timprove internals plot - sphere - GPU-based 3D discrete element method algorit… | |
git clone git://src.adamsgaard.dk/sphere | |
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--- | |
commit fd4eb344b8af1b8de25c5a2c587c01f94fd9adb4 | |
parent 9d9e5ba4f59c0dbafc66116261bd5766e48f380f | |
Author: Anders Damsgaard <[email protected]> | |
Date: Thu, 16 Apr 2015 11:48:55 +0200 | |
improve internals plot | |
Diffstat: | |
M python/halfshear-darcy-internals.py | 373 +++++++++++++++++------------… | |
M python/sphere.py | 9 +++++++-- | |
2 files changed, 207 insertions(+), 175 deletions(-) | |
--- | |
diff --git a/python/halfshear-darcy-internals.py b/python/halfshear-darcy-inter… | |
t@@ -13,213 +13,240 @@ 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.set(style='ticks', palette='Blues') | |
+ | |
#sigma0 = float(sys.argv[1]) | |
sigma0 = 20000.0 | |
#k_c = 3.5e-13 | |
-k_c = float(sys.argv[1]) | |
- | |
-if k_c == 3.5e-15: | |
- steps = [1232, 1332, 1433, 1534, 1635] | |
-elif k_c == 3.5e-13: | |
- steps = [100, 200, 300, 410, 515] | |
-else: | |
- steps = [10, 50, 100, 1000, 1999] | |
+#k_c = float(sys.argv[1]) | |
+k_c_list = [3.5e-13, 3.5e-14, 3.5e-15] | |
+ | |
+#if k_c == 3.5e-15: | |
+# steps = [1232, 1332, 1433, 1534, 1635] | |
+#elif k_c == 3.5e-13: | |
+# steps = [100, 200, 300, 410, 515] | |
+#else: | |
+# steps = [10, 50, 100, 1000, 1999] | |
nsteps_avg = 1 # no. of steps to average over | |
#nsteps_avg = 100 # no. of steps to average over | |
+steps = [1, 50, 100, 150, 200] | |
-sid = 'halfshear-darcy-sigma0=' + str(sigma0) + '-k_c=' + str(k_c) + \ | |
- '-mu=1.797e-06-velfac=1.0-shear' | |
-sim = sphere.sim(sid, fluid=True) | |
-sim.readfirst(verbose=False) | |
+for k_c in k_c_list: | |
-# particle z positions | |
-zpos_p = numpy.zeros((len(steps), sim.np)) | |
+ sid = 'halfshear-darcy-sigma0=' + str(sigma0) + '-k_c=' + str(k_c) + \ | |
+ '-mu=1.797e-06-velfac=1.0-shear' | |
+ sim = sphere.sim(sid, fluid=True) | |
+ sim.readfirst(verbose=False) | |
-# cell midpoint cell positions | |
-zpos_c = numpy.zeros((len(steps), sim.num[2])) | |
-dz = sim.L[2]/sim.num[2] | |
-for i in numpy.arange(sim.num[2]): | |
- zpos_c[:,i] = i*dz + 0.5*dz | |
+ # particle z positions | |
+ zpos_p = numpy.zeros((len(steps), sim.np)) | |
-# particle x displacements | |
-xdisp = numpy.zeros((len(steps), sim.np)) | |
+ # cell midpoint cell positions | |
+ zpos_c = numpy.zeros((len(steps), sim.num[2])) | |
+ dz = sim.L[2]/sim.num[2] | |
+ for i in numpy.arange(sim.num[2]): | |
+ zpos_c[:,i] = i*dz + 0.5*dz | |
-# particle z velocity | |
-v_z_p = numpy.zeros((len(steps), sim.np)) | |
+ # particle x displacements | |
+ xdisp = numpy.zeros((len(steps), sim.np)) | |
-# fluid permeability | |
-k = numpy.zeros((len(steps), sim.num[0], sim.num[1], sim.num[2])) | |
-k_bar = numpy.zeros((len(steps), sim.num[2])) | |
+ # particle z velocity | |
+ v_z_p = numpy.zeros((len(steps), sim.np)) | |
-# pressure | |
-p = numpy.zeros((len(steps), sim.num[2])) | |
+ # fluid permeability | |
