addressing comments

Author: PrajaktaPMohite

cookbooks/continental_compression_with_imposed_faults/continental_compression_with_imposed_faults.prm

@@ -1,4 +1,4 @@
-# Continental Compression with Imposed Faults Cookbooks
+# Continental Compression with Imposed Faults Cookbook
 # This cookbook builds on the continental extension cookbook
 # and a recent paper investigating rift inversion (Vasey et al., 2024,
 # https://doi.org/10.1130/G51489.1) to demonstrate how to design
@@ -266,8 +266,7 @@ end
 # Values for most rheological parameters are specified for a background material and
 # each compositional field.  Values for viscous deformation are based on dislocation
 # creep flow-laws, with distinct values for the upper crust (wet quartzite), lower
-# crust (wet anorthite) and mantle (dry olivine).  Table 1 of Naliboff and Buiter (2015),
-# Earth Planet. Sci. Lett., v.421, p. 58-67 contains values for each of these flow laws.
+# crust (wet anorthite) and mantle (dry olivine).
 subsection Material model
   set Model name = visco plastic
 
@@ -378,7 +377,9 @@ subsection Material model
     set Cohesions                   = 20.e6
 
     # The parameters below weaken the friction and cohesion by a
-    # a factor of 4 between plastic strain values of 0.5 and 1.5.
+    # a factor of 4 between plastic strain values of 0.5 and 1.5,
+    # and the pre-yield viscosity by a factor of 10 over the same
+    # strain interval.
     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

cookbooks/continental_compression_with_imposed_faults/doc/continental_compression_with_imposed_faults.md

@@ -1,17 +1,16 @@
 (sec:cookbooks:Continental-Compression-with-imposed-faults)=
 # Continental Compression with Pre-Existing Fault inheritance
 
-*This section was contributed by Prajakta Mohite & John Naliboff.*
+*This section was contributed by Prajakta Mohite and John Naliboff.*
 
 Recent numerical modeling investigations have demonstrated the influence of extensional phases of deformation on the subsequent evolution of continental collision zones (eg., {cite}`Vasey:etal:2024`,{cite}`Zwaan:etal:2025`). Motivated by these studies and a wide range of observations that highlight fault reactivation processes during the Wilson cycle, this cookbook implements a 2D visco-plastic model of continental compression that incorporates pre-existing fault zones into the initial conditions.
 
 The cookbook builds directly on components of the continental extension cookbook, and the primary goal here is to
 1. Highlight techniques for imposing fault zones in the initial conditions of a lithospheric deformation simulation and
-
 2. Demonstrate their effect on the evolution of deformation patterns.
 
 # 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 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.
 
@@ -20,19 +19,17 @@ The initial lithological structure includes distinct layers representing the upp
 ```{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. In addition to defined fault locations with constant strain values, randomized zones of plastic and brittle strain 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.
+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. Plastic strain within the faults is limited to the upper 40 km where brittle deformation occurs, while viscous strain within the faults extends to the base of the lithosphere. In addition to defined fault locations with constant strain values, randomized zones of plastic and brittle strain 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.
 
 Following Howard et al. (2023), 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
-<img src="initial_plastic_and_viscous_strain.svg" style="width:50.0%" />
+```{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 (left) and viscous (right) strain highlighting the location of defined fault zones and randomized strain across a broader region in the upper 100 km.
+ Initial plastic (left), viscous (right) strain and density (bottom) highlighting the location of defined fault zones and randomized strain across a broader region in the upper 100 km.
 ```
 
-The observed reduction in plastic strain with depth arises from the implementation of depth-dependent rheological behavior and initial conditions. Initial plastic strain is prescribed only within the upper 40 km of the crust, limiting potential for strain localization in deeper regions. The lithosphere is layered compositionally as upper and lower crust  with rheologically weaker materials, while mantle lithosphere has higher strength and supports viscous deformation. Temperature dependent dislocation creep becomes dominant at deeper depth due to high temperatures, further suppressing brittle failure. Strain weakening is initiated only after the plastic strain threshold is exceeded. As a result, the model demonstrates a depth-dependent rheological transition from brittle to ductile behavior, as indicated by the substantially lower plastic strain magnitudes observed in the deeper lithospheric domains.
-
-The position, dip angle and direction, thickness (5 km), and composition (plastic and viscous strain) of each fault are defined with the GWB, with the section of code below illustrating this approach for a single fault.
+The position, dip angle and direction, thickness (5 km), and composition (plastic and viscous strain) of each fault are defined with the [Geodynamic World Builder fault feature](https://geodynamicworldbuilder.github.io), which is illustrated below for a single fault.
 
 ```{literalinclude} single_fault_imposed.part.wb
 ```
@@ -42,14 +39,15 @@ The position, dip angle and direction, thickness (5 km), and composition (plasti
 ```{figure-md} fig:strain_rate_and_density_0_myr
 <img src="strain_rate_and_density_0_myr.svg" style="width:50.0%" />
 
- Strain rate and density distribution at timestep 0 Myr in a 2D continental compression model. Strain localizes in the upper crust along pre-defined fault zones, while density increases with depth, reflecting the compositional and thermal stratification of the lithosphere.
+ Strain rate (left) and density distribution (right) at 0 Myr in a 2D continental compression model. Strain localizes in the upper crust along pre-defined fault zones, while density increases with depth, reflecting the compositional and thermal stratification of the lithosphere.
 ```
 
 ```{figure-md} fig:strain_rate_and_density_35_myr
 <img src="strain_rate_and_density_35_myr.svg" style="width:50.0%" />
 
- Strain rate and density distribution at timestep 35 Myr in a 2D continental compression model. Strain localizes in the upper crust along pre-defined fault zones, while density increases with depth, reflecting the compositional and thermal stratification of the lithosphere.
+ Strain rate (left) and density (rigth) distributions  with temperature contours after 35 Myr of deformation.
 ```
 
 Deformation preferentially localizes along the two pre-existing shear zones forming a grabben-like geometry (Figure 2), which reflects their optimal orientation and position within the model domain to accommodate the imposed convergence. While additional smaller-structures develop after 35 Myr of convergence (Figure 3), deformation remains strongly localized along these faults with crustal shortening and thickening occurring between them.
+
 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.

cookbooks/continental_compression_with_imposed_faults/doc/continental_compression_with_imposed_faults.prm

@@ -1,4 +1,4 @@
-# Continental Compression with Imposed Faults Cookbooks
+# Continental Compression with Imposed Faults Cookbook
 # This cookbook builds on the continental extension cookbook
 # and a recent paper investigating rift inversion (Vasey et al., 2024,
 # https://doi.org/10.1130/G51489.1) to demonstrate how to design
@@ -266,8 +266,7 @@ end
 # Values for most rheological parameters are specified for a background material and
 # each compositional field.  Values for viscous deformation are based on dislocation
 # creep flow-laws, with distinct values for the upper crust (wet quartzite), lower
-# crust (wet anorthite) and mantle (dry olivine).  Table 1 of Naliboff and Buiter (2015),
-# Earth Planet. Sci. Lett., v.421, p. 58-67 contains values for each of these flow laws.
+# crust (wet anorthite) and mantle (dry olivine).
 subsection Material model
   set Model name = visco plastic
 
@@ -378,7 +377,9 @@ subsection Material model
     set Cohesions                   = 20.e6
 
     # The parameters below weaken the friction and cohesion by a
-    # a factor of 4 between plastic strain values of 0.5 and 1.5.
+    # a factor of 4 between plastic strain values of 0.5 and 1.5,
+    # and the pre-yield viscosity by a factor of 10 over the same
+    # strain interval.
     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