mod
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jeremias
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0dd4e01188
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2d3873605d
@ -132,7 +132,6 @@ def Plot_Histogram(meshnames,paths,colors,outpath):
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ind = 0
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for nm in range(len(meshnames)):
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if 'box' in meshnames[nm]:
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# VOXEL SEQUENCE SIZE
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Lx = 64
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@ -167,13 +166,11 @@ def Plot_Histogram(meshnames,paths,colors,outpath):
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heights_method = False
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for k in range(mesh.num_cells()):
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# Coordinates of each cell (A,B,C,D)
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A = Points[Cells[k]][0]
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B = Points[Cells[k]][1]
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C = Points[Cells[k]][2]
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D = Points[Cells[k]][3]
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if heights_method:
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hs = np.zeros([4])
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for l in range(4):
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@ -1412,127 +1409,79 @@ def ROUTINE(options):
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if 'Error-curves' in options:
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if options['Error-curves']['apply']:
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print('--- Error curves ---')
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meas = {}
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corrs = {}
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times = {}
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norm = options['Error-curves']['norm']
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colorset = options['Error-curves']['colors']
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for resol in options['Error-curves']['resol']:
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meas[resol] = {}
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corrs[resol] = {}
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times[resol] = {}
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for dts in options['Error-curves']['times']:
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path = options['Error-curves']['folder'] + \
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resol + '/dt' + dts
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try:
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corrs[resol][dts] = np.loadtxt(
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path + '/w_' + str(norm) + 'norm.txt')
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except IOError:
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print('no curve for ' + resol + '/' + dts)
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try:
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meas[resol][dts] = np.loadtxt(
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path + '/u_' + str(norm) + 'norm.txt')
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times[resol][dts] = np.loadtxt(
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path + '/times_' + str(norm) + 'norm.txt')
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except IOError:
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print('no meas for ' + resol + '/' + dts)
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if 'meas' in options['Error-curves']['mode']:
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for resol in options['Error-curves']['resol']:
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for dts in meas[resol].keys():
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if resol == 'H1':
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print('--- Error-curves analysis ---')
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ratio = False
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for types in options['Error-curves']['type']:
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if types=='mean_ratio':
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types = 'mean'
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ratio = True
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if types=='max_ratio':
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types = 'max'
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ratio = True
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nc = 0
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elif resol == 'H2':
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nc = 1
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elif resol == 'H3':
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nc = 2
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plt.plot(times[resol][dts], meas[resol]
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[dts], color=colorset[nc], label='$' + resol + '/' + dts + '$')
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#plt.ylim([0, 1.1])
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plt.ylabel('$||u||_2$', fontsize=18)
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plt.xlabel('$time \ \ (s)$', fontsize=18)
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plt.legend(fontsize=16)
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plt.savefig(options['Error-curves']['outpath'] + 'meas_' +dts + '.png',
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dpi=500, bbox_inches='tight')
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plt.show()
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if 'corrs' in options['Error-curves']['mode']:
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for resol in options['Error-curves']['resol']:
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for dts in corrs[resol].keys():
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if resol == 'H1':
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nc = 0
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elif resol == 'H2':
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nc = 1
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elif resol == 'H3':
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nc = 2
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plt.plot(times[resol][dts], corrs[resol]
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[dts], color = colorset[nc],label='$' + resol + '/' + dts + '$')
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plt.ylim([0, 16.2])
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plt.ylabel('$||w||_2$', fontsize=18)
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plt.xlabel('$time \ \ (s)$', fontsize=18)
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plt.legend(fontsize=16)
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plt.savefig(options['Error-curves']['outpath'] + 'corrs_' +dts + '.png',
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dpi=500, bbox_inches='tight')
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plt.show()
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if 'fracs' in options['Error-curves']['mode']:
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for resol in options['Error-curves']['resol']:
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for dts in corrs[resol].keys():
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if resol == 'H1':
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nc = 0
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elif resol == 'H2':
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nc = 1
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elif resol == 'H3':
