Clean Up Figures

src/docs/sphinx/basicExamples/gravityInducedStressInitialization/Example.rst

@@ -131,7 +131,7 @@ In the ``Tasks`` section, ``SinglePhasePoromechanicsInitialization`` tasks are d
     :start-after: <!-- SPHINX_TASKS -->
     :end-before: <!-- SPHINX_TASKS_END -->
 
-The initialization is triggered into action using the ``Event`` management section, where the ``soloEvent`` function calls the task at the target time (in this case -1e10s).
+The initialization is triggered into action using the ``Event`` management section, where the ``soloEvent`` function calls the task at the target time (in this case -1e10\u00A0s).
 
 .. literalinclude:: ../../../../../inputFiles/initialization/gravityInducedStress_initialization_benchmark.xml
     :language: xml
@@ -197,11 +197,11 @@ The parameters used in the simulation are summarized in the following table.
 Inspecting Results
 ---------------------------------
 
-In the example, we request vtk output files for time-series (time history). We use paraview to visualize the outcome at the time 0s.
+In the example, we request vtk output files for time-series (time history). We use paraview to visualize the outcome at the time 0\u00A0s.
 The following figure shows the final gradient of pressure and of the effective vertical stress after initialization is completed.
 
 .. _problemInitializationPres:
-.. figure:: vertical_grad.png
+.. figure:: pressure_field.png
    :align: center
    :width: 500
    :figclass: align-center

src/docs/sphinx/basicExamples/gravityInducedStressInitialization/gravityInitializationFigure.py

@@ -51,7 +51,7 @@ def getHydromechanicalParametersFromXML(xmlFilePath):
 
 def main():
 	# File path
-	xmlFile1Path = "../../../../../inputFiles/initialization/gravityInducedStress_initialization_base.xml"
+ 	xmlFile1Path = "../../../../../inputFiles/initialization/gravityInducedStress_initialization_base.xml"
 	xmlFile2Path = "../../../../../inputFiles/initialization/gravityInducedStress_initialization_benchmark.xml"
 
 	hydromechanicalParameters = getHydromechanicalParametersFromXML(xmlFile1Path)
@@ -66,18 +66,23 @@ def main():
 	traction = hydromechanicalParameters["traction"]
 	gravity = 9.81 
 
+	# rename this file to the name of your Paraview output file
 	file = open("simulation_result_0.csv")
 	csvreader = csv.reader(file)
 	header = next(csvreader)
+	header_index = {column_name: index for index, column_name in enumerate(header)}
 
 	rows = []
 	for row in csvreader:
 		rows.append(row)
 	file.close() 
 
-
+	zloc_index = header_index["elementCenter:2"]
+	pressure_index = header_index["pressure"]
+	tsxx_index = header_index["rockSolid_stress:0"] # the solidModelName="rockSolid" has been defined in the gravityInducedStress_initialization_base.xml file, please change if you have a different solidModelName 
+	tsyy_index = header_index["rockSolid_stress:1"]
+	tszz_index = header_index["rockSolid_stress:2"]
 
-	z_analytical= np.linspace(0, 1000, 100)
 
 	rows = np.array(rows)
 	zloc_0 = np.empty(len(rows[:,1]))
@@ -86,13 +91,11 @@ def main():
 	tsyy_0 = np.empty(len(rows[:,1]))
 	tszz_0 = np.empty(len(rows[:,1]))
 	for i in range(0,len(rows[:,1])):
-		zloc_0[i]=-(float(rows[i,2]))
-		pressure_0[i]=float(rows[i,3])		
-		tsxx_0[i]=-(float(rows[i,4])-BiotCoefficient*pressure_0[i])/1.0e6
-		tsyy_0[i]=-(float(rows[i,5])-BiotCoefficient*pressure_0[i])/1.0e6
-		tszz_0[i]=-(float(rows[i,6])-BiotCoefficient*pressure_0[i])/1.0e6
-
-
+		zloc_0[i]=-(float(rows[i,zloc_index]))
+		pressure_0[i]=float(rows[i,pressure_index])		
+		tsxx_0[i]=-(float(rows[i,tsxx_index])-BiotCoefficient*pressure_0[i])/1.0e6
+		tsyy_0[i]=-(float(rows[i,tsyy_index])-BiotCoefficient*pressure_0[i])/1.0e6
+		tszz_0[i]=-(float(rows[i,tszz_index])-BiotCoefficient*pressure_0[i])/1.0e6
 
 
 	z_analytical= np.linspace(0, 1000, 100)

src/docs/sphinx/basicExamples/userTableStressInitialization/Example.rst

@@ -67,17 +67,24 @@ In addition to generating the files listed above, the script prints out the resu
 Inspecting Results
 ---------------------------------
 
