Merge pull request #187 from marcfehling/codespell

Run codespell on repository.

CeresFE/CMakeLists.txt

@@ -48,7 +48,7 @@ FIND_LIBRARY(ARMADILLO_LIBRARY NAMES armadillo
   )
 
 #
-# Are all dependencies fullfilled?
+# Are all dependencies fulfilled?
 #
 
 IF(NOT DEAL_II_WITH_UMFPACK)

CeresFE/Readme.md

@@ -4,7 +4,7 @@ Readme file for CeresFE
 Motivation for project
 ----------------------
 
-This code was made to simulate the evolution of global-scale topography on planetary bodies.  Specifically, it is designed to compute the rates of topography relaxation on the dwarf planet Ceres.  The NASA Dawn mission, in orbit around Ceres since March, 2015, has produced a high resolution shape model of its surface.  As on other planets including the Earth, topography on Ceres is subject to decay over time due to processes such as viscous flow and brittle failure.  Because the efficiency of these processes is dependent on the material properties of the body at depth, simulating the decay of topography and comparing it to the observed shape model permits insights into Ceres' internal stucture. 
+This code was made to simulate the evolution of global-scale topography on planetary bodies.  Specifically, it is designed to compute the rates of topography relaxation on the dwarf planet Ceres.  The NASA Dawn mission, in orbit around Ceres since March, 2015, has produced a high resolution shape model of its surface.  As on other planets including the Earth, topography on Ceres is subject to decay over time due to processes such as viscous flow and brittle failure.  Because the efficiency of these processes is dependent on the material properties of the body at depth, simulating the decay of topography and comparing it to the observed shape model permits insights into Ceres' internal structure. 
 
 Some previous applications of this basic idea- using topography to constrain internal structure- may be found in the following references:  
 
@@ -49,7 +49,7 @@ Description of files in repo
 ----------------------------
 
 * src/ceres.cc                     Main code
-* support_code/config_in.h         Reads config file and intializes system parameters
+* support_code/config_in.h         Reads config file and initializes system parameters
 * support_code/ellipsoid_fit.h     Finds best-fit ellipse for surface and internal density boundaries.  Also uses deal.II
 * support_code/ellipsoid_grav.h    Analytically computes self gravity of layered ellipsoids structure
 * support_code/local_math.h        Defines some constants for convenience

Distributed_LDG_Method/CMakeLists.txt

@@ -30,7 +30,7 @@ IF(NOT ${deal.II_FOUND})
 ENDIF()
 
 #
-# Are all dependencies fullfilled?
+# Are all dependencies fulfilled?
 #
 IF( NOT DEAL_II_WITH_MPI OR
     NOT DEAL_II_WITH_P4EST OR

Distributed_LDG_Method/Functions.cc

@@ -50,7 +50,7 @@ class TrueSolution : public Function<dim>
   {}
 
   virtual void vector_value(const Point<dim> &p,
-                            Vector<double> &valuess) const override;
+                            Vector<double> &values) const override;
 };
 
 template <int dim>

Distributed_LDG_Method/LDGPoisson.cc

@@ -64,7 +64,7 @@
 #include <deal.II/lac/trilinos_solver.h>
 
 
-// The functions class contains all the defintions of the functions we
+// The functions class contains all the definitions of the functions we
 // will use, i.e. the right hand side function, the boundary conditions
 // and the test functions.
 #include "Functions.cc"
@@ -75,7 +75,7 @@ using namespace dealii;
 // Here is the main class for the Local Discontinuous Galerkin method
 // applied to Poisson's equation, we won't explain much of the
 // the class and method declarations, but dive deeper into describing the
-// functions when they are defined.  The only thing I will menion
+// functions when they are defined.  The only thing I will mention
 // about the class declaration is that this is where I labeled
 // the different types of boundaries using enums.
 template <int dim>
@@ -170,7 +170,7 @@ class LDGPoissonProblem
 // @sect4{Class constructor and destructor}
 // The constructor and destructor for this class is very much like the
 // like those for step-40.  The difference being that we'll be passing
-// in an integer, <code>degree</code>, which tells us the maxiumum order
+// in an integer, <code>degree</code>, which tells us the maximum order
 // of the polynomial to use as well as <code>n_refine</code> which is the
 // global number of times we refine our mesh.  The other main differences
 // are that we use a FESystem object for our choice of basis
@@ -183,15 +183,15 @@ class LDGPoissonProblem
 //       FE_DGQ<dim>(degree),                          1)
 // </code>
 //
-// which tells us that the basis functions contain discontinous polynomials
+// which tells us that the basis functions contain discontinuous polynomials
 // of order <code>degree</code> in each of the <code>dim</code> dimensions
 // for the vector field.  For the scalar unknown we
 // use a discontinuous polynomial of the order <code>degree</code>.
 // The LDG method for Poisson equations solves for both the primary variable
 // as well as its gradient, just like the mixed finite element method.
 // However, unlike the mixed method, the LDG method uses discontinuous
 // polynomials to approximate both variables.
-// The other difference bewteen our constructor and that of step-40 is that
+// The other difference between our constructor and that of step-40 is that
 // we all instantiate our linear solver in the constructor definition.
 template <int dim>
 LDGPoissonProblem<dim>::
@@ -253,7 +253,7 @@ make_grid()
       // the domain.  This was just to show that
       // the LDG method is working with local
       // refinement and discussions on building
-      // more realistic refinement stategies are
+      // more realistic refinement strategies are
       // discussed elsewhere in the deal.ii
       // documentation.
       for (; cell != endc; ++cell)
@@ -274,7 +274,7 @@ make_grid()
   // type, i.e. Dirichlet or Neumann,
   // we loop over all the cells in the mesh and then over
   // all the faces of each cell.  We then have to figure out
-  // which faces are on the bounadry and set all faces
+  // which faces are on the boundary and set all faces
   // on the boundary to have
   // <code>boundary_id</code> to be <code>Dirichlet</code>.
   // We remark that one could easily set more complicated
@@ -320,7 +320,7 @@ make_dofs()
   // with a distributed triangulation!
   dof_handler.distribute_dofs(fe);
 
