tadd shear strain figure with different shear velocities - 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 56af4aacf999712c3c11b456d93f6cf5d51af926
(DIR) parent 570befea3f48d138c03d8eab59c6e60366c36d52
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Wed, 6 May 2015 14:18:03 +0200
add shear strain figure with different shear velocities
Diffstat:
A python/halfshear-darcy-strain-rate… | 204 +++++++++++++++++++++++++++++++
1 file changed, 204 insertions(+), 0 deletions(-)
---
(DIR) diff --git a/python/halfshear-darcy-strain-rate.py b/python/halfshear-darcy-strain-rate.py
t@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+import matplotlib
+matplotlib.use('Agg')
+matplotlib.rcParams.update({'font.size': 18, 'font.family': 'serif'})
+matplotlib.rc('text', usetex=True)
+matplotlib.rcParams['text.latex.preamble']=[r"\usepackage{amsmath}"]
+import shutil
+
+import os
+import numpy
+import sphere
+from permeabilitycalculator import *
+import matplotlib.pyplot as plt
+from matplotlib.ticker import MaxNLocator
+
+import seaborn as sns
+#sns.set(style='ticks', palette='Set2')
+#sns.set(style='ticks', palette='colorblind')
+sns.set(style='ticks', palette='Set2')
+sns.despine() # remove chartjunk
+
+sigma0_list = [20000.0, 80000.0]
+#cvals = ['dry', 1.0, 0.1, 0.01]
+#cvals = ['dry', 3.5e-13, 3.5e-15]
+#cvals = ['dry', 3.5e-13, 3.5e-14, 3.5e-15]
+#cvals = ['dry', 3.5e-13, 3.5e-14, 3.5e-15]
+#cvals = ['dry', 1.0]
+c = 3.5e-15
+muvals = ['dry', 1.797e-06, 1.797e-07, 1.797e-08]
+#step = 1999
+
+for sigma0 in sigma0_list:
+
+ sim = sphere.sim('halfshear-sigma0=' + str(sigma0) + '-shear')
+ sim.readfirst(verbose=False)
+
+
+ # particle z positions
+ zpos_p = [[], [], [], []]
+
+ # cell midpoint cell positions
+ zpos_c = [[], [], [], []]
+
+ # particle x displacements
+ xdisp = [[], [], [], []]
+ xdisp_mean = [[], [], [], []]
+
+ s = 0
+ for mu in muvals:
+
+ if mu == 'dry':
+ fluid = False
+ sid = 'halfshear-sigma0=' + str(sigma0) + '-shear'
+ else:
+ fluid = True
+ sid = 'halfshear-darcy-sigma0=' + str(sigma0) + '-k_c=' + str(c) + \
+ '-mu=' + str(mu) + '-velfac=1.0-shear'
+
+ sim = sphere.sim(sid, fluid=fluid)
+
+ if os.path.isfile('../output/' + sid + '.status.dat'):
+
+ sim.readlast(verbose=False)
+
+ zpos_c[s] = numpy.zeros(sim.num[2]*2)
+ dz = sim.L[2]/(sim.num[2]*2)
+ for i in numpy.arange(sim.num[2]*2):
+ zpos_c[s][i] = i*dz + 0.5*dz
+
+ xdisp[s] = numpy.zeros(sim.np)
+ xdisp_mean[s] = numpy.zeros(sim.num[2]*2)
+
+
+ zpos_p[s][:] = sim.x[:,2]
+
+ xdisp[s][:] = sim.xyzsum[:,0]
+
+ #shear_strain[s] += sim.shearStrain()/nsteps_avg
+
+ # calculate mean values of xdisp and f_pf
+ for iz in numpy.arange(sim.num[2]*2):
+ z_bot = iz*dz
+ z_top = (iz+1)*dz
+ I = numpy.nonzero((zpos_p[s][:] >= z_bot) & (zpos_p[s][:] < z_top))
+ if len(I) > 0:
+ xdisp_mean[s][iz] = numpy.mean(xdisp[s][I])
+
+ # normalize distance
+ max_dist = numpy.nanmax(xdisp_mean[s])
+ xdisp_mean[s] /= max_dist
+
+ else:
+ print(sid + ' not found')
+ s += 1
+
+
+ #fig = plt.figure(figsize=(8,4*(len(steps))+1))
+ #fig = plt.figure(figsize=(8,5*(len(steps))+1))
+ #fig = plt.figure(figsize=(8/2,6/2))
+ fig = plt.figure(figsize=(3.74,3.47)) # 3.14 inch = 80 mm, 3.74 = 95 mm
+ #fig = plt.figure(figsize=(8,6))
+
+ ax = []
+ #linetype = ['-', '--', '-.']
