timprove friction,dilation,pressure vs rate plot - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
(HTM) git clone git://src.adamsgaard.dk/sphere
(DIR) Log
(DIR) Files
(DIR) Refs
(DIR) LICENSE
---
(DIR) commit e1ca057c3a2749911d17d6f9356f67e8470be834
(DIR) parent e05f1f05655a65d9f3920854b5e072c227285260
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Tue, 14 Apr 2015 16:02:19 +0200
improve friction,dilation,pressure vs rate plot
Diffstat:
M python/halfshear-darcy-strength-di… | 393 +++++++++++++++++++++----------
1 file changed, 275 insertions(+), 118 deletions(-)
---
(DIR) diff --git a/python/halfshear-darcy-strength-dilation-rate.py b/python/halfshear-darcy-strength-dilation-rate.py
t@@ -23,6 +23,8 @@ sns.despine() # remove right and top spines
pressures = True
zflow = False
contact_forces = False
+smooth_friction = True
+smooth_window = 30
#sigma0_list = numpy.array([1.0e3, 2.0e3, 4.0e3, 10.0e3, 20.0e3, 40.0e3])
sigma0 = 20000.0
t@@ -32,10 +34,72 @@ k_c = 3.5e-15
# 5.0e-8 results present
#mu_f_vals = [1.797e-06, 1.204e-06, 5.0e-8, 1.797e-08]
-mu_f_vals = [1.797e-06, 1.204e-06, 3.594e-07, 1.797e-08]
+#mu_f_vals = [1.797e-06, 1.204e-06, 3.594e-07, 1.797e-08]
+#mu_f_vals = [1.797e-06, 1.797-07, 1.797e-08]
+#mu_f_vals = [1.797e-06, 1.797-07, 1.797e-08]
#mu_f_vals = [1.797e-06, 1.204e-06, 1.797e-08]
+mu_f_vals = [1.797e-06, 3.594e-07, 1.797e-08]
velfac = 1.0
+# return a smoothed version of in. The returned array is smaller than the
+# original input array
+def smooth(x, window_len=10, window='hanning'):
+ """smooth the data using a window with requested size.
+
+ This method is based on the convolution of a scaled window with the signal.
+ The signal is prepared by introducing reflected copies of the signal
+ (with the window size) in both ends so that transient parts are minimized
+ in the begining and end part of the output signal.
+
+ input:
+ x: the input signal
+ window_len: the dimension of the smoothing window
+ window: the type of window from 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'
+ flat window will produce a moving average smoothing.
+
+ output:
+ the smoothed signal
+
+ example:
+
+ import numpy as np
+ t = np.linspace(-2,2,0.1)
+ x = np.sin(t)+np.random.randn(len(t))*0.1
+ y = smooth(x)
+
+ see also:
+
+ numpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve
+ scipy.signal.lfilter
+
+ TODO: the window parameter could be the window itself if an array instead of a string
+ """
+
+ if x.ndim != 1:
+ raise ValueError, "smooth only accepts 1 dimension arrays."
+
+ if x.size < window_len:
+ raise ValueError, "Input vector needs to be bigger than window size."