+ k = numpy.zeros((len(steps), sim.num[0], sim.num[1], sim.num[2])) | |
+ k_bar = numpy.zeros((len(steps), sim.num[2])) | |
-# mean per-particle values | |
-v_z_p_bar = numpy.zeros((len(steps), sim.num[2])) | |
-v_z_f_bar = numpy.zeros((len(steps), sim.num[2])) | |
+ # pressure | |
+ p = numpy.zeros((len(steps), sim.num[2])) | |
-# particle-fluid force per particle | |
-f_pf = numpy.zeros_like(xdisp) | |
+ # mean per-particle values | |
+ v_z_p_bar = numpy.zeros((len(steps), sim.num[2])) | |
+ v_z_f_bar = numpy.zeros((len(steps), sim.num[2])) | |
-# pressure - hydrostatic pressure | |
-#dev_p = numpy.zeros((len(steps), sim.num[2])) | |
+ # particle-fluid force per particle | |
+ f_pf = numpy.zeros_like(xdisp) | |
-# mean porosity | |
-phi_bar = numpy.zeros((len(steps), sim.num[2])) | |
+ # pressure - hydrostatic pressure | |
+ #dev_p = numpy.zeros((len(steps), sim.num[2])) | |
-# mean porosity change | |
-dphi_bar = numpy.zeros((len(steps), sim.num[2])) | |
+ # mean porosity | |
+ phi_bar = numpy.zeros((len(steps), sim.num[2])) | |
-# mean per-particle values | |
-xdisp_mean = numpy.zeros((len(steps), sim.num[2])) | |
-f_pf_mean = numpy.zeros((len(steps), sim.num[2])) | |
+ # mean porosity change | |
+ dphi_bar = numpy.zeros((len(steps), sim.num[2])) | |
-shear_strain_start = numpy.zeros(len(steps)) | |
-shear_strain_end = numpy.zeros(len(steps)) | |
+ # mean per-particle values | |
+ xdisp_mean = numpy.zeros((len(steps), sim.num[2])) | |
+ f_pf_mean = numpy.zeros((len(steps), sim.num[2])) | |
-#fig = plt.figure(figsize=(8,4*(len(steps))+1)) | |
-fig = plt.figure(figsize=(8,4.5)) | |
-ax = [] | |
-n = 4 | |
-ax.append(plt.subplot(1, n, 1)) # 0: xdisp | |
-ax.append(plt.subplot(1, n, 2, sharey=ax[0])) # 3: k | |
-ax.append(plt.subplot(1, n, 3, sharey=ax[0])) # 5: p_f | |
-ax.append(plt.subplot(1, n, 4, sharey=ax[0])) # 6: f_pf_z | |
+ shear_strain_start = numpy.zeros(len(steps)) | |
+ shear_strain_end = numpy.zeros(len(steps)) | |
-s = 0 | |
-for step_str in steps: | |
+ #fig = plt.figure(figsize=(8,4*(len(steps))+1)) | |
+ #fig = plt.figure(figsize=(8,4.5)) | |
+ fig = plt.figure(figsize=(3.74*2,4.5)) | |
+ ax = [] | |
+ n = 4 | |
+ ax.append(plt.subplot(1, n, 1)) # 0: xdisp | |
+ ax.append(plt.subplot(1, n, 2, sharey=ax[0])) # 3: k | |
+ ax.append(plt.subplot(1, n, 3, sharey=ax[0])) # 5: p_f | |
+ ax.append(plt.subplot(1, n, 4, sharey=ax[0])) # 6: f_pf_z | |
- step = int(step_str) | |
+ s = 0 | |
+ for step_str in steps: | |
- if os.path.isfile('../output/' + sid + '.status.dat'): | |
+ step = int(step_str) | |
- for substep in numpy.arange(nsteps_avg): | |
+ if os.path.isfile('../output/' + sid + '.status.dat'): | |
- if step + substep > sim.status(): | |
- raise Exception( | |
- 'Simulation step %d not available (sim.status = %d).' | |
- % (step + substep, sim.status())) | |
+ for substep in numpy.arange(nsteps_avg): | |
- sim.readstep(step + substep, verbose=False) | |
+ if step + substep > sim.status(): | |
+ raise Exception( | |
+ 'Simulation step %d not available (sim.status = %d… | |
+ % (step + substep, sim.status())) | |