-In the example, we request vtk output files for time-series (time history). We use Python scripts to visualize the outcome at the time 0s.
-The following figure shows the final gradient of pressure after initialization is completed.
+In the example, we request vtk output files for time-series (time history). We use Python scripts to visualize the outcome at the time 0\u00A0s.
+The following figure shows the final gradient of pressure and of the effective vertical stress after initialization is completed.
 
 .. _problemInitializationPres:
-.. figure:: pressure_gradient.png
+.. figure:: pressure_field.png
    :align: center
    :width: 500
    :figclass: align-center
 
    Simulation result of pressure
 
+.. _problemInitializationSZZ:
+.. figure:: stressZZ_field.png
+   :align: center
+   :width: 500
+   :figclass: align-center
+
+   Simulation result of effective vertical stress
 
 The figure below shows the comparisons between the numerical predictions (marks) and the corresponding user-provided stress gradients.
 

src/docs/sphinx/basicExamples/userTableStressInitialization/tableInitializationFigure.py

@@ -62,6 +62,7 @@ def main():
 	xmlFile1Path = "../../../../../inputFiles/initialization/userdefinedStress_initialization_base.xml"
 	xmlFile2Path = "../../../../../inputFiles/initialization/userdefinedStress_initialization_benchmark.xml"
 
+
 	hydromechanicalParameters = getHydromechanicalParametersFromXML(xmlFile1Path)
 	stress_gradients = inputStressGradientsMPa(0.17,0.27,0.24,0.1)
 	sxx_grad = stress_gradients["stressXX"]
@@ -78,27 +79,36 @@ def main():
 	traction = hydromechanicalParameters["traction"]
 	gravity = 9.81 
 
+	# rename this file to the name of your Paraview output file
 	file = open("simulation_result_0.csv")
 	csvreader = csv.reader(file)
 	header = next(csvreader)
+	header_index = {column_name: index for index, column_name in enumerate(header)}
 
 	rows = []
 	for row in csvreader:
 		rows.append(row)
 	file.close() 
 
+	zloc_index = header_index["elementCenter:2"]
+	pressure_index = header_index["pressure"]
+	tsxx_index = header_index["rockSolid_stress:0"] # the solidModelName="rockSolid" has been defined in the gravityInducedStress_initialization_base.xml file, please change if you have a different solidModelName 
+	tsyy_index = header_index["rockSolid_stress:1"]
+	tszz_index = header_index["rockSolid_stress:2"]
+
+
 	rows = np.array(rows)
 	zloc_0 = np.empty(len(rows[:,1]))
 	pressure_0 = np.empty(len(rows[:,1]))
 	tsxx_0 = np.empty(len(rows[:,1]))
 	tsyy_0 = np.empty(len(rows[:,1]))
 	tszz_0 = np.empty(len(rows[:,1]))
 	for i in range(0,len(rows[:,1])):
-		zloc_0[i]=-(float(rows[i,2]))
-		pressure_0[i]=float(rows[i,3])		
-		tsxx_0[i]=-(float(rows[i,4])-BiotCoefficient*pressure_0[i])/1.0e6
-		tsyy_0[i]=-(float(rows[i,5])-BiotCoefficient*pressure_0[i])/1.0e6
-		tszz_0[i]=-(float(rows[i,6])-BiotCoefficient*pressure_0[i])/1.0e6
+		zloc_0[i]=-(float(rows[i,zloc_index]))
+		pressure_0[i]=float(rows[i,pressure_index])		
+		tsxx_0[i]=-(float(rows[i,tsxx_index])-BiotCoefficient*pressure_0[i])/1.0e6
+		tsyy_0[i]=-(float(rows[i,tsyy_index])-BiotCoefficient*pressure_0[i])/1.0e6
+		tszz_0[i]=-(float(rows[i,tszz_index])-BiotCoefficient*pressure_0[i])/1.0e6
 
 
 	z_analytical= np.linspace(0, 1000, 100)