tuse seaborn to improve figures - 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 e05f1f05655a65d9f3920854b5e072c227285260
(DIR) parent 90c69f56c42d99b499c64fc131309115f962253a
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Tue, 14 Apr 2015 14:59:48 +0200
use seaborn to improve figures
Diffstat:
M python/halfshear-darcy-strain.py | 8 +++++---
M python/halfshear-darcy-strength-di… | 150 +++++++++++++++++++++----------
2 files changed, 109 insertions(+), 49 deletions(-)
---
(DIR) diff --git a/python/halfshear-darcy-strain.py b/python/halfshear-darcy-strain.py
t@@ -14,6 +14,8 @@ 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
t@@ -113,11 +115,11 @@ for s in numpy.arange(len(cvals)):
if cvals[s] == 'dry':
legend = 'dry'
elif cvals[s] == 3.5e-13:
- legend = 'wet, relatively permeable'
+ legend = 'wet, high permeability'
elif cvals[s] == 3.5e-14:
legend = 'wet, intermediate permeability'
elif cvals[s] == 3.5e-15:
- legend = 'wet, relatively impermeable'
+ legend = 'wet, low permeability'
else:
legend = 'wet, $k_c$ = ' + str(cvals[s]) + ' m$^2$'
t@@ -179,7 +181,7 @@ ax[0].legend(handles[::-1], labels[::-1], loc='best')
#ax[0].legend(loc='best')
#ax[0].grid()
#ax[0].set_xlim([-0.05, 1.01])
-ax[0].set_xlim([-0.05, 1.04])
+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()
(DIR) diff --git a/python/halfshear-darcy-strength-dilation-rate.py b/python/halfshear-darcy-strength-dilation-rate.py
t@@ -14,8 +14,11 @@ from permeabilitycalculator import *
import matplotlib.pyplot as plt
import seaborn as sns
-sns.set(style='ticks', palette='Set2')
-sns.despine() # remove chartjunk
+#sns.set(style='ticks', palette='Set2')
+sns.set(style='ticks', palette='colorblind')
+#sns.set(style='ticks', palette='muted')
+#sns.set(style='ticks', palette='pastel')
+sns.despine() # remove right and top spines
pressures = True
zflow = False
t@@ -48,6 +51,7 @@ fluid=True
# wet shear
for c in numpy.arange(0,len(mu_f_vals)):
+#for c in numpy.arange(len(mu_f_vals)-1, -1, -1):
mu_f = mu_f_vals[c]
# halfshear-darcy-sigma0=20000.0-k_c=3.5e-13-mu=1.797e-06-velfac=1.0-shear
t@@ -58,43 +62,56 @@ for c in numpy.arange(0,len(mu_f_vals)):
if os.path.isfile('../output/' + sid + '.status.dat'):
sim = sphere.sim(sid, fluid=fluid)
- shear_strain[c] = numpy.zeros(sim.status())
+ n = sim.status()
+ #n = 20
+ shear_strain[c] = numpy.zeros(n)
friction[c] = numpy.zeros_like(shear_strain[c])
dilation[c] = numpy.zeros_like(shear_strain[c])
+ '''
sim.readlast(verbose=False)
- sim.visualize('shear')
+ #sim.visualize('shear')
shear_strain[c] = sim.shear_strain
#shear_strain[c] = numpy.arange(sim.status()+1)
- #friction[c] = sim.tau/sim.sigma_eff
- friction[c] = sim.tau/1000.0#/sim.sigma_eff
+ #friction[c] = sim.tau/1000.0#/sim.sigma_eff
+ friction[c] = sim.shearStress('effective')/sim.currentNormalStress('defined')
dilation[c] = sim.dilation
+ '''
# fluid pressures and particle forces
- if pressures or contact_forces:
- p_mean[c] = numpy.zeros_like(shear_strain[c])
- p_min[c] = numpy.zeros_like(shear_strain[c])
- p_max[c] = numpy.zeros_like(shear_strain[c])
- f_n_mean[c] = numpy.zeros_like(shear_strain[c])
- f_n_max[c] = numpy.zeros_like(shear_strain[c])
- for i in numpy.arange(sim.status()):
- if pressures:
- sim.readstep(i, verbose=False)
- iz_top = int(sim.w_x[0]/(sim.L[2]/sim.num[2]))-1
- p_mean[c][i] = numpy.mean(sim.p_f[:,:,0:iz_top])/1000
- p_min[c][i] = numpy.min(sim.p_f[:,:,0:iz_top])/1000
- p_max[c][i] = numpy.max(sim.p_f[:,:,0:iz_top])/1000
-
- if contact_forces:
- sim.findNormalForces()
- f_n_mean[c][i] = numpy.mean(sim.f_n_magn)
- f_n_max[c][i] = numpy.max(sim.f_n_magn)
+ p_mean[c] = numpy.zeros_like(shear_strain[c])
+ p_min[c] = numpy.zeros_like(shear_strain[c])
+ p_max[c] = numpy.zeros_like(shear_strain[c])