- zpos_p[s,:] += sim.x[:,2]/nsteps_avg | |
+ sim.readstep(step + substep, verbose=False) | |
- xdisp[s,:] += sim.xyzsum[:,0]/nsteps_avg | |
+ zpos_p[s,:] += sim.x[:,2]/nsteps_avg | |
- ''' | |
- for i in numpy.arange(sim.np): | |
- f_pf[s,i] += \ | |
- sim.f_sum[i].dot(sim.f_sum[i])/nsteps_avg | |
- ''' | |
- f_pf[s,:] += sim.f_p[:,2] | |
+ xdisp[s,:] += sim.xyzsum[:,0]/nsteps_avg | |
- dz = sim.L[2]/sim.num[2] | |
- wall0_iz = int(sim.w_x[0]/dz) | |
+ ''' | |
+ for i in numpy.arange(sim.np): | |
+ f_pf[s,i] += \ | |
+ sim.f_sum[i].dot(sim.f_sum[i])/nsteps_avg | |
+ ''' | |
+ f_pf[s,:] += sim.f_p[:,2] | |
- p[s,:] += numpy.average(numpy.average(sim.p_f[:,:,:], axis=0),\ | |
- axis=0)/nsteps_avg | |
+ dz = sim.L[2]/sim.num[2] | |
+ wall0_iz = int(sim.w_x[0]/dz) | |
- sim.findPermeabilities() | |
- k[s,:] += sim.k[:,:,:]/nsteps_avg | |
+ p[s,:] += numpy.average(numpy.average(sim.p_f[:,:,:], axis=0),\ | |
+ axis=0)/nsteps_avg | |
- k_bar[s,:] += \ | |
- numpy.average(numpy.average(sim.k[:,:,:], axis=0), axis=0)\ | |
- /nsteps_avg | |
+ sim.findPermeabilities() | |
+ k[s,:] += sim.k[:,:,:]/nsteps_avg | |
- if substep == 0: | |
- shear_strain_start[s] = sim.shearStrain() | |
- else: | |
- shear_strain_end[s] = sim.shearStrain() | |
- | |
- # calculate mean values of xdisp and f_pf | |
- for iz in numpy.arange(sim.num[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]) | |
- f_pf_mean[s,iz] = numpy.mean(f_pf[s,I]) | |
+ k_bar[s,:] += \ | |
+ numpy.average(numpy.average(sim.k[:,:,:], axis=0), axi… | |
+ /nsteps_avg | |
- #ax[0].plot(xdisp[s], zpos_p[s], ',', color = '#888888') | |
- ax[0].plot(xdisp_mean[s], zpos_c[s], label='$\gamma$ = %.2f' % | |
- (shear_strain_start[s])) | |
+ if substep == 0: | |
+ shear_strain_start[s] = sim.shearStrain() | |
+ else: | |
+ shear_strain_end[s] = sim.shearStrain() | |
+ | |
+ # calculate mean values of xdisp and f_pf | |
+ for iz in numpy.arange(sim.num[2]): | |
+ z_bot = iz*dz | |
+ z_top = (iz+1)*dz | |
+ I = numpy.nonzero((zpos_p[s,:] >= z_bot) & (zpos_p[s,:] < z_to… | |
+ if len(I) > 0: | |
+ xdisp_mean[s,iz] = numpy.mean(xdisp[s,I]) | |
+ f_pf_mean[s,iz] = numpy.mean(f_pf[s,I]) | |
- ax[1].semilogx(k_bar[s], zpos_c[s], label='$\gamma$ = %.2f' % | |
- (shear_strain_start[s])) | |
- | |
- ax[2].plot(p[s]/1000.0, zpos_c[s], label='$\gamma$ = %.2f' % | |
- (shear_strain_start[s])) | |
- | |
- # remove particles with 0.0 pressure force | |
- I = numpy.nonzero(numpy.abs(f_pf[s]) > .01) | |
- f_pf_nonzero = f_pf[s][I] | |
- zpos_p_nonzero = zpos_p[s][I] | |
- I = numpy.nonzero(numpy.abs(f_pf_mean[s]) > .01) | |
- f_pf_mean_nonzero = f_pf_mean[s][I] | |
- zpos_c_nonzero = zpos_c[s][I] | |
- | |
- #ax[3].plot(f_pf_nonzero, zpos_p_nonzero, ',', alpha=0.5, | |
- #color='#888888') | |
- ax[3].plot(f_pf_mean_nonzero, zpos_c_nonzero, label='$\gamma$ = %.2f' % | |
- (shear_strain_start[s])) | |
- | |
- else: | |
- print(sid + ' not found') | |
- s += 1 | |
- | |
- | |
- | |
-max_z = numpy.max(zpos_p) | |
-ax[0].set_ylim([0, max_z]) | |
-ax[0].set_xlim([0, 0.5]) | |