-  // We now renumber the dofs so that the vector of unkonwn dofs
+  // We now renumber the dofs so that the vector of unknown dofs
   // that we are solving for, <code>locally_relevant_solution</code>,
   // corresponds to a vector of the form,
   //
@@ -332,7 +332,7 @@ make_dofs()
   // matrix and vectors that we will write to.
   const IndexSet &locally_owned_dofs = dof_handler.locally_owned_dofs();
 
-  // In additon to the locally owned dofs, we also need the the locally
+  // In addition to the locally owned dofs, we also need the the locally
   // relevant dofs.  These are the dofs that have read access to and we
   // need in order to do computations on our processor, but, that
   // we do not have the ability to write to.
@@ -356,7 +356,7 @@ make_dofs()
 
   // Just like step-40 we create a dynamic sparsity pattern
   // and distribute it to the processors.  Notice how we do not have to
-  // explictly mention that we are using a FESystem for system of
+  // explicitly mention that we are using a FESystem for system of
   // variables instead of a FE_DGQ for a scalar variable
   // or that we are using a discributed DoFHandler.  All these specifics
   // are taken care of under the hood by the deal.ii library.
@@ -459,7 +459,7 @@ assemble_system()
   // for evaluating the basis functions
   // on one side of an element face as well as another FEFaceValues object,
   // <code>fe_neighbor_face_values</code>, for evaluating the basis functions
-  // on the opposite side of the face, i.e. on the neighoring element's face.
+  // on the opposite side of the face, i.e. on the neighboring element's face.
   // In addition, we also introduce a FESubfaceValues object,
   // <code>fe_subface_values</code>, that
   // will be used for dealing with faces that have multiple refinement
@@ -495,7 +495,7 @@ assemble_system()
   FullMatrix<double>      ve_ue_matrix(dofs_per_cell, dofs_per_cell);
   // As explained in the section on the LDG method we take our test
   // function to be v and multiply it on the left side of our differential
-  // equation that is on u and peform integration by parts as explained in the
+  // equation that is on u and perform integration by parts as explained in the
   // introduction. Using this notation for test and solution function,
   // the matrices below will then stand for:
   //
@@ -727,7 +727,7 @@ assemble_system()
                       // At this point we know that this cell and the neighbor
                       // of this cell are on the same refinement level and
                       // the work to assemble the interior flux matrices
-                      // is very much the same as before. Infact it is
+                      // is very much the same as before. In fact it is
                       // much simpler since we do not have to loop through the
                       // subfaces.  However, we have to check that we do
                       // not compute the same contribution twice. This would
@@ -800,7 +800,7 @@ assemble_system()
 
 
           // Now that have looped over all the faces for this
-          // cell and computed as well as disributed the local
+          // cell and computed as well as distributed the local
           // flux matrices to the <code>system_matrix</code>, we
           // can finally distribute the cell's <code>local_matrix</code>
           // and <code>local_vector</code> contribution to the
@@ -812,7 +812,7 @@ assemble_system()
           // the faces on the boundary of the domain contribute
           // to the <code>local_matrix</code>
           // and <code>system_rhs</code>.  We could distribute
-          // the local contributions for each component seperately,
+          // the local contributions for each component separately,
           // but writing to the distributed sparse matrix and vector
           // is expensive and want to to minimize the number of times
           // we do so.
@@ -909,7 +909,7 @@ assemble_cell_terms(
 // Here we have the function that builds the <code>local_matrix</code>
 // contribution
 // and local right hand side vector, <code>local_vector</code>
-// for the Dirichlet boundary condtions.
+// for the Dirichlet boundary conditions.
 template<int dim>
 void
 LDGPoissonProblem<dim>::
@@ -981,7 +981,7 @@ assemble_Dirichlet_boundary_terms(
 