+
+ if window_len < 3:
+ return x
+
+ if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']:
+ raise ValueError, "Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'"
+
+ s=numpy.r_[2*x[0]-x[window_len:1:-1], x, 2*x[-1]-x[-1:-window_len:-1]]
+ #print(len(s))
+
+ if window == 'flat': #moving average
+ w = numpy.ones(window_len,'d')
+ else:
+ w = getattr(numpy, window)(window_len)
+ y = numpy.convolve(w/w.sum(), s, mode='same')
+ return y[window_len-1:-window_len+1]
+
+
+smooth_window = 10
+
shear_strain = [[], [], [], []]
friction = [[], [], [], []]
t@@ -123,37 +187,39 @@ for c in numpy.arange(0,len(mu_f_vals)):
if zflow or pressures:
#fig = plt.figure(figsize=(8,10))
- fig = plt.figure(figsize=(3.74, 2*3.74))
+ #fig = plt.figure(figsize=(3.74, 2*3.74))
+ fig = plt.figure(figsize=(2*3.74, 2*3.74))
else:
fig = plt.figure(figsize=(8,8)) # (w,h)
#fig = plt.figure(figsize=(8,12))
#fig = plt.figure(figsize=(8,16))
-fig.subplots_adjust(hspace=0.0)
#plt.subplot(3,1,1)
#plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
-if zflow or pressures:
- ax1 = plt.subplot(311)
- ax2 = plt.subplot(312, sharex=ax1)
- ax3 = plt.subplot(313, sharex=ax1)
-else:
- ax1 = plt.subplot(211)
- ax2 = plt.subplot(212, sharex=ax1)
-#ax3 = plt.subplot(413, sharex=ax1)
-#ax4 = plt.subplot(414, sharex=ax1)
-#alpha = 0.5
-alpha = 1.0
-#ax1.plot(shear_strain[0], friction[0], label='dry', linewidth=1, alpha=alpha)
-#ax2.plot(shear_strain[0], dilation[0], label='dry', linewidth=1)
-#ax4.plot(shear_strain[0], f_n_mean[0], '-', label='dry', color='blue')
-#ax4.plot(shear_strain[0], f_n_max[0], '--', color='blue')
-
-#color = ['b','g','r','c']
-#color = ['g','r','c']
-color = sns.color_palette()
-#for c, mu_f in enumerate(mu_f_vals):
-for c in numpy.arange(len(mu_f_vals)-1, -1, -1):
+for c in numpy.arange(0,len(mu_f_vals)):
+
+ if zflow or pressures:
+ ax1 = plt.subplot(3, len(mu_f_vals), 1+c)
+ ax2 = plt.subplot(3, len(mu_f_vals), 4+c, sharex=ax1)
+ ax3 = plt.subplot(3, len(mu_f_vals), 7+c, sharex=ax1)
+ else:
+ ax1 = plt.subplot(211)
+ ax2 = plt.subplot(212, sharex=ax1)
+ #ax3 = plt.subplot(413, sharex=ax1)
+ #ax4 = plt.subplot(414, sharex=ax1)
+ #alpha = 0.5
+ alpha = 1.0
+ #ax1.plot(shear_strain[0], friction[0], label='dry', linewidth=1, alpha=alpha)
+ #ax2.plot(shear_strain[0], dilation[0], label='dry', linewidth=1)
+ #ax4.plot(shear_strain[0], f_n_mean[0], '-', label='dry', color='blue')
+ #ax4.plot(shear_strain[0], f_n_max[0], '--', color='blue')
+
+ #color = ['b','g','r','c']
+ #color = ['g','r','c']
+ color = sns.color_palette()
+ #for c, mu_f in enumerate(mu_f_vals):
+ #for c in numpy.arange(len(mu_f_vals)-1, -1, -1):
mu_f = mu_f_vals[c]
if numpy.isclose(mu_f, 1.797e-6):
t@@ -164,12 +230,20 @@ for c in numpy.arange(len(mu_f_vals)-1, -1, -1):
#label = 'ref. shear velocity$\\times$0.01'
else:
#label = '$\\mu_\\text{{f}}$ = {:.3e} Pa s'.format(mu_f)
- label = 'ref. shear velocity$\\times${:.2}'.format(mu_f/mu_f_vals[0])
+ label = 'shear velocity$\\times${:.2}'.format(mu_f/mu_f_vals[0])
+
+ # unsmoothed
+ ax1.plot(shear_strain[c][1:], friction[c][1:], \
+ label=label, linewidth=1,
+ alpha=0.2, color='gray')
+ #alpha=alpha, color=color[c])
- ax1.plot(shear_strain[c], friction[c], \
+ # smoothed
+ ax1.plot(shear_strain[c][1:], smooth(friction[c], smooth_window)[1:], \
label=label, linewidth=1,
alpha=alpha, color=color[c])
+
ax2.plot(shear_strain[c], dilation[c], \
label=label, linewidth=1,
color=color[c])
t@@ -179,111 +253,194 @@ for c in numpy.arange(len(mu_f_vals)-1, -1, -1):
label=label, linewidth=1)