- | |
-if k_c == 3.5e-15: | |
- #ax[1].set_xlim([1e-14, 1e-12]) | |
- ax[1].set_xlim([1e-16, 1e-14]) | |
-elif k_c == 3.5e-13: | |
- #ax[1].set_xlim([1e-12, 1e-10]) | |
- ax[1].set_xlim([1e-14, 1e-12]) | |
- | |
-ax[0].set_ylabel('Vertical position $z$ [m]') | |
-ax[0].set_xlabel('$\\bar{\\boldsymbol{x}}^x_\\text{p}$ [m]') | |
-ax[1].set_xlabel('$\\bar{k}$ [m$^{2}$]') | |
-ax[2].set_xlabel('$\\bar{p_\\text{f}}$ [kPa]') | |
-ax[3].set_xlabel('$\\boldsymbol{f}^z_\\text{i}$ [N]') | |
- | |
-# align x labels | |
-labely = -0.3 | |
-ax[0].xaxis.set_label_coords(0.5, labely) | |
-ax[1].xaxis.set_label_coords(0.5, labely) | |
-ax[2].xaxis.set_label_coords(0.5, labely) | |
-ax[3].xaxis.set_label_coords(0.5, labely) | |
- | |
-plt.setp(ax[1].get_yticklabels(), visible=False) | |
-plt.setp(ax[2].get_yticklabels(), visible=False) | |
-plt.setp(ax[3].get_yticklabels(), visible=False) | |
- | |
-plt.setp(ax[0].xaxis.get_majorticklabels(), rotation=90) | |
-plt.setp(ax[1].xaxis.get_majorticklabels(), rotation=90) | |
-plt.setp(ax[2].xaxis.get_majorticklabels(), rotation=90) | |
-plt.setp(ax[3].xaxis.get_majorticklabels(), rotation=90) | |
- | |
-ax[0].grid() | |
-ax[1].grid() | |
-ax[2].grid() | |
-ax[3].grid() | |
- | |
-legend_alpha=0.5 | |
-ax[0].legend(loc='lower center', prop={'size':12}, fancybox=True, | |
- framealpha=legend_alpha) | |
- | |
-#plt.subplots_adjust(wspace = .05) # doesn't work with tight_layout() | |
-plt.tight_layout() | |
-#plt.MaxNLocator(nbins=1) # doesn't work? | |
-ax[0].locator_params(nbins=3) | |
-ax[2].locator_params(nbins=3) | |
-ax[3].locator_params(nbins=3) | |
- | |
-filename = 'halfshear-darcy-internals-k_c=%.0e.pdf' % (k_c) | |
-plt.savefig(filename) | |
-shutil.copyfile(filename, '/home/adc/articles/own/2/graphics/' + filename) | |
-print(filename) | |
+ k_bar[s][0] = k_bar[s][1] | |
+ | |
+ | |
+ | |
+ #ax[0].plot(xdisp[s], zpos_p[s], ',', color = '#888888') | |
+ ax[0].plot(xdisp_mean[s], zpos_c[s], label='$\gamma$ = %.2f' % | |
+ (shear_strain_start[s])) | |
+ | |
+ ax[1].semilogx(k_bar[s], zpos_c[s], label='$\gamma$ = %.2f' % | |
+ (shear_strain_start[s])) | |
+ | |
+ ax[2].plot(p[s]/1000.0, zpos_c[s], label='$\gamma$ = %.2f' % | |
+ (shear_strain_start[s])) | |
+ | |
+ # remove particles with 0.0 pressure force | |
+ I = numpy.nonzero(numpy.abs(f_pf[s]) > .01) | |
+ f_pf_nonzero = f_pf[s][I] | |
+ zpos_p_nonzero = zpos_p[s][I] | |
+ I = numpy.nonzero(numpy.abs(f_pf_mean[s]) > .01) | |
+ f_pf_mean_nonzero = f_pf_mean[s][I] | |
+ zpos_c_nonzero = zpos_c[s][I] | |
+ | |
+ #ax[3].plot(f_pf_nonzero, zpos_p_nonzero, ',', alpha=0.5, | |
+ #color='#888888') | |
+ ax[3].plot(f_pf_mean_nonzero, zpos_c_nonzero, label='$\gamma$ = %.… | |
+ (shear_strain_start[s])) | |
+ | |
+ else: | |
+ print(sid + ' not found') | |
+ s += 1 | |
+ | |
+ | |
+ max_z = numpy.max(zpos_p) | |
+ ax[0].set_ylim([0, max_z]) | |
+ #ax[0].set_xlim([0, 0.5]) | |
+ ax[0].set_xlim([0, 0.05]) | |
+ | |
+ if k_c == 3.5e-15: | |
+ #ax[1].set_xlim([1e-14, 1e-12]) | |
+ ax[1].set_xlim([1e-16, 1e-14]) | |
