addressing Daniel's comments

Author: PrajaktaPMohite

cookbooks/continental_compression_with_imposed_faults/continental_compression_with_imposed_faults.prm

@@ -44,6 +44,10 @@ subsection Formulation
   set Temperature equation = reference density profile
 end
 
+# constraining adiabatic temperature profile in compositional fields. 
+# each component referring to compositional fields. First three
+# components are referring to strain and then chemical composition fields. 
+# see subsection Compositional fields
 subsection Adiabatic conditions model
   subsection Compute profile
     set Composition reference profile = function
@@ -63,6 +67,10 @@ subsection Discretization
   set Composition polynomial degree           = 2
   set Stokes velocity polynomial degree       = 2
   set Temperature polynomial degree           = 2
+  # The gradient at quadrature points will not be a precise approximation of the true gradient 
+  # since it excludes the contribution of jumps in the compositional field between cells.
+  # Even though the finite element solution varies from cell to cell, the gradient of the 
+  # solution at quadrature locations inside each cell will always be precisely zero.
   set Use discontinuous composition discretization = true
 end
 
@@ -113,8 +121,8 @@ subsection Mesh deformation
 end
 
 # Velocity on boundaries characterized by functions
-# The combined horizontal velocity (x-direction) magnitude on the left and right walls is 0.2 cm/year
-# The vertical velocity at the base is 0.2 cm/year (balances outflow on sides)
+# A horizontal velocity (x-direction) of 0.1 cm/year is applied to the left and right walls 
+# resulting in inflow, which is balanced by the 0.2 cm/yr vertical (y-direction) outflow on the bottom boundary.
 # Velocity components parallel to the base (x-velocity) and side walls (y-velocity)
 # are unconstrained (i.e. 'free').
 subsection Boundary velocity model
@@ -166,8 +174,8 @@ end
 
 # Initial values of different compositional fields
 # The upper crust (20 km thick), lower crust (20 km thick)
-# and mantle (60 km thick) are continuous horizontal layers
-# of constant thickness. The non initial plastic strain is
+# and mantle lithosphere(40 km thick) and asthenosphere (320 km thick )are continuous 
+# horizontal layers of constant thickness. The non initial plastic strain is
 # set to 0, while the initial plastic and viscous strain is
 # randomized between 0.5 and 1.5.
 subsection Initial composition model
@@ -187,7 +195,7 @@ subsection Initial composition model
   end
 end
 
-# Composition: fixed on bottom (inflow boundary), free on sides and top
+# Composition: fixed on the bottom (outflow boundary) and side boundary, and free on top
 subsection Boundary composition model
   set Fixed composition boundary indicators = bottom, left, right
   set List of model names = initial composition
@@ -199,6 +207,7 @@ end
 # Note that while temperatures are specified for the model sides, these values are
 # not used as the sides are not specified "Fixed temperature boundaries".  Rather,
 # these boundaries are insulating (zero net heat flux).
+# Initial temperature model can be computed using plugin from continental_extension cookbook
 subsection Boundary temperature model
   set Fixed temperature boundary indicators = bottom, top
   set List of model names = box

cookbooks/continental_compression_with_imposed_faults/doc/continental_compression_with_imposed_faults.md

@@ -12,21 +12,21 @@ The cookbook builds directly on components of the {ref}`sec:cookbooks:crustal-de
 # Model Design
 The model domain spans 400 km x 400 km and uses adaptive refinement to resolve deformation patterns in the regions where faults are imposed at the onset of deformation. The initial thermal structure follows a conductive, continental-style geothermal through the lithosphere and an initial adiabatic profile in the asthenosphere. The governing equations follow the extended Boussinesq approximation, which includes both adiabatic and shear heating.
 