if pressures:
- #ax3.plot(shear_strain[c][1:], p_max[c][1:], '-', color=color[c],
- #alpha=0.5)
+ #ax3.plot(shear_strain[c], p_max[c], '-', color=color[c], alpha=0.5)
+
ax3.plot(shear_strain[c], p_mean[c], '-', color=color[c], \
label=label, linewidth=1)
- #ax3.plot(shear_strain[c][1:], p_min[c][1:], '-', color=color[c],
- #alpha=0.5)
- #ax3.fill_between(shear_strain[c][1:], p_min[c][1:], p_max[c][1:],
- #where=p_min[c][1:]<=p_max[c][1:], facecolor=color[c],
- #interpolate=True, alpha=0.5)
+ #ax3.plot(shear_strain[c], p_min[c], '-', color=color[c], alpha=0.5)
+
+
+ ax3.fill_between(shear_strain[c], p_min[c], p_max[c],
+ where=p_min[c]<=p_max[c], facecolor=color[c],
+ interpolate=True, alpha=0.5)
#ax4.plot(shear_strain[c][1:], f_n_mean[c][1:], '-' + color[c],
#label='$c$ = %.2f' % (cvals[c-1]), linewidth=2)
#ax4.plot(shear_strain[c][1:], f_n_max[c][1:], '--' + color[c])
#label='$c$ = %.2f' % (cvals[c-1]), linewidth=2)
-#ax4.set_xlabel('Shear strain $\\gamma$ [-]')
-if zflow or pressures:
- ax3.set_xlabel('Shear strain $\\gamma$ [-]')
-else:
- ax2.set_xlabel('Shear strain $\\gamma$ [-]')
+ #ax4.set_xlabel('Shear strain $\\gamma$ [-]')
+ if zflow or pressures:
+ ax3.set_xlabel('Shear strain $\\gamma$ [-]')
+ else:
+ ax2.set_xlabel('Shear strain $\\gamma$ [-]')
-ax1.set_ylabel('Shear friction $\\tau/\\sigma_0$ [-]')
-#ax1.set_ylabel('Shear stress $\\tau$ [kPa]')
-ax2.set_ylabel('Dilation $\\Delta h/(2r)$ [-]')
-if zflow:
- ax3.set_ylabel('$\\boldsymbol{v}_\\text{f}^z h$ [ms$^{-1}$]')
-if pressures:
- ax3.set_ylabel('Mean fluid pressure $\\bar{p}_\\text{f}$ [kPa]')
-#ax4.set_ylabel('Particle contact force $||\\boldsymbol{f}_\\text{p}||$ [N]')
+ if c == 0:
+ ax1.set_ylabel('Shear friction $\\tau/\\sigma_0$ [-]')
+ #ax1.set_ylabel('Shear stress $\\tau$ [kPa]')
+ ax2.set_ylabel('Dilation $\\Delta h/(2r)$ [-]')
+ if zflow:
+ ax3.set_ylabel('$\\boldsymbol{v}_\\text{f}^z h$ [ms$^{-1}$]')
+ if pressures:
+ ax3.set_ylabel('Mean fluid pressure $\\bar{p}_\\text{f}$ [kPa]')
+ #ax4.set_ylabel('Particle contact force $||\\boldsymbol{f}_\\text{p}||$ [N]')
+
+ #ax1.set_xlim([200,300])
+ #ax3.set_ylim([595,608])
+
+ plt.setp(ax1.get_xticklabels(), visible=False)
+ if zflow or pressures:
+ plt.setp(ax2.get_xticklabels(), visible=False)
+ #plt.setp(ax2.get_xticklabels(), visible=False)
+ #plt.setp(ax3.get_xticklabels(), visible=False)
+
+ '''
+ ax1.grid()
+ ax2.grid()
+ if zflow or pressures:
+ ax3.grid()
+ #ax4.grid()
+ '''
+
+ if c == 0: # left
+ # remove box at top and right
+ ax1.spines['top'].set_visible(False)
+ ax1.spines['bottom'].set_visible(False)
+ ax1.spines['right'].set_visible(False)
+ #ax1.spines['left'].set_visible(True)
+ # remove ticks at top and right
+ ax1.get_xaxis().set_ticks_position('none')
+ ax1.get_yaxis().set_ticks_position('none')
+ ax1.get_yaxis().tick_left()
+
+ # remove box at top and right
+ ax2.spines['top'].set_visible(False)
+ ax2.spines['right'].set_visible(False)
+ ax2.spines['bottom'].set_visible(False)
+ # remove ticks at top and right
+ ax2.get_xaxis().set_ticks_position('none')
+ ax2.get_yaxis().set_ticks_position('none')
+ ax2.get_yaxis().tick_left()
+
+ # remove box at top and right
+ ax3.spines['top'].set_visible(False)
+ ax3.spines['right'].set_visible(False)
+ # remove ticks at top and right
+ ax3.get_xaxis().set_ticks_position('none')
+ ax3.get_yaxis().set_ticks_position('none')
+ ax3.get_xaxis().tick_bottom()
+ ax3.get_yaxis().tick_left()
+
+ elif c == len(mu_f_vals)-1: # right
+ # remove box at top and right
+ ax1.spines['top'].set_visible(False)