+ elif k_c == 3.5e-14: | |
+ ax[1].set_xlim([1e-15, 1e-13]) | |
+ elif k_c == 3.5e-13: | |
+ #ax[1].set_xlim([1e-12, 1e-10]) | |
+ ax[1].set_xlim([1e-14, 1e-12]) | |
+ | |
+ ax[0].set_ylabel('Vertical position $z$ [m]') | |
+ ax[0].set_xlabel('$\\bar{\\boldsymbol{x}}^x_\\text{p}$ [m]') | |
+ ax[1].set_xlabel('$\\bar{k}$ [m$^{2}$]') | |
+ ax[2].set_xlabel('$\\bar{p_\\text{f}}$ [kPa]') | |
+ ax[3].set_xlabel('$\\boldsymbol{f}^z_\\text{i}$ [N]') | |
+ | |
+ # align x labels | |
+ labely = -0.3 | |
+ ax[0].xaxis.set_label_coords(0.5, labely) | |
+ ax[1].xaxis.set_label_coords(0.5, labely) | |
+ ax[2].xaxis.set_label_coords(0.5, labely) | |
+ ax[3].xaxis.set_label_coords(0.5, labely) | |
+ | |
+ plt.setp(ax[1].get_yticklabels(), visible=False) | |
+ plt.setp(ax[2].get_yticklabels(), visible=False) | |
+ plt.setp(ax[3].get_yticklabels(), visible=False) | |
+ | |
+ plt.setp(ax[0].xaxis.get_majorticklabels(), rotation=90) | |
+ plt.setp(ax[1].xaxis.get_majorticklabels(), rotation=90) | |
+ plt.setp(ax[2].xaxis.get_majorticklabels(), rotation=90) | |
+ plt.setp(ax[3].xaxis.get_majorticklabels(), rotation=90) | |
+ | |
+ ''' | |
+ ax[0].grid() | |
+ ax[1].grid() | |
+ ax[2].grid() | |
+ ax[3].grid() | |
+ ''' | |
+ | |
+ for i in range(4): | |
+ # vertical grid lines | |
+ ax[i].get_xaxis().grid(True, linestyle=':', linewidth=0.5) | |
+ # horizontal grid lines | |
+ ax[i].get_yaxis().grid(True, linestyle=':', linewidth=0.5) | |
+ | |
+ legend_alpha=0.5 | |
+ ax[0].legend(loc='lower center', prop={'size':12}, fancybox=True, | |
+ framealpha=legend_alpha) | |
+ | |
+ #plt.subplots_adjust(wspace = .05) # doesn't work with tight_layout() | |
+ plt.tight_layout() | |
+ #plt.MaxNLocator(nbins=1) # doesn't work? | |
+ ax[0].locator_params(nbins=5) | |
+ ax[2].locator_params(nbins=5) | |
+ ax[3].locator_params(nbins=5) | |
+ | |
+ sns.despine() # remove chartjunk | |
+ | |
+ filename = 'halfshear-darcy-internals-k_c=%.0e.pdf' % (k_c) | |
+ plt.savefig(filename) | |
+ shutil.copyfile(filename, '/home/adc/articles/own/2/graphics/' + filename) | |
+ print(filename) | |
diff --git a/python/sphere.py b/python/sphere.py | |
t@@ -6785,7 +6785,8 @@ class sim: | |
i_max = sb.status() | |
# use largest difference in p from 0 as +/- limit on colormap | |
#print i_min, i_max | |
- p_ext = numpy.max(numpy.abs(pres)) | |
+ #p_ext = numpy.max(numpy.abs(pres)) | |
+ p_ext = numpy.max(numpy.abs(pres[0:9,:])) # for article2 | |
if sb.wmode[0] == 3: | |
x = t | |
t@@ -6803,7 +6804,8 @@ class sim: | |
else: | |
im1 = ax.pcolormesh( | |
x, zpos_c, pres, | |
- cmap=matplotlib.cm.get_cmap('bwr'), | |
+ #cmap=matplotlib.cm.get_cmap('bwr'), | |
+ cmap=matplotlib.cm.get_cmap('RdBu_r'), | |
#cmap=matplotlib.cm.get_cmap('coolwarm'), | |
vmin=-p_ext, vmax=p_ext, | |
rasterized=True) | |
t@@ -6824,6 +6826,9 @@ class sim: | |
if xlim: | |
ax.set_xlim([x[0], x[-1]]) | |
+ # for article2 | |
+ ax.set_ylim([zpos_c[0], zpos_c[9]]) | |
+ | |
cb = plt.colorbar(im1) | |
cb.set_label('$p_\\text{f}$ [kPa]') | |
cb.solids.set_rasterized(True) |