+
	+if (initialization):
	+
	+ # Run sphere
	+ init.run(dry=True)
	+ init.run(device=device)
	+
	+ if (plots):
	+ # Make a graph of energies
	+ init.visualize('energy')
	+
	+ init.writeVTKall()
	+
	+ if (rendering):
	+ # Render images with raytracer
	+ init.render(method="angvel", max_val=0.3, verbose=False)
	+
	+
	+# For each normal stress, consolidate and subsequently shear the material
	+for devs in devslist:
	+
	+ ### CONSOLIDATION ###
	+
	+ # New class
	+ cons = sphere.sim(
	+ np=init.np,
	+ nw=1,
	+ sid=sim_id +
	+ "-cons-devs{}".format(devs))
	+
	+ # Read last output file of initialization step
	+ lastf = sphere.status(sim_id + "-init")
	+ cons.readbin(
	+ "../output/" +
	+ sim_id +
	+ "-init.output{:0=5}.bin".format(lastf),
	+ verbose=False)
	+
	+ # Periodic x and y boundaries
	+ cons.periodicBoundariesXY()
	+
	+ # Setup consolidation experiment
	+ cons.consolidate(normal_stress=devs)
	+
	+ # Set duration of simulation
	+ cons.initTemporal(total=3.0, epsilon=0.07)
	+
	+ """
	+ cons.w_m[0] *= 0.001
	+ cons.mu_s[0] = 0.0
	+ cons.mu_d[0] = 0.0
	+ cons.gamma_wn[0] = 1e4
	+ cons.gamma_wt[0] = 1e4
	+ cons.contactmodel[0] = 1
	+ """
	+
	+ if (consolidation):
	+
	+ # Run sphere
	+ cons.run(dry=True) # show values, don't run
	+ cons.run(device=device) # run
	+
	+ if (plots):
	+ # Make a graph of energies
	+ cons.visualize('energy')
	+ cons.visualize('walls')
	+
	+ cons.writeVTKall()
	+
	+ if (rendering):
	+ # Render images with raytracer
	+ cons.render(method="pres", max_val=2.0*devs, verbose=False)
	+
	+ ### SHEARING ###
	+
	+ # New class
	+ shear = sphere.sim(
	+ np=cons.np,
	+ nw=cons.nw,
	+ sid=sim_id +
	+ "-shear-devs{}".format(devs))
	+
	+ # Read last output file of initialization step
	+ lastf = sphere.status(sim_id + "-cons-devs{}".format(devs))
	+ shear.readbin(
	+ "../output/" + sim_id + "-cons-devs{}.output{:0=5}.bin".format(devs,
	+ lastf),…
	+
	+ # Periodic x and y boundaries
	+ shear.periodicBoundariesXY()
	+
	+ # Setup shear experiment
	+ shear.shear(shear_strain_rate=0.05)
	+
	+ shear.gamma_wn[0] = 1.0e5
	+ shear.w_m[0] = shear.totalMass()
	+
	+ # Set duration of simulation
	+ shear.initTemporal(total=240.0, epsilon=0.07)
	+
	+ if (shearing):
	+
	+ # Run sphere
	+ shear.run(dry=True)
	+ shear.run(device=device)
	+
	+ if (plots):
	+ # Make a graph of energies
	+ shear.visualize('energy')
	+ shear.visualize('shear')
	+
	+ shear.writeVTKall()
	+
	+ if (rendering):
	+ # Render images with raytracer
	+ shear.render(method="pres", max_val=2.0*devs, verbose=False)
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -3915,6 +3915,17 @@ class sim:
	'''
	return self.rho[0]*self.volume(idx)

	+ def totalMass(self):
	+ '''
	+ Returns the total mass of all particles.
	+
	+ :returns: The total mass in [kg]
	+ '''
	+ m = 0.0
	+ for i in range(self.np):
	+ m += self.mass(i)
	+ return m
	+
	def smallestMass(self):
	'''
	Returns the mass of the leightest particle.