add jupyter notebook example; finetuning of various output writing

JuliaGeodynamics · Jul 21, 2023 · dddb51a · dddb51a
1 parent 74a7a15
commit dddb51a
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Showing 5 changed files with 6,924 additions and 4 deletions.
diff --git a/notebooks/subduction_example.ipynb b/notebooks/subduction_example.ipynb
diff --git a/src/LaMEM_ModelGeneration/Grid.jl b/src/LaMEM_ModelGeneration/Grid.jl
@@ -159,10 +159,11 @@ function  Create_Grid(nmark_x, nmark_y, nmark_z, nel_x, nel_y, nel_z, coord_x, c
     nump_z    = nel_z_tot*nmark_z;
 
     # Create 1D coordinate vectors (either regular or refined)
+
     xn, x = GeophysicalModelGenerator.Create1D_grid_vector(coord_x, nel_x, nmark_x, nseg_x, bias_x)
     yn, y = GeophysicalModelGenerator.Create1D_grid_vector(coord_y, nel_y, nmark_y, nseg_y, bias_y)
     zn, z = GeophysicalModelGenerator.Create1D_grid_vector(coord_z, nel_z, nmark_z, nseg_z, bias_z)
-
+    
     # node grid
     Xn,Yn,Zn = GeophysicalModelGenerator.XYZGrid(xn, yn, zn); 
 

diff --git a/src/LaMEM_ModelGeneration/LaMEM_Model.jl b/src/LaMEM_ModelGeneration/LaMEM_Model.jl
@@ -17,7 +17,7 @@ function write_vec(data)
     if !isa(data,String)
         str = ""; for d in data; str = str*" $d" end
     else
-        str = data
+        str = " "*data
     end
 
     return str

diff --git a/src/LaMEM_ModelGeneration/ModelSetup.jl b/src/LaMEM_ModelGeneration/ModelSetup.jl
@@ -164,7 +164,13 @@ function Write_LaMEM_InputFile(io, d::ModelSetup)
     for f in fields
         if getfield(d,f) != getfield(Reference,f)  ||
             (f == :bg_phase) ||
-            (f == :msetup)
+            (f == :msetup) ||
+            (f == :rand_noise) ||
+            (f == :nmark_lim) ||
+            (f == :mark_ctrl)
+
+
+
 
             if (f != :geom_primitives)
                 # only print if value differs from reference value

diff --git a/src/LaMEM_ModelGeneration/Output.jl b/src/LaMEM_ModelGeneration/Output.jl
@@ -48,10 +48,13 @@ Base.@kwdef mutable struct Output
     "effective pressure"
     out_eff_press       = 0     
 
+    "out_over_press"
     out_over_press      = 0
 
+    "lithospheric pressure"
     out_litho_press     = 0
 
+    "pore pressure"
     out_pore_press      = 0
 
     "temperature"
@@ -69,10 +72,13 @@ Base.@kwdef mutable struct Output
     "second invariant of strain rate tensor"
     out_j2_strain_rate  = 0     
 
+    "sh max"
     out_shmax           = 0
 
+    "eh max"
     out_ehmax           = 0
 
+    "yield stress"
     out_yield           = 0
 
     "relative proportion of diffusion creep strainrate"
@@ -93,20 +99,28 @@ Base.@kwdef mutable struct Output
     "plastic dissipation"
     out_plast_dissip    = 0     
 
+    "total displacement"
     out_tot_displ       = 0
 
+    "momentum residual"
     out_moment_res      = 0
 
+    "continuity residual"
     out_cont_res        = 0
 
+    "energy residual"
     out_energ_res       = 0
 
+    "Melt fraction"
     out_melt_fraction   = 0
 
+    "fluid density"
     out_fluid_density   = 0
 
+    "conductivity"
     out_conductivity    = 0
 
+    "velocity gradient tensor"
     out_vel_gr_tensor   = 0 
 
     "activate surface output"
@@ -200,7 +214,16 @@ function Write_LaMEM_InputFile(io, d::Output)
 
     # Write all fields that are active
     for f in fields
-        if getfield(d,f) == 1
+
+        # write "out_*" always
+        write_always = false
+        if length(String(f))>3
+            if String(f)[1:3]=="out"
+                write_always = true
+            end
+        end
+
+        if getfield(d,f) == 1 || write_always
             # only print if value differs from reference value
             name = rpad(String(f),15)
             comment = get_doc(Output, f)