tadded script for simulations with modulating stresses - 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 d2028121eff909fff835dbe760771c2d87dd5c6c
 (DIR) parent 665811d1559586641cc8d1d12ce32dde5d5982ae
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       Date:   Wed, 21 Jan 2015 11:39:59 +0100
       
       added script for simulations with modulating stresses
       
       Diffstat:
         A python/halfshear-darcy-stress-mod-… |      93 +++++++++++++++++++++++++++++++
       
       1 file changed, 93 insertions(+), 0 deletions(-)
       ---
 (DIR) diff --git a/python/halfshear-darcy-stress-mod-starter.py b/python/halfshear-darcy-stress-mod-starter.py
       t@@ -0,0 +1,93 @@
       +#!/usr/bin/env python
       +import sphere
       +import numpy
       +import sys
       +
       +# launch with:
       +# $ ipython halfshear-darcy-stress-starter.py <device> <fluid> <c_phi> <k_c> <sigma_0> <mu> <shear_stress> <mod_A> <mod_f>
       +
       +device = int(sys.argv[1])
       +wet = int(sys.argv[2])
       +c_phi = float(sys.argv[3])
       +k_c = float(sys.argv[4])
       +sigma0 = float(sys.argv[5])
       +mu = float(sys.argv[6])
       +shear_stress = float(sys.argv[7])
       +mod_A = float(sys.argv[8])
       +mod_f = float(sys.argv[9])
       +
       +if wet == 1:
       +    fluid = True
       +else:
       +    fluid = False
       +    
       +sim = sphere.sim('halfshear-sigma0=' + str(sigma0), fluid=False)
       +print('Input: ' + sim.sid)
       +sim.readlast()
       +
       +sim.fluid = fluid
       +if fluid:
       +    sim.id('halfshear-darcy-sigma0=' + str(sigma0) + '-k_c=' + str(k_c) +
       +            '-mu=' + str(mu) + '-ss=' + str(shear_stress) + '-A=' + str(mod_A)
       +            + '-f=' + str(mod_f))
       +else:
       +    sim.id('halfshear-sigma0=' + str(sigma0) + '-ss=' + str(shear_stress) + \
       +            '-shear')
       +
       +sim.checkerboardColors(nx=6,ny=3,nz=6)
       +sim.cleanup()
       +sim.adjustUpperWall()
       +sim.zeroKinematics()
       +
       +#sim.shear(0.0/20.0)
       +#sim.shear(1.0/20.0 * velfac)
       +sim.shear(shear_stress = shear_stress)
       +K_q_real = 36.4e9
       +K_w_real =  2.2e9
       +K_q_sim  = 1.16e9
       +K_w_sim  = K_w_real/K_q_real * K_q_sim
       +
       +if fluid:
       +    #sim.num[2] *= 2
       +    sim.num[:] /= 2
       +    #sim.L[2] *= 2.0
       +    #sim.initFluid(mu = 1.787e-6, p = 600.0e3, cfd_solver = 1)
       +    sim.initFluid(mu = mu, p = 0.0, cfd_solver = 1)
       +    sim.setFluidBottomNoFlow()
       +    sim.setFluidTopFixedPressure()
       +    #sim.setDEMstepsPerCFDstep(10)
       +    sim.setMaxIterations(2e5)
       +    sim.setPermeabilityPrefactor(k_c)
       +    sim.setFluidCompressibility(1.0/K_w_sim)
       +    sim.setFluidPressureModulation(A=mod_A, f=mod_f)
       +
       +sim.w_sigma0[0] = sigma0
       +sim.w_m[0] = numpy.abs(sigma0*sim.L[0]*sim.L[1]/sim.g[2])
       +sim.setTopWallNormalStressModulation(A=mod_A, f=mod_f)
       +
       +#sim.setStiffnessNormal(36.4e9 * 0.1 / 2.0)
       +#sim.setStiffnessTangential(36.4e9/3.0 * 0.1 / 2.0)
       +sim.setStiffnessNormal(K_q_sim)
       +sim.setStiffnessTangential(K_q_sim)
       +sim.mu_s[0] = 0.5
       +sim.mu_d[0] = 0.5
       +sim.setDampingNormal(0.0)
       +sim.setDampingTangential(0.0)
       +#sim.deleteAllParticles()
       +#sim.fixvel[:] = -1.0
       +
       +sim.initTemporal(total = 20.0, file_dt = 0.01, epsilon=0.07)
       +#sim.initTemporal(total = 20.0, file_dt = 0.00001, epsilon=0.07)
       +#sim.time_dt[0] *= 1.0e-2
       +#sim.initTemporal(total = 1.0e-4, file_dt = 1.0e-5, epsilon=0.07)
       +
       +# 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')