-Deformation is driven by horizontal velocity applied at the model sides (2 mm/yr), which are balanced by outflow at the model base. A free surface allows topography to develop through time, which is diffused at each time step to approximate landscape evolution processes and stabilize both linear and nonlinear solver behavior.
+Deformation is driven by horizontal velocity applied at the model sides (1 mm/yr), which are balanced by outflow at the model base (2 mm/yr). A free surface allows topography to develop through time, which is diffused at each time step to approximate landscape evolution processes and stabilize both linear and nonlinear solver behavior.
 
 The initial lithological structure includes distinct layers representing the upper crust (20 km), lower crust (20 km), mantle lithosphere (40 km), and asthenosphere (320 km). Each layer is represented by a nonlinear viscoplastic rheology combining dislocation creep and pressure-dependent plasticity. Respectively, the pre-yield viscosity and brittle material parameters (cohesion, friction) weaken by a factor of 10 and 4 as a function of accumulated viscous and brittle strain over strain intervals of 0.5-1.5.
 
 ```{literalinclude} strain_weakening_mechanism.part.prm
 ```
 
-Faults are correspondingly integrated into the model initial conditions as zones of initial strain defined in the Geodynamic World Builder. Four faults extending to the base of the lithosphere with constant dip angles are included, two of which dip at 60 degrees toward each other in a style representing pre-existing normal faults. A third vertical fault (i.e., approximating a strike-slip fault) is centrally located between the two dipping faults, while the fourth fault is located to the right of two normal faults and dips at a higher angle. The faults maintain a constant width of 5 km and extend to a depth of 100 km. In addition to defined fault locations with constant strain values, randomized zones of plastic (0-40 km depth) and viscous strain (0-100 km depth) are imposed across a 300 km wide zone in the upper to approximate pervasive off-fault damage observed in many regions that have undergone significant tectonic deformation. The plastic and viscous strain compositions value within the faults is the sum of the value defined in the world builder and the randomized values defined in these zones.
+Faults are correspondingly integrated into the model initial conditions as zones of initial strain defined in the Geodynamic World Builder. Four faults extending to the base of the lithosphere with constant dip angles are included, two of which dip at 60 degrees toward each other in a style representing pre-existing normal faults. A third vertical fault (i.e., approximating a strike-slip fault) is centrally located between the two dipping faults, while the fourth fault is located to the right of two normal faults and dips at a higher angle. The faults maintain a constant width of 5 km and extend to a depth of 100 km. In addition to defined fault locations with constant strain values, randomized zones of plastic (0-40 km depth) and viscous strain (0-100 km depth) are imposed across a 300 km wide zone in the upper to approximate pervasive off-fault damage observed in many regions that have undergone significant tectonic deformation. The faults are setting in the middle of the randomized strain zones, fault1 in wb file is located at x = 250km. The plastic and viscous strain compositions value within the faults is the sum of the value defined in the world builder and the randomized values defined in these zones. 
 
 Following Howard et al. (2003), the configuration of these faults is motivated by the inferred tectonic history of the Dzereg basin in the Mongolia Altai, which has been undergoing relatively slow compression since the onset of the India-Asia collision following a period of extensional deformation.
 
 ```{figure-md} fig:initial_plastic_and_viscous_strain_and_density
 <img src="initial_plastic_and_viscous_strain_and_density.svg" style="width:50.0%" />
 
- Initial plastic (top left), viscous (top right) strain and density (bottom) highlighting the location of defined fault zones and randomized strain across a broader region in the upper 100 km.
+  Initial plastic strain (top left), viscous strain (top right) and density (bottom) highlighting the location of defined fault zones and randomized strain across a broader region in the upper 100 km.
  The density plot contains temperature contours at intervals of 200 K, beginning at 373 K and ending at 1573 K (LAB temperature).
 ```
 