+ ax1.spines['bottom'].set_visible(False)
+ ax1.spines['right'].set_visible(True)
+ ax1.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax1.get_xaxis().set_ticks_position('none')
+ ax1.get_yaxis().set_ticks_position('none')
+ ax1.get_yaxis().tick_right()
+
+ # remove box at top and right
+ ax2.spines['top'].set_visible(False)
+ ax2.spines['right'].set_visible(True)
+ ax2.spines['bottom'].set_visible(False)
+ ax2.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax2.get_xaxis().set_ticks_position('none')
+ ax2.get_yaxis().set_ticks_position('none')
+ #ax2.get_yaxis().tick_left()
+ ax2.get_yaxis().tick_right()
+
+ # remove box at top and right
+ ax3.spines['top'].set_visible(False)
+ ax3.spines['right'].set_visible(True)
+ ax3.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax3.get_xaxis().set_ticks_position('none')
+ ax3.get_yaxis().set_ticks_position('none')
+ ax3.get_xaxis().tick_bottom()
+ #ax3.get_yaxis().tick_left()
+ ax3.get_yaxis().tick_right()
+
+ else: # middle
+ # remove box at top and right
+ ax1.spines['top'].set_visible(False)
+ ax1.spines['bottom'].set_visible(False)
+ ax1.spines['right'].set_visible(False)
+ ax1.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax1.get_xaxis().set_ticks_position('none')
+ ax1.get_yaxis().set_ticks_position('none')
+ #ax1.get_yaxis().tick_left()
+ plt.setp(ax1.get_yticklabels(), visible=False)
+
+ # remove box at top and right
+ ax2.spines['top'].set_visible(False)
+ ax2.spines['right'].set_visible(False)
+ ax2.spines['bottom'].set_visible(False)
+ ax2.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax2.get_xaxis().set_ticks_position('none')
+ ax2.get_yaxis().set_ticks_position('none')
+ #ax2.get_yaxis().tick_left()
+ plt.setp(ax2.get_yticklabels(), visible=False)
+
+ # remove box at top and right
+ ax3.spines['top'].set_visible(False)
+ ax3.spines['right'].set_visible(False)
+ ax3.spines['left'].set_visible(False)
+ # remove ticks at top and right
+ ax3.get_xaxis().set_ticks_position('none')
+ ax3.get_yaxis().set_ticks_position('none')
+ ax3.get_xaxis().tick_bottom()
+ #ax3.get_yaxis().tick_left()
+ plt.setp(ax3.get_yticklabels(), visible=False)
+
+
+ # vertical grid lines
+ ax1.get_xaxis().grid(True, linestyle=':', linewidth=0.5)
+ ax2.get_xaxis().grid(True, linestyle=':', linewidth=0.5)
+ ax3.get_xaxis().grid(True, linestyle=':', linewidth=0.5)
+
+
+ # horizontal grid lines
+ ax1.get_yaxis().grid(True, linestyle=':', linewidth=0.5)
+ ax2.get_yaxis().grid(True, linestyle=':', linewidth=0.5)
+ ax3.get_yaxis().grid(True, linestyle=':', linewidth=0.5)
+
+ ax1.set_title(label)
+ #ax1.legend(loc='best')
+ #legend_alpha=0.5
+ #ax1.legend(loc='upper right', prop={'size':18}, fancybox=True,
+ #framealpha=legend_alpha)
+ #ax2.legend(loc='lower right', prop={'size':18}, fancybox=True,
+ #framealpha=legend_alpha)
+ #if zflow or pressures:
+ #ax3.legend(loc='upper right', prop={'size':18}, fancybox=True,
+ #framealpha=legend_alpha)
+ #ax4.legend(loc='best', prop={'size':18}, fancybox=True,
+ #framealpha=legend_alpha)
-#ax1.set_xlim([200,300])
-#ax3.set_ylim([595,608])
+ #ax1.set_xlim([0.0, 0.09])
+ #ax2.set_xlim([0.0, 0.09])
+ #ax2.set_xlim([0.0, 0.2])
-plt.setp(ax1.get_xticklabels(), visible=False)
-if zflow or pressures:
- plt.setp(ax2.get_xticklabels(), visible=False)
-#plt.setp(ax2.get_xticklabels(), visible=False)
-#plt.setp(ax3.get_xticklabels(), visible=False)
+ #ax1.set_ylim([-7, 45])
+ ax1.set_xlim([0.0, 1.0])
+ ax1.set_ylim([0.0, 1.0])
+ ax2.set_ylim([0.0, 1.0])
+ ax3.set_ylim([-200., 200.])
