final v2.1 updates

applications/grainGrowth_dream3d/equations.cc

@@ -15,17 +15,26 @@
 
 void variableAttributeLoader::loadVariableAttributes(){
 
+    // For the input file 'parameters.in'
     for (unsigned int var_index=0; var_index<8; var_index++){
+
+    // For the input file 'parameters_large_2D.in'
+    //for (unsigned int var_index=0; var_index<12; var_index++){
         std::string var_name = "n";
         var_name.append(std::to_string(var_index));
 
         set_variable_name				(var_index,var_name);
     	set_variable_type				(var_index,SCALAR);
     	set_variable_equation_type		(var_index,EXPLICIT_TIME_DEPENDENT);
 
+        // For the input file 'parameters.in'
         set_dependencies_value_term_RHS(var_index, "n0, n1, n2, n3, n4, n5, n6, n7");
         set_dependencies_gradient_term_RHS(var_index, "grad(n0), grad(n1), grad(n2), grad(n3), grad(n4), grad(n5), grad(n6), grad(n7)");
 
+        // For the input file 'parameters_large_2D.in'
+        //set_dependencies_value_term_RHS(var_index, "n0, n1, n2, n3, n4, n5, n6, n7 , n8, n9, n10, n11");
+        //set_dependencies_gradient_term_RHS(var_index, "grad(n0), grad(n1), grad(n2), grad(n3), grad(n4), grad(n5), grad(n6), grad(n7), grad(n8), grad(n9), grad(n10), grad(n11)");
+
     }
 
 }

applications/grainGrowth_dream3d/parameters.in

@@ -41,7 +41,7 @@ set Max refinement level = 7
 set Min refinement level = 4
 
 # Set the fields used to determine the refinement using their index.
-set Refinement criteria fields = n0,n1,n2,n3,n4,n5,n6
+set Refinement criteria fields = n0,n1,n2,n3,n4,n5,n6,n7
 
 # Set the maximum and minimum value of the fields where the mesh should be refined
 set Refinement window max = 0.999,0.999,0.999,0.999,0.999,0.999,0.999,0.999
@@ -58,7 +58,7 @@ set Time step = 0.05
 
 # The simulation ends when either the number of time steps is reached or the
 # simulation time is reached.
-set Number of time steps = 4000
+set Number of time steps = 10000 #4000
 
 # =================================================================================
 # Set the output parameters

applications/grainGrowth_dream3d/parameters_large_2D.in

@@ -58,7 +58,7 @@ set Time step = 0.05
 
 # The simulation ends when either the number of time steps is reached or the
 # simulation time is reached.
-set Number of time steps = 400
+set Number of time steps = 40000
 
 # =================================================================================
 # Set the output parameters
@@ -80,12 +80,12 @@ set Skip print steps = 50
 
 set Activate grain reassignment = true
 set Order parameter fields for grain reassignment = n0, n1, n2, n3, n4, n5, n6, n7, n8, n9, n10, n11
-set Time steps between grain reassignments = 1000
+set Time steps between grain reassignments = 500
 set Order parameter cutoff for grain identification = 1e-2
 set Buffer between grains before reassignment = 2.0
 
 set Load grain structure = true
-set Grain structure filename = initial_grain_structure_large_2D
+set Grain structure filename = resampled_2048x2048_738g_us #initial_grain_structure_large_2D
 set Grain structure variable name = FeatureIds
 set Number of smoothing cycles after grain structure loading = 2
 set Minimum radius for loaded grains = 1.0

applications/grainGrowth_dream3d/postprocess.cc

@@ -14,7 +14,12 @@ void variableAttributeLoader::loadPostProcessorVariableAttributes(){
 	set_variable_name				(0,"feature_ids");
 	set_variable_type				(0,SCALAR);
 
+    // For the input file 'parameters.in'
     set_dependencies_value_term_RHS(0, "n0, n1, n2, n3, n4, n5, n6, n7");
+
+    // For the input file 'parameters_large_2D.in'
+    //set_dependencies_value_term_RHS(0, "n0, n1, n2, n3, n4, n5, n6, n7, n8, n9, n10, n11");
+
     set_dependencies_gradient_term_RHS(0, "");
 
     set_output_integral         	(0,false);
@@ -23,7 +28,12 @@ void variableAttributeLoader::loadPostProcessorVariableAttributes(){
     set_variable_name				(1,"op_ids");
 	set_variable_type				(1,SCALAR);
 
+    // For the input file 'parameters.in'
     set_dependencies_value_term_RHS(1, "n0, n1, n2, n3, n4, n5, n6, n7");
+
+    // For the input file 'parameters_large_2D.in'
+    //set_dependencies_value_term_RHS(1, "n0, n1, n2, n3, n4, n5, n6, n7, n8, n9, n10, n11");
+
     set_dependencies_gradient_term_RHS(1, "");
 
     set_output_integral         	(1,false);

applications/grainGrowth_dream3d/vtk_converter.py

@@ -4,10 +4,10 @@
 shift_y = 0.125
 shift_z = 0
 
-rl_grid_filename = 'resampled_2048x2048_738g.vtk'
+rl_grid_filename = 'initial_grain_structure_large_2D.vtk'
 target_variable = 'FeatureIds'
 
-us_grid_filename = "resampled_2048x2048_738g_us.vtk"
+us_grid_filename = "initial_grain_structure_large_2D_us.vtk"
 
 # Parse the rectilinear grid vtk file
 f = open(rl_grid_filename)

version

@@ -1 +1 @@
-2.1 (pre)
+2.1

version_changes.md

@@ -1,5 +1,5 @@
-# Version 2.1pre
-Moderate-level update to v2.0, to be released in August 2018. The largest changes involve a restructuring of the functions in equations.cc and ICs_and_BCs.cc. Grain remapping was also introduced to permit simulations with hundreds/thousands of grains.
+# Version 2.1
+Moderate-level update to v2.0, released in August 2018. The largest changes involve a restructuring of the functions in equations.cc and ICs_and_BCs.cc. Grain remapping was also introduced to permit simulations with hundreds/thousands of grains.
 
 Changes to the example applications:
 - New application: CHAC_performance_test. This app is very similar to 'coupledCahnHilliardAllenCahn', but is 3D and was designed for scaling and performance comparisons to a finite difference code.
@@ -22,9 +22,10 @@ Added functionality:
 - The user can now specify a parameters file other than 'parameters.in'. The syntax is: './main -i other_parameters_file.in'
 
 Bug fixes:
-- A typo has been fixed in the expression for 'faccV' in precipitateEvolution
+- A typo has been fixed in the expression for 'faccV' in the precipitateEvolution app
 
 Other changes:
+- The pdf user guide has been removed as well as the Doxygen files. A Doxygen-based user guide is now hosted on [a separate site](https://prisms-center.github.io/phaseField/doxygen_files/manual.html) to provide a more interactive experience. The repo for the new user guide can be found [here](https://github.com/prisms-center/prismspf-manual).
 - Changed how the equation dependencies are input, making them more specific and more intuitive.
 - Previously, there were separate initial condition functions and non-uniform Dirichlet BC functions for scalar fields and vector fields. These have been merged so that there is one initial condition function and one non-uniform Dirichlet BC function. These functions are now part of customPDE and have direct access to the model parameters declared in customPDE.h.
 - Renamed the functions in the equation file, removing references to 'residuals'. Instead, everything is referred to as a term in the governing equation.