Updating user parameters & Removing need for postprocessed fields to …

…have boundary conditions (#443) * script that remove comments from *.prm * removed comments * remove some misc stuff * postprocess fields don't need boundary conditions
prisms-center · Feb 20, 2025 · b78d45d · b78d45d
1 parent 64b20eb
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diff --git a/applications/CHAC_anisotropy/ICs_and_BCs.cc b/applications/CHAC_anisotropy/ICs_and_BCs.cc
@@ -23,24 +23,24 @@ customPDE<dim, degree>::setInitialCondition([[maybe_unused]] const Point<dim>  &
       r = 0.0;
       for (unsigned int dir = 0; dir < dim; dir++)
         {
-          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
-               (p[dir] - userInputs.domain_size[dir] / 2.0);
+          r +=
+            (p[dir] - userInputs.size[dir] / 2.0) * (p[dir] - userInputs.size[dir] / 2.0);
         }
-      r         = std::sqrt(r);
-      double n  = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
-      scalar_IC = 0.082 * 16.0 / (userInputs.domain_size[0] / 4.0) +
-                  (3.0 * n * n - 2.0 * n * n * n);
+      r        = std::sqrt(r);
+      double n = 0.5 * (1.0 - std::tanh((r - userInputs.size[0] / 4.0) / 4.0));
+      scalar_IC =
+        0.082 * 16.0 / (userInputs.size[0] / 4.0) + (3.0 * n * n - 2.0 * n * n * n);
     }
   else
     {
       r = 0.0;
       for (unsigned int dir = 0; dir < dim; dir++)
         {
-          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
-               (p[dir] - userInputs.domain_size[dir] / 2.0);
+          r +=
+            (p[dir] - userInputs.size[dir] / 2.0) * (p[dir] - userInputs.size[dir] / 2.0);
         }
       r         = std::sqrt(r);
-      scalar_IC = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
+      scalar_IC = 0.5 * (1.0 - std::tanh((r - userInputs.size[0] / 4.0) / 4.0));
     }
 
   // --------------------------------------------------------------------------

diff --git a/applications/CHAC_anisotropy/parameters.prm b/applications/CHAC_anisotropy/parameters.prm
@@ -1,119 +1,47 @@
-# =================================================================================
-# Set the number of dimensions (2 or 3 for a 2D or 3D calculation)
-# =================================================================================
 set Number of dimensions = 2
 
-# =================================================================================
-# Set the length of the domain in all three dimensions
-# (Domain size Z ignored in 2D)
-# =================================================================================
-# Each axes spans from zero to the specified length
 set Domain size X = 100
 set Domain size Y = 100
 set Domain size Z = 100
 
-# =================================================================================
-# Set the element parameters
-# =================================================================================
-# The number of elements in each direction is 2^(refineFactor) * subdivisions
-# Subdivisions Z ignored in 2D
-# For optimal performance, use refineFactor primarily to determine the element size
 set Subdivisions X = 1
 set Subdivisions Y = 1
 set Subdivisions Z = 1
 
 set Refine factor = 7
 
-# Set the polynomial degree of the element (allowed values: 1, 2, or 3)
 set Element degree = 1
 
-# =================================================================================
-# Set the adaptive mesh refinement parameters
-# =================================================================================
-# Set the flag determining if adaptive meshing is activated
 set Mesh adaptivity = true
 
-# Set the maximum and minimum level of refinement
-# When adaptive meshing is enabled, the refine factor set in the block above is
-# only used to generate the first pass of the mesh as the initial conditions are
-# applied. It should be set somewhere between the max and min levels below.
 set Max refinement level = 7
 set Min refinement level = 4
 
-# Set the number of time steps between remeshing operations
 set Steps between remeshing operations = 1000
 
-# Set the criteria for adapting the mesh
 subsection Refinement criterion: n
-    # Select whether the mesh is refined based on the variable value (VALUE),
-    # its gradient (GRADIENT), or both (VALUE_AND_GRADIENT)
     set Criterion type = VALUE
-    # Set the lower and upper bounds for the value-based refinement window
     set Value lower bound = 0.001
     set Value upper bound = 0.999
 end
 
-# =================================================================================
-# Set the time step parameters
-# =================================================================================
-# The size of the time step
 set Time step = 1.0e0
 
-# The simulation ends when either the number of time steps is reached or the
-# simulation time is reached.
 set Number of time steps = 10000
 