+ f_n_mean[c] = numpy.zeros_like(shear_strain[c])
+ f_n_max[c] = numpy.zeros_like(shear_strain[c])
+
+ for i in numpy.arange(n):
+
+ sim.readstep(i, verbose=False)
+
+ shear_strain[c][i] = sim.shearStrain()
+ friction[c][i] = sim.shearStress('effective')/sim.currentNormalStress('defined')
+ dilation[c][i] = sim.w_x[0]
+
+ if pressures:
+ iz_top = int(sim.w_x[0]/(sim.L[2]/sim.num[2]))-1
+ p_mean[c][i] = numpy.mean(sim.p_f[:,:,0:iz_top])/1000
+ p_min[c][i] = numpy.min(sim.p_f[:,:,0:iz_top])/1000
+ p_max[c][i] = numpy.max(sim.p_f[:,:,0:iz_top])/1000
+
+ if contact_forces:
+ sim.findNormalForces()
+ f_n_mean[c][i] = numpy.mean(sim.f_n_magn)
+ f_n_max[c][i] = numpy.max(sim.f_n_magn)
if zflow:
v_f_z_mean[c] = numpy.zeros_like(shear_strain[c])
- for i in numpy.arange(sim.status()):
+ for i in numpy.arange(n):
v_f_z_mean[c][i] = numpy.mean(sim.v_f[:,:,:,2])
+ dilation[c] =\
+ (dilation[c] - dilation[c][0])/(numpy.mean(sim.radius)*2.0)
+
else:
print(sid + ' not found')
t@@ -105,7 +122,8 @@ for c in numpy.arange(0,len(mu_f_vals)):
if zflow or pressures:
- fig = plt.figure(figsize=(8,10))
+ #fig = plt.figure(figsize=(8,10))
+ fig = plt.figure(figsize=(3.74, 2*3.74))
else:
fig = plt.figure(figsize=(8,8)) # (w,h)
#fig = plt.figure(figsize=(8,12))
t@@ -133,7 +151,10 @@ alpha = 1.0
#color = ['b','g','r','c']
#color = ['g','r','c']
-for c, mu_f in enumerate(mu_f_vals):
+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):
label = 'ref. shear velocity'
t@@ -145,27 +166,29 @@ for c, mu_f in enumerate(mu_f_vals):
#label = '$\\mu_\\text{{f}}$ = {:.3e} Pa s'.format(mu_f)
label = 'ref. shear velocity$\\times${:.2}'.format(mu_f/mu_f_vals[0])
- ax1.plot(shear_strain[c][1:], friction[c][1:], \
+ ax1.plot(shear_strain[c], friction[c], \
label=label, linewidth=1,
alpha=alpha, color=color[c])
- ax2.plot(shear_strain[c][1:], dilation[c][1:], \
+ ax2.plot(shear_strain[c], dilation[c], \
label=label, linewidth=1,
color=color[c])
if zflow:
- ax3.plot(shear_strain[c][1:], v_f_z_mean[c][1:],
+ ax3.plot(shear_strain[c], v_f_z_mean[c],
label=label, linewidth=1)
if pressures:
- ax3.plot(shear_strain[c][1:], p_max[c][1:], '-' + color[c], alpha=0.5)
- #ax3.plot(shear_strain[c][1:], p_mean[c][1:], '-' + color[c], \
- #label=label, linewidth=1)
- ax3.plot(shear_strain[c][1:], p_min[c][1:], '-' + color[c], alpha=0.5)
+ #ax3.plot(shear_strain[c][1:], p_max[c][1:], '-', 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.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)
#ax4.plot(shear_strain[c][1:], f_n_mean[c][1:], '-' + color[c],
#label='$c$ = %.2f' % (cvals[c-1]), linewidth=2)
t@@ -178,8 +201,8 @@ if zflow or pressures:
else:
ax2.set_xlabel('Shear strain $\\gamma$ [-]')
-#ax1.set_ylabel('Shear friction $\\tau/\\sigma\'$ [-]')
-ax1.set_ylabel('Shear stress $\\tau$ [kPa]')
+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$^{-1}$]')
t@@ -204,9 +227,42 @@ if zflow or pressures:
#ax4.grid()
'''
-legend_alpha=0.5
-ax1.legend(loc='upper right', prop={'size':18}, fancybox=True,
- framealpha=legend_alpha)
+
+# 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:
t@@ -219,19 +275,21 @@ ax1.legend(loc='upper right', prop={'size':18}, fancybox=True,
#ax2.set_xlim([0.0, 0.09])
#ax2.set_xlim([0.0, 0.2])
-ax1.set_ylim([-7, 45])
+#ax1.set_ylim([-7, 45])
ax2.set_ylim([0.0, 0.8])
#ax1.set_ylim([0.0, 1.0])
-if pressures:
+#if pressures:
#ax3.set_ylim([-1400, 900])
- ax3.set_ylim([-200, 200])
+ #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=0.05)
+plt.subplots_adjust(hspace=0.15)
#filename = 'shear-' + str(int(sigma0/1000.0)) + 'kPa-stress-dilation.pdf'
filename = 'halfshear-darcy-rate.pdf'
#print(os.getcwd() + '/' + filename)
plt.savefig(filename)
shutil.copyfile(filename, '/home/adc/articles/own/2/graphics/' + filename)
+plt.close()
print(filename)