@@ -49,8 +49,8 @@ The position, dip angle and direction, thickness (5 km), and composition (plasti
  Strain rate (left) and density (right) distributions with temperature contours after 35 Myr of deformation.
 ```
 
-Deformation preferentially localizes along the two pre-existing shear zones forming a grabben-like geometry ({numref}`fig:strain_rate_and_density_0_myr`), which reflects their optimal orientation and position within the model domain to accommodate the imposed convergence. After 35 Myr of convergence ({numref}`fig:strain_rate_and_density_35_myr`) deformation remains strongly localized along these faults,  with crustal shortening and thickening occurring between them forming approximately symmetric orogenic wedge. Some degree of asymmetry develops on the right side of the wedge, where the fault farthest to the right remains active in the upper crust and connects to the fault bounding the wedge near the brittle-ductile transition zone.
+Deformation preferentially localizes along the two pre-existing shear zones forming a grabben-like geometry ({numref}`fig:strain_rate_and_density_0_myr`), which reflects their optimal orientation and position within the model domain to accommodate the imposed convergence. After 35 Myr of convergence ({numref}`fig:strain_rate_and_density_35_myr`) deformation remains strongly localized along these faults,  with crustal shortening and thickening occurring between them forming an approximately symmetric orogenic wedge. Some degree of asymmetry develops on the right side of the wedge, where the fault farthest to the right remains active in the upper crust and connects to the fault bounding the wedge near the brittle-ductile transition zone.
 
 Given the nonlinearity of the rheology and governing equations, minor variations in fault strength, geometry, lithospheric structure, and boundary velocities may lead to significant variations in the spatiotemporal evolution of deformation. This cookbook provides a flexible framework for exploring the effects of these parameters, and application to hypothesis-driven questions such as fault reactivation, inversion of rift basins, or the partitioning of strain in complex orogens.
 
-These results demonstrate the potential key role of pre-existing faults in guiding the evolution of lithospheric deformation. However, given the nonlinearity of the rheology and governing equations, minor variations in fault strength, geometry, lithospheric structure, and boundary velocities may lead to significant variations in the spatiotemporal evolution of deformation. Similarly, changing the numerical resolution is likely to also affect the results, as the brittle shear band width by introduced by the plastic damper (1e21 Pa s) is still likely not fully resolved at the maximum resolution of 1e21 Pa s. Furthermore, varying degrees of minor variations in the model results will likely occur if a stricter nonlinear solver tolerance is selected. This cookbook provides a flexible framework for exploring the effects of these parameters, and application to hypothesis-driven questions such as fault reactivation, inversion of rift basins, or the partitioning of strain in complex orogens.
+Similarly, changing the numerical resolution is likely to also affect the results, as the brittle shear band width by introduced by the plastic damper (1e21 Pa s) is still likely not fully resolved at the maximum resolution of 2.5 km. Furthermore, varying degrees of minor variations in the model results will likely occur if a stricter nonlinear solver tolerance is selected. This cookbook provides a flexible framework for exploring the effects of these parameters, and application to hypothesis-driven questions such as fault reactivation, inversion of rift basins, or the partitioning of strain in complex orogens.

cookbooks/continental_compression_with_imposed_faults/doc/strain_weakening_mechanism.part.prm

@@ -1,8 +1,12 @@
-set Strain weakening mechanism                   =  plastic weakening with plastic strain and viscous weakening with viscous strain
-set Start plasticity strain weakening intervals  = 0.5
-set End plasticity strain weakening intervals    = 1.5
-set Cohesion strain weakening factors            = 0.25
-set Friction strain weakening factors            = 0.25
-set Start prefactor strain weakening intervals   = 0.5
-set End prefactor strain weakening intervals     = 1.5
-set Prefactor strain weakening factors           = 0.1
+subsection Material model
+    subsection Visco Plastic
+        set Strain weakening mechanism                   =  plastic weakening with plastic strain and viscous weakening with viscous strain
+        set Start plasticity strain weakening intervals  = 0.5
+        set End plasticity strain weakening intervals    = 1.5
+        set Cohesion strain weakening factors            = 0.25
+        set Friction strain weakening factors            = 0.25
+        set Start prefactor strain weakening intervals   = 0.5
+        set End prefactor strain weakening intervals     = 1.5
+        set Prefactor strain weakening factors           = 0.1
+    end
+end