-# =================================================================================
-# Set the boundary conditions
-# =================================================================================
-# Set the boundary condition for each variable, where each variable is given by
-# its name, as defined in equations.h. The four boundary condition
-# types are NATURAL, DIRICHLET, NON_UNIFORM_DIRICHLET and PERIODIC. If all
-# of the boundaries have the same boundary condition, only one boundary condition
-# type needs to be given. If multiple boundary condition types are needed, give a
-# comma-separated list of the types. The order is the miniumum of x, maximum of x,
-# minimum of y, maximum of y, minimum of z, maximum of z (i.e left, right, bottom,
-# top in 2D and left, right, bottom, top, front, back in 3D). The value of a
-# Dirichlet BC is specfied in the following way -- DIRCHILET: val -- where 'val' is
-# the desired value. If the boundary condition is NON_UNIFORM_DIRICHLET, the
-# boundary condition should be specified in the appropriate function in 'ICs_and_BCs.h'.
-# Example 1: All periodic BCs for variable 'c'
-# set Boundary condition for variable c = PERIODIC
-# Example 2: Zero-derivative BCs on the left and right, Dirichlet BCs with value
-# 1.5 on the top and bottom for variable 'n' in 2D
-# set Boundary condition for variable n = NATURAL, NATURAL, DIRICHLET: 1.5, DIRICHLET: 1.5
 
 set Boundary condition for variable c = NATURAL
 set Boundary condition for variable n = NATURAL
 
-# =================================================================================
-# Set the model constants
-# =================================================================================
-# Set the user-defined model constants, which must have a counter-part given in
-# customPDE.h. These are most often used in the residual equations in equations.h,
-# but may also be used for initial conditions and nucleation calculations. The type
-# options currently are DOUBLE, INT, BOOL, TENSOR, and [symmetry] ELASTIC CONSTANTS
-# where [symmetry] is ISOTROPIC, TRANSVERSE, ORTHOTROPIC, or ANISOTROPIC.
 
-# The CH mobility, McV in equations.h
 set Model constant McV = 1.0, DOUBLE
 
-# The AC mobility, MnV in equations.h
 set Model constant MnV = 0.1, DOUBLE
 
-# Anisotropy parameter
 set Model constant epsilonM = 0.06, DOUBLE
 
-# =================================================================================
-# Set the output parameters
-# =================================================================================
-# Type of spacing between outputs ("EQUAL_SPACING", "LOG_SPACING", "N_PER_DECADE",
-# or "LIST")
 set Output condition = EQUAL_SPACING
 
-# Number of times the program outputs the fields (total number for "EQUAL_SPACING"
-# and "LOG_SPACING", number per decade for "N_PER_DECADE", ignored for "LIST")
 set Number of outputs = 10
 
-# The number of time steps between updates being printed to the screen
 set Skip print steps = 1000
diff --git a/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc b/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc
@@ -23,24 +23,24 @@ customPDE<dim, degree>::setInitialCondition([[maybe_unused]] const Point<dim>  &
       r = 0.0;
       for (unsigned int dir = 0; dir < dim; dir++)
         {
-          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
-               (p[dir] - userInputs.domain_size[dir] / 2.0);
+          r +=
+            (p[dir] - userInputs.size[dir] / 2.0) * (p[dir] - userInputs.size[dir] / 2.0);
         }
-      r         = std::sqrt(r);
-      double n  = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
-      scalar_IC = 0.082 * 16.0 / (userInputs.domain_size[0] / 4.0) +
-                  (3.0 * n * n - 2.0 * n * n * n);
+      r        = std::sqrt(r);
+      double n = 0.5 * (1.0 - std::tanh((r - userInputs.size[0] / 4.0) / 4.0));
+      scalar_IC =
+        0.082 * 16.0 / (userInputs.size[0] / 4.0) + (3.0 * n * n - 2.0 * n * n * n);
     }
   else if (index == 1)
     {
       r = 0.0;
       for (unsigned int dir = 0; dir < dim; dir++)
         {
-          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
-               (p[dir] - userInputs.domain_size[dir] / 2.0);
+          r +=
+            (p[dir] - userInputs.size[dir] / 2.0) * (p[dir] - userInputs.size[dir] / 2.0);
         }
       r         = std::sqrt(r);
-      scalar_IC = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
+      scalar_IC = 0.5 * (1.0 - std::tanh((r - userInputs.size[0] / 4.0) / 4.0));
     }
   else
     {

diff --git a/applications/CHAC_anisotropyRegularized/parameters.prm b/applications/CHAC_anisotropyRegularized/parameters.prm
@@ -1,123 +1,50 @@
-# =================================================================================
-# Set the number of dimensions (2 or 3 for a 2D or 3D calculation)
-# =================================================================================
 set Number of dimensions = 2
 
-# =================================================================================
-# Set the length of the domain in all three dimensions
-# (Domain size Z ignored in 2D)
-# =================================================================================
-# Each axes spans from zero to the specified length
 set Domain size X = 100
 set Domain size Y = 100
 set Domain size Z = 100
 