 // @sect4{assemble_Neumann_boundary_terms}
 // Here we have the function that builds the <code>local_matrix</code>
-// and <code>local_vector</code> for the Neumann boundary condtions.
+// and <code>local_vector</code> for the Neumann boundary conditions.
 template<int dim>
 void
 LDGPoissonProblem<dim>::
@@ -1027,7 +1027,7 @@ assemble_Neumann_boundary_terms(
             }
 
           // We also compute the contribution for the flux for
-          // $\widehat{q}$ on the Neumann bounary which is the
+          // $\widehat{q}$ on the Neumann boundary which is the
           // Neumann boundary condition and enters the right
           // hand side vector as
           //
@@ -1328,17 +1328,17 @@ distribute_local_flux_to_global(
 // As mentioned earlier I used a direct solver to solve
 // the linear system of equations resulting from the LDG
 // method applied to the Poisson equation. One could also
-// use a iterative sovler, however, we then need to use
-// a preconditoner and that was something I did not wanted
+// use a iterative solver, however, we then need to use
+// a preconditioner and that was something I did not wanted
 // to get into. For information on preconditioners
 // for the LDG Method see this
 // <a href="http://epubs.siam.org/doi/abs/10.1137/S1064827502410657">
-// paper</a>. The uses of a direct sovler here is
+// paper</a>. The uses of a direct solver here is
 // somewhat of a limitation.  The built-in distributed
 // direct solver in Trilinos reduces everything to one
 // processor, solves the system and then distributes
 // everything back out to the other processors.  However,
-// by linking to more advanced direct sovlers through
+// by linking to more advanced direct solvers through
 // Trilinos one can accomplish fully distributed computations
 // and not much about the following function calls will
 // change.
@@ -1359,7 +1359,7 @@ solve()
   TrilinosWrappers::MPI::Vector
   completely_distributed_solution(system_rhs);
 
-  // Now we can preform the solve on the completeley distributed
+  // Now we can perform the solve on the completeley distributed
   // right hand side vector, system matrix and the completely
   // distributed solution.
   solver.solve(system_matrix,
@@ -1382,11 +1382,11 @@ solve()
 }
 
 // @sect4{output_results}
-// This function deals with the writing of the reuslts in parallel
+// This function deals with the writing of the results in parallel
 // to disk.  It is almost exactly the same as
-// in step-40 and we wont go into it.  It is noteworthy
+// in step-40 and we won't go into it.  It is noteworthy
 // that in step-40 the output is only the scalar solution,
-// while in our situation, we are outputing both the scalar
+// while in our situation, we are outputting both the scalar
 // solution as well as the vector field solution. The only
 // difference between this function and the one in step-40
 // is in the <code>solution_names</code> vector where we have to add

Distributed_LDG_Method/README.md

@@ -21,7 +21,7 @@ I could not use this framework for solving my research problem and I
 needed to write the LDG method from scratch. I thought it 
 would be helpful for others to have access to 
 this example that goes through writing a discontinuous Galerkin method from 
-scatch and also shows how to do it in a distributed setting using the 
+scratch and also shows how to do it in a distributed setting using the 
 <a href="https://www.trilinos.org">Trilinos</a> library. This example may also
 be of interest to users that wish to use the LDG method, as the method is 
 distinctly different from the 
@@ -137,7 +137,7 @@ $\textbf{q}$:
 f(\textbf{x}) && \text{in} \ \Omega, \label{eq:Primary} \\
 \textbf{q}
 \; &= \;
- -\nabla u && \text{in} \ \Omega,  \label{eq:Auxillary} \\
+ -\nabla u && \text{in} \ \Omega,  \label{eq:Auxiliary} \\
 \textbf{q}  \cdot \textbf{n} 
 \; &= \; g_{N}(\textbf{x}) && \text{on} \ \partial \Omega_{N},\\
 u &= g_{D}(\textbf{x}) && \mbox{on}\ \partial \Omega_{D}.
@@ -275,7 +275,7 @@ parameter that is defined as,
 
 
 with $\tilde{\sigma}$ being a positive constant.  There are other choices of
-penalty values $\sigma$, but the one above produces in appoximations to solutions
+penalty values $\sigma$, but the one above produces in approximations to solutions
 that are the most accurate, see this 
 <a href="http://epubs.siam.org/doi/abs/10.1137/S0036142900371003">
 reference</a> for more info.