-'''
-ax1.grid()
-ax2.grid()
-if zflow or pressures:
- ax3.grid()
-#ax4.grid()
-'''
-
-
-# remove box at top and right
-ax1.spines['top'].set_visible(False)
-ax1.spines['bottom'].set_visible(False)
-ax1.spines['right'].set_visible(False)
-#ax1.spines['left'].set_visible(True)
-# remove ticks at top and right
-ax1.get_xaxis().set_ticks_position('none')
-ax1.get_yaxis().set_ticks_position('none')
-ax1.get_yaxis().tick_left()
-ax1.get_xaxis().grid(True, linestyle='--', linewidth=0.5)
-
-# remove box at top and right
-ax2.spines['top'].set_visible(False)
-ax2.spines['right'].set_visible(False)
-ax2.spines['bottom'].set_visible(False)
-# remove ticks at top and right
-ax2.get_xaxis().set_ticks_position('none')
-ax2.get_yaxis().set_ticks_position('none')
-ax2.get_yaxis().tick_left()
-ax2.get_xaxis().grid(True, linestyle='--', linewidth=0.5)
-
-# remove box at top and right
-ax3.spines['top'].set_visible(False)
-ax3.spines['right'].set_visible(False)
-# remove ticks at top and right
-ax3.get_xaxis().set_ticks_position('none')
-ax3.get_yaxis().set_ticks_position('none')
-ax3.get_xaxis().tick_bottom()
-ax3.get_yaxis().tick_left()
-ax3.get_xaxis().grid(True, linestyle='--', linewidth=0.5)
-
-ax1.legend(loc='best')
-#legend_alpha=0.5
-#ax1.legend(loc='upper right', prop={'size':18}, fancybox=True,
- #framealpha=legend_alpha)
-#ax2.legend(loc='lower right', prop={'size':18}, fancybox=True,
- #framealpha=legend_alpha)
-#if zflow or pressures:
- #ax3.legend(loc='upper right', prop={'size':18}, fancybox=True,
- #framealpha=legend_alpha)
-#ax4.legend(loc='best', prop={'size':18}, fancybox=True,
- #framealpha=legend_alpha)
-
-#ax1.set_xlim([0.0, 0.09])
-#ax2.set_xlim([0.0, 0.09])
-#ax2.set_xlim([0.0, 0.2])
-
-#ax1.set_ylim([-7, 45])
-ax2.set_ylim([0.0, 0.8])
-#ax1.set_ylim([0.0, 1.0])
-#if pressures:
- #ax3.set_ylim([-1400, 900])
- #ax3.set_ylim([-200, 200])
- #ax3.set_xlim([0.0, 0.09])
-
-plt.tight_layout()
+ #ax1.set_ylim([0.0, 1.0])
+ #if pressures:
+ #ax3.set_ylim([-1400, 900])
+ #ax3.set_ylim([-200, 200])
+ #ax3.set_xlim([0.0, 0.09])
+
+#plt.tight_layout()
#plt.subplots_adjust(hspace=0.05)
plt.subplots_adjust(hspace=0.15)
#filename = 'shear-' + str(int(sigma0/1000.0)) + 'kPa-stress-dilation.pdf'