-# =================================================================================
-# Set the element parameters
-# =================================================================================
-# The number of elements in each direction is 2^(refineFactor) * subdivisions
-# Subdivisions Z ignored in 2D
-# For optimal performance, use refineFactor primarily to determine the element size
 set Subdivisions X = 1
 set Subdivisions Y = 1
 set Subdivisions Z = 1
 
 set Refine factor = 7
 
-# Set the polynomial degree of the element (allowed values: 1, 2, or 3)
 set Element degree = 1
 
-# =================================================================================
-# Set the adaptive mesh refinement parameters
-# =================================================================================
-# Set the flag determining if adaptive meshing is activated
 set Mesh adaptivity = true
 
-# Set the maximum and minimum level of refinement
-# When adaptive meshing is enabled, the refine factor set in the block above is
-# only used to generate the first pass of the mesh as the initial conditions are
-# applied. It should be set somewhere between the max and min levels below.
 set Max refinement level = 7
 set Min refinement level = 4
 
-# Set the number of time steps between remeshing operations
 set Steps between remeshing operations = 1000
 
-# Set the criteria for adapting the mesh
 subsection Refinement criterion: n
-    # Select whether the mesh is refined based on the variable value (VALUE),
-    # its gradient (GRADIENT), or both (VALUE_AND_GRADIENT)
     set Criterion type = VALUE
-    # Set the lower and upper bounds for the value-based refinement window
     set Value lower bound = 0.001
     set Value upper bound = 0.999
 end
 
-# =================================================================================
-# Set the time step parameters
-# =================================================================================
-# The size of the time step
 set Time step = 5.0e-2
 
-# The simulation ends when either the number of time steps is reached or the
-# simulation time is reached.
 set Number of time steps = 40000
 
-# =================================================================================
-# Set the boundary conditions
-# =================================================================================
-# Set the boundary condition for each variable, where each variable is given by
-# its name, as defined in equations.h. The four boundary condition
-# types are NATURAL, DIRICHLET, NON_UNIFORM_DIRICHLET and PERIODIC. If all
-# of the boundaries have the same boundary condition, only one boundary condition
-# type needs to be given. If multiple boundary condition types are needed, give a
-# comma-separated list of the types. The order is the miniumum of x, maximum of x,
-# minimum of y, maximum of y, minimum of z, maximum of z (i.e left, right, bottom,
-# top in 2D and left, right, bottom, top, front, back in 3D). The value of a
-# Dirichlet BC is specfied in the following way -- DIRCHILET: val -- where 'val' is
-# the desired value. If the boundary condition is NON_UNIFORM_DIRICHLET, the
-# boundary condition should be specified in the appropriate function in 'ICs_and_BCs.h'.
-# Example 1: All periodic BCs for variable 'c'
-# set Boundary condition for variable c = PERIODIC
-# Example 2: Zero-derivative BCs on the left and right, Dirichlet BCs with value
-# 1.5 on the top and bottom for variable 'n' in 2D
-# set Boundary condition for variable n = NATURAL, NATURAL, DIRICHLET: 1.5, DIRICHLET: 1.5
 
 set Boundary condition for variable c = NATURAL
 set Boundary condition for variable n = NATURAL
 set Boundary condition for variable biharm = NATURAL
 
-# =================================================================================
-# Set the model constants
-# =================================================================================
-# Set the user-defined model constants, which must have a counter-part given in
-# customPDE.h. These are most often used in the residual equations in equations.h,
-# but may also be used for initial conditions and nucleation calculations. The type
-# options currently are DOUBLE, INT, BOOL, TENSOR, and [symmetry] ELASTIC CONSTANTS
-# where [symmetry] is ISOTROPIC, TRANSVERSE, ORTHOTROPIC, or ANISOTROPIC.
 
-# The CH mobility, McV in equations.h
 set Model constant McV = 1.0, DOUBLE
 
-# The AC mobility, MnV in equations.h
 set Model constant MnV = 0.1, DOUBLE
 
-# Anisotropy parameter
 set Model constant epsilonM = 0.2, DOUBLE
 
-# Regularization parameter
 set Model constant delta2 = 1.0, DOUBLE
 
-# =================================================================================
-# Set the output parameters
-# =================================================================================
-# Type of spacing between outputs ("EQUAL_SPACING", "LOG_SPACING", "N_PER_DECADE",
-# or "LIST")
 set Output condition = EQUAL_SPACING
 
-# Number of times the program outputs the fields (total number for "EQUAL_SPACING"
-# and "LOG_SPACING", number per decade for "N_PER_DECADE", ignored for "LIST")
 set Number of outputs = 10
 
-# The number of time steps between updates being printed to the screen
 set Skip print steps = 1000