+ #linetype = ['-', '-', '-', '-']
+ linetype = ['-', '--', '-.', ':']
+ #color = ['b','g','c','y']
+ #color = ['k','g','c','y']
+ color = ['y','g','c','k']
+ #color = ['c','m','y','k']
+ for s in numpy.arange(len(muvals)):
+ #for s in numpy.arange(len(cvals)-1, -1, -1):
+
+ ax.append(plt.subplot(111))
+ #ax.append(plt.subplot(len(steps)*100 + 31 + s*3))
+ #ax.append(plt.subplot(len(steps)*100 + 32 + s*3, sharey=ax[s*4+0]))
+ #ax.append(plt.subplot(len(steps)*100 + 33 + s*3, sharey=ax[s*4+0]))
+ #ax.append(ax[s*4+2].twiny())
+
+ if muvals[s] == 'dry':
+ legend = 'dry'
+ elif muvals[s] == 1.797e-06:
+ legend = 'wet, ref. shear vel.'
+ elif muvals[s] == 1.797e-07:
+ legend = 'wet, shear vel. $\\times$ 0.1'
+ elif muvals[s] == 1.797e-08:
+ legend = 'wet, shear vel. $\\times$ 0.01'
+ else:
+ legend = 'wet, $k_c$ = ' + str(muvals[s]) + ' m$^2$'
+
+ #ax[0].plot(xdisp[s], zpos_p[s], ',', color = '#888888')
+ #ax[0].plot(xdisp[s], zpos_p[s], ',', color=color[s], alpha=0.5)
+ ax[0].plot(xdisp_mean[s], zpos_c[s], linetype[s],
+ label=legend)#,
+ #color=color[s],
+ #linewidth=2.0)
+
+ ax[0].set_ylabel('Vertical position $z$ [m]')
+ #ax[0].set_xlabel('$\\boldsymbol{x}^x_\\text{p}$ [m]')
+ ax[0].set_xlabel('Normalized horizontal movement')
+
+ #ax[s*4+0].get_xaxis().set_major_locator(MaxNLocator(nbins=5))
+ #ax[s*4+1].get_xaxis().set_major_locator(MaxNLocator(nbins=5))
+ #ax[s*4+2].get_xaxis().set_major_locator(MaxNLocator(nbins=5))
+
+ #plt.setp(ax[s*4+0].xaxis.get_majorticklabels(), rotation=90)
+ #plt.setp(ax[s*4+1].xaxis.get_majorticklabels(), rotation=90)
+ #plt.setp(ax[s*4+2].xaxis.get_majorticklabels(), rotation=90)
+ #plt.setp(ax[s*4+3].xaxis.get_majorticklabels(), rotation=90)
+
+ #if s == 0:
+ #y = 0.95
+ #if s == 1:
+ #y = 0.55
+
+ #strain_str = 'Shear strain $\\gamma = %.3f$' % (shear_strain[s])
+ #fig.text(0.1, y, strain_str, horizontalalignment='left', fontsize=22)
+ #ax[s*4+0].annotate(strain_str, xytext=(0,1.1), textcoords='figure fraction',
+ #horizontalalignment='left', fontsize=22)
+ #plt.text(0.05, 1.06, strain_str, horizontalalignment='left', fontsize=22,
+ #transform=ax[s*4+0].transAxes)
+ #ax[s*4+0].set_title(strain_str)
+
+ #ax[s*4+0].grid()
+ #ax[s*4+1].grid()
+ #ax[s*4+2].grid()
+ #ax1.legend(loc='lower right', prop={'size':18})
+ #ax2.legend(loc='lower right', prop={'size':18})
+
+ # remove box at top and right
+ ax[0].spines['top'].set_visible(False)
+ ax[0].spines['right'].set_visible(False)
+ # remove ticks at top and right
+ ax[0].get_xaxis().tick_bottom()
+ ax[0].get_yaxis().tick_left()
+ ax[0].get_xaxis().grid(False) # horizontal grid lines
+ #ax[0].get_yaxis().grid(True, linestyle='--', linewidth=0.5) # vertical grid lines
+ ax[0].get_xaxis().grid(True, linestyle=':', linewidth=0.5) # vertical grid lines
+ ax[0].get_yaxis().grid(True, linestyle=':', linewidth=0.5) # vertical grid lines
+
+ # reverse legend order
+ handles, labels = ax[0].get_legend_handles_labels()
+ ax[0].legend(handles[::-1], labels[::-1], loc='best')
+
+ #legend_alpha=0.5
+ #ax[0].legend(loc='lower right', prop={'size':18}, fancybox=True, framealpha=legend_alpha)
+ #ax[0].legend(loc='best', prop={'size':18}, fancybox=True, framealpha=legend_alpha)
+ #ax[0].legend(loc='best')
+ #ax[0].grid()
+ #ax[0].set_xlim([-0.05, 1.01])
+ ax[0].set_xlim([-0.05, 1.05])
+ #ax[0].set_ylim([0.0, 0.47])
+ ax[0].set_ylim([0.20, 0.47])
+ plt.tight_layout()
+ plt.subplots_adjust(wspace = .05)
+ plt.MaxNLocator(nbins=4)
+
+ filename = 'halfshear-darcy-strain-rate.pdf'
+ if sigma0 == 80000.0:
+ filename = 'halfshear-darcy-strain-N80-rate.pdf'
+ plt.savefig(filename)
+ #shutil.copyfile(filename, '/Users/adc/articles/own/2/graphics/' + filename)
+ shutil.copyfile(filename, '/home/adc/articles/own/2/graphics/' + filename)
+ print(filename)