tadded script to start shear2 simulations - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
 (HTM) git clone git://src.adamsgaard.dk/sphere
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       ---
 (DIR) commit 42b7039c127fbf0f3ac1938530e333d450284af2
 (DIR) parent 8e72814af7eb96dd3b6673e10ce7567023829e5d
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       Date:   Thu,  2 Oct 2014 13:54:53 +0200
       
       added script to start shear2 simulations
       
       Diffstat:
         A python/shear2-starter.py            |      74 +++++++++++++++++++++++++++++++
       
       1 file changed, 74 insertions(+), 0 deletions(-)
       ---
 (DIR) diff --git a/python/shear2-starter.py b/python/shear2-starter.py
       t@@ -0,0 +1,74 @@
       +#!/usr/bin/env python
       +import sphere
       +import numpy
       +import sys
       +
       +# launch with:
       +# $ python shear-starter.py <DEVICE> <FLUID> <C_PHI> <C_GRAD_P> <SIGMA_0>
       +
       +device = int(sys.argv[1])
       +wet = int(sys.argv[2])
       +c_phi = float(sys.argv[3])
       +c_grad_p = float(sys.argv[4])
       +sigma0 = float(sys.argv[5])
       +
       +#sim = sphere.sim('diffusivity-sigma0=' + str(sigma0) + '-c_phi=' + \
       +#        str(c_phi) + '-c_grad_p=' + str(c_grad_p), fluid=True)
       +if wet == 1:
       +    fluid = True
       +else:
       +    fluid = False
       +    
       +sim = sphere.sim('cons2-20kPa', fluid=False)
       +sim.readlast()
       +
       +#if sigma0 == 20.0e3 and c_phi == 1.0 and c_grad_p == 0.1:
       +#    sim.sid = 'shear-sigma0=20000.0-c_phi=1.0-c_grad_p=0.1-hi_mu-lo_visc-hw-noshear'
       +#    sim.readlast()
       +
       +if fluid:
       +    sim.id('shear2-sigma0=' + str(sigma0) + '-c_phi=' + str(c_phi) + \
       +            '-c_grad_p=' + str(c_grad_p) + '-hi_mu-lo_visc-hw')
       +else:
       +    sim.id('shear2-sigma0=' + str(sigma0) + '-hw')
       +
       +print(sim.sid)
       +sim.fluid = fluid
       +
       +sim.checkerboardColors(nx=6,ny=6,nz=6)
       +sim.cleanup()
       +sim.adjustUpperWall()
       +sim.zeroKinematics()
       +
       +sim.shear(1.0/20.0)
       +#sim.shear(0.0)
       +
       +if fluid:
       +    #sim.num[2] *= 2
       +    #sim.L[2] *= 2.0
       +    sim.initFluid(mu = 1.787e-6, p = 600.0e3, hydrostatic = True)
       +    #sim.initFluid(mu = 17.87e-4, p = 1.0e5, hydrostatic = True)
       +    sim.setFluidBottomNoFlow()
       +    sim.setFluidTopFixedPressure()
       +    sim.setDEMstepsPerCFDstep(10)
       +    sim.setMaxIterations(2e5)
       +    sim.c_phi[0] = c_phi
       +    sim.c_grad_p[0] = c_grad_p
       +    sim.w_devs[0] = sigma0
       +
       +sim.initTemporal(total = 20.0, file_dt = 0.01, epsilon=0.07)
       +#sim.initTemporal(total = 20.0, file_dt = 0.01, epsilon=0.05)
       +sim.w_m[0] = numpy.abs(sigma0*sim.L[0]*sim.L[1]/sim.g[2])
       +sim.mu_s[0] = 0.5
       +sim.mu_d[0] = 0.5
       +
       +# Fix lowermost particles
       +dz = sim.L[2]/sim.num[2]
       +I = numpy.nonzero(sim.x[:,2] < 1.5*dz)
       +sim.fixvel[I] = 1
       +
       +sim.run(dry=True)
       +sim.run(device=device)
       +#sim.writeVTKall()
       +#sim.visualize('walls')
       +#sim.visualize('fluid-pressure')