ElastoplasticTorsion/ElastoplasticTorsion.cc

@@ -500,7 +500,7 @@ namespace nsp
 
 
   /*************************************************************/
-// formating
+// formatting
 
   template <int dim>
   void ElastoplasticTorsion<dim>::format_convergence_tables()
@@ -624,7 +624,7 @@ namespace nsp
   }
 
   /***************************************************************************************/
-  /* the coeffcients W, W' and G defining the problem.
+  /* the coefficients W, W' and G defining the problem.
 
      Min_u \int W(|Du|^2) dx
 
@@ -1054,7 +1054,7 @@ namespace nsp
       }
     if (!done)
       {
-        std::cerr << ", max. no. of iterations reached wiht steplength= "<< alpha
+        std::cerr << ", max. no. of iterations reached with steplength= "<< alpha
                   << ", fcn value= "<< phi_alpha<<std::endl;
         return false;
       }
@@ -1206,7 +1206,7 @@ namespace nsp
     double ptime=0.0;
     timer.start ();
 
-    // initalize mesh for the selected domain
+    // initialize mesh for the selected domain
     init_mesh();
 
     // setup FE space

Linear_Elastic_Active_Skeletal_Muscle_Model/Linear_active_muscle_model.cc

@@ -754,7 +754,7 @@ namespace LMM
   {
     // Values from previous state
     // These were the values that were used in the assembly,
-    // so we must use them in the update step to be consistant.
+    // so we must use them in the update step to be consistent.
     // Need to compute these before we overwrite epsilon_c_t1
     const double m_s = get_m_s();
     const double beta = get_beta(dt);
@@ -900,7 +900,7 @@ namespace LMM
     // Provides the muscle direction at the point @p pt
     // in the real geometry (one that has undergone the
     // transformation given by the profile() function)
-    // and subequent grid rescaling.
+    // and subsequent grid rescaling.
     // The directions are given by the gradient of the
     // transformation function (i.e. the fibres are
     // orientated by the curvature of the muscle).

Linear_Elastic_Active_Skeletal_Muscle_Model/README.md

@@ -53,7 +53,7 @@ a diameter of `80mm` at its mid-point.
 We assume that there exists a single muscle fibre family orientated axially.
 The orientation of the underlying muscle fibres is, however, not parallel,
 but rather follows the curvature of the macroscopic anatomy.
-The longitudinal profile of the muscle is generated using a trignometric
+The longitudinal profile of the muscle is generated using a trigonometric
 function, as opposed to being extracted from medical images.
 The benefit to doing so is that the geometry can be (parametrically) created
 in `deal.II` itself and the associated microstructural orientation can be

MCMC-Laplace/Readme.md

@@ -214,8 +214,8 @@ that may take into account the current time, the amount of data
 written to disk over the past hour, the amount of internet traffic
 that has gone through the machine in the last hour, and similar pieces
 of pretty much random information. As a consequence, the seed is then
-pretty much guaranteed to be different from program invokation to
-program invokation, and consequently we will get different random
+pretty much guaranteed to be different from program invocation to
+program invocation, and consequently we will get different random
 number sequences every time. The output file is tagged with a string
 representation of this random seed, so that it is safe to run the same
 program multiple times at the same time in the same directory, with

MultipointFluxMixedFiniteElementMethods/mfmfe.cc

@@ -115,7 +115,7 @@ namespace MFMFE
     // Next, since this particular program allows for the use of
     // multiple threads, the helper CopyData structures
     // are defined. There are two kinds of these, one is used
-    // for the copying cell-wise contributions to the corresponging
+    // for the copying cell-wise contributions to the corresponding
     // node-associated data structures...
     template <int dim>
     struct NodeAssemblyCopyData
@@ -145,7 +145,7 @@ namespace MFMFE
     // Similarly, two ScratchData classes are defined.
     // One for the assembly part, where we need
     // FEValues, FEFaceValues, Quadrature and storage
-    // for the basis fuctions...
+    // for the basis functions...
     template <int dim>
     struct NodeAssemblyScratchData
     {
@@ -367,7 +367,7 @@ namespace MFMFE
 
   // First, the function that copies local cell contributions to the corresponding nodal
   // matrices and vectors is defined. It places the values obtained from local cell integration
-  // into the correct place in a matrix/vector corresponging to a specific node.
+  // into the correct place in a matrix/vector corresponding to a specific node.
   template <int dim>
   void MultipointMixedDarcyProblem<dim>::copy_cell_to_node(const DataStructures::NodeAssemblyCopyData<dim> &copy_data)
   {