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nc = 2
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plt.plot(times[resol][dts], corrs[resol][dts]/meas[resol][dts],
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color=colorset[nc], label='$' + resol + '/' + dts + '$')
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plt.ylim([0, 1])
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plt.ylabel('$||w||_2/||u||_2$', fontsize=18)
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plt.xlabel('$time \ \ (s)$', fontsize=18)
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plt.legend(fontsize=16)
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plt.savefig(options['Error-curves']['outpath'] + 'fracs_' +dts + '.png',
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dpi=500, bbox_inches='tight')
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plt.show()
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if 'Components' in options:
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if options['Components']['apply']:
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print('--- Components analysis ---')
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for types in options['Components']['type']:
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nc = 0
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for subf in options['Components']['subfolders']:
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if len(options['Error-curves']['subfolders'])==0:
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ucomp = []
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wcomp = []
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colorset = options['Components']['colors']
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path = options['Components']['folder'] + subf + '/'
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colorset = options['Error-curves']['colors']
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path = options['Error-curves']['folder']
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try:
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ucomp = np.loadtxt(path + '/u'+types+'.txt')
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wcomp = np.loadtxt(path + '/w'+types+'.txt')
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times = np.loadtxt(path + '/times.txt')
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except IOError:
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print('no components for ' + subf)
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print('no Error-curves for ' + subf)
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if not ratio:
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plt.plot(
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times, ucomp, color=colorset[nc], linestyle='-', label= '$u$' )
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plt.plot(
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times, wcomp, color=colorset[nc], linestyle='--', label='$w$')
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else:
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plt.plot(
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times, ucomp, color=colorset[nc], linestyle='-', label= '$u$' )
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plt.plot(
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times, wcomp, color=colorset[nc], linestyle='--', label='$w$')
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nc +=1
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else:
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for subf in options['Error-curves']['subfolders']:
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ucomp = []
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wcomp = []
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colorset = options['Error-curves']['colors']
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labelset = options['Error-curves']['labels']
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path = options['Error-curves']['folder'] + subf + '/'
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try:
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ucomp = np.loadtxt(path + '/u'+types+'.txt')
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wcomp = np.loadtxt(path + '/w'+types+'.txt')
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times = np.loadtxt(path + '/times.txt')
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except IOError:
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print('no cError-curves for ' + subf)
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if not ratio:
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plt.plot(
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times, ucomp, color=colorset[nc], linestyle='-', label= '$u'+ subf +'$' )
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plt.plot(
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times, wcomp, color=colorset[nc], linestyle='--', label='$w'+subf+'$')
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else:
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wu = wcomp/ucomp
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plt.plot(
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times, wu, color=colorset[nc], linestyle='-', label= '$'+ labelset[nc] +'$' )
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nc +=1
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#plt.ylim([0, 170])
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plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
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plt.xlabel('$time \ \ (s)$', fontsize=18)
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plt.legend(fontsize=16)
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plt.savefig(options['Components']['outpath'] + types + '.png', dpi=500, bbox_inches='tight')
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if options['Error-curves']['title']:
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plt.title(options['Error-curves']['title'], fontsize=18)
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if not ratio:
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plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
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plt.savefig(options['Error-curves']['outpath'] + types + '.png', dpi=500, bbox_inches='tight')
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else:
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plt.ylabel('$w/u$', fontsize=18)
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if 'max' in types:
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plt.ylim([0, 1.8])
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plt.savefig(options['Error-curves']['outpath'] + types + '_ratio.png', dpi=500, bbox_inches='tight')
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plt.show()
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@ -175,6 +175,37 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
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for bb in bnds:
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QQ[bb] = []
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if mode == 'Histograms':
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u = Function(W)
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if 'w_COR' in filename:
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h5name = 'w/vector_0'
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else:
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h5name = 'u/vector_0'
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ValuesTime = np.zeros([len(indexes),len(u.vector().get_local())])
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ValuesPeak = np.zeros([len(u.vector().get_local())])
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ix = int(0)
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for k in indexes:
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path = checkpoint_path + str(k) + '/'+filename+'.h5'
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hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
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print('Reading checkpoint ',indexes[k])
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hdf.read(u, h5name)
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time = hdf.attributes(h5name).to_dict()['timestamp']
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hdf.close()
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uvec = u.vector().get_local()
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ValuesTime[ix,:] = np.abs(uvec)
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ix +=1
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CoordPeak = np.where(ValuesTime==np.max(ValuesTime))
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ValuesPeak = np.abs(ValuesTime[CoordPeak[0],:])
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freq,edges = np.histogram(ValuesPeak, bins=80, density=True)
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#Saving the histogram
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print('Saving at ' + output_path)
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np.savetxt(output_path + 'hist_frew.txt', freq)
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np.savetxt(output_path + 'hist_edges.txt', edges)
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if mode == 'perturbation':
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u = Function(W)
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unew = Function(W)
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@ -216,10 +247,10 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
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ufactor = options['Perturbation']['type']['phase_contrast']/100
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VENC = np.max(np.abs(uvec))*ufactor
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gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
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#B0 = 1.5 # Tesla Magnetic Field Strenght
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B0 = 1.5 # Tesla Magnetic Field Strenght
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TE = 5e-3 # Echo-time
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Phi1 = gamma*10*TE + 0*uvec
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Phi2 = gamma*10*TE + np.pi*uvec/VENC
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Phi1 = 1*B0*TE + 0*uvec
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Phi2 = 1*B0*TE + np.pi*uvec/VENC
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M1 = np.cos(Phi1) + 1j*np.sin(Phi1)
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M2 = np.cos(Phi2) + 1j*np.sin(Phi2)
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@ -476,7 +507,10 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
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u.rename('meas', 'meas')
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w.rename('w', 'w')
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hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
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if 'w' in comname:
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hdf_w.read(w, 'w/vector_0')
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else:
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hdf_w.read(w, 'u/vector_0')
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hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
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hdf_u.read(u, 'u/vector_0')
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hdf_u.close()
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@ -917,7 +951,6 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
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unsort_indexes = os.listdir(checkpoint_path)
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indexes = [int(x) for x in unsort_indexes]
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indexes.sort()
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QQ = {}
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PP = {}
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ds = Measure('ds', domain=MESH['mesh'], subdomain_data=MESH['boundaries'])
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@ -930,11 +963,6 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
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for k in range(0, len(indexes)):
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path_u = checkpoint_path + str(indexes[k]) + '/'+filename[0]+'.h5'
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path_p = checkpoint_path + str(indexes[k]) + '/'+filename[1]+'.h5'
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if indexes[k] < 10:
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path_u = checkpoint_path + '0' + \
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str(indexes[k]) + '/'+filename[0]+'.h5'
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path_p = checkpoint_path + '0' + \
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str(indexes[k]) + '/'+filename[1]+'.h5'
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u = Function(V)
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p = Function(W)
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@ -946,7 +974,7 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
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hdf_p.read(p, 'p/vector_0')
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hdf_p.close()
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print('Computing flows and pressures at timestep number ' + str(k))
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print('Computing flows and pressures at timestep number ' + str(indexes[k]))
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for bb in bnds:
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if bb == 2:
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QQ[bb].append(-assemble(dot(u, n)*ds(bb)))
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@ -1134,9 +1162,20 @@ def ROUTINE(options):
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MESH = LOADmesh(options['Perturbation']['meshpath'])
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checkpath = options['Perturbation']['checkpath'] + 'checkpoint/'
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out_check = options['Perturbation']['checkpath'] + 'Perturbation/'
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name_folder = 'SNR' +options['Perturbation']['type']['SNR'] + 'V' + str(options['Perturbation']['type']['phase_contrast'])
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out_check = options['Perturbation']['checkpath'] + name_folder + '/'
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READcheckpoint(MESH,'perturbation', out_check,checkpath,'u','u',options)
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if 'Histograms' in options:
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if options['Histograms']['apply']:
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if rank==0:
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print('--- Histograms in measurements ---')
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MESH = LOADmesh(options['Histograms']['meshpath'])
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checkpath = options['Histograms']['checkpath'] + 'checkpoint/'
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outpath = options['Histograms']['checkpath']
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field_name = options['Histograms']['field_name']
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READcheckpoint(MESH,'Histograms', outpath, checkpath,field_name,field_name,options)
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if __name__ == '__main__':
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