Minor edits to the programs added today.

Crystal_Growth_Phase_Field_Model/README.md

@@ -12,7 +12,7 @@ quickly go through the governing equations and the boundary conditions solved in
 \tau \frac{\partial p}{\partial t} = \nabla \cdot( \left(\epsilon^2\right)\nabla p) + p(1-p)(p-\frac{1}{2}+m) \label{heateq} \\
 \frac{\partial T}{\partial t}=\nabla^2T+K\frac{\partial p}{\partial t}
 @f}
-where $m(t) = \frac{a}{\pi}\tan^{-1}(\gamma(T_e-T))$
+where $m(T) = \frac{a}{\pi}\tan^{-1}(\gamma(T_e-T))$
 
 The problem is subjected to the boundary conditions:
 @f{align*}{
@@ -27,11 +27,11 @@ T(x,y,0)= T_\gamma -\Delta T
 Here, $\Delta T$ is the degree of undercooling.
 
 ### Dendritic Growth
-Using this code, we have reproduced one of the study from Koabayashi's work regarding the dendritic 
+Using this code, we have reproduced one of the study from Kobayashi's work regarding the dendritic 
 behaviour during directional solidification. The latent heat parameter 'K' in the equation determines 
 the amount of heat released as the phase solidifies. If this value is high enough, we would observe an 
 unstable interface between the solid and liquid phase, which would lead to the formation of dendrites 
-as shown in these images. To assist this growth we need to add a random perterbation term 
+as shown in these images. To assist this growth we need to add a random perturbation term 
 '$a \chi p (1-p)$' to the dynamic term of the phase field equation.
 
 ![Screenshot](./doc/images/K=1v1.2v1.4.gif)

TravelingWaves/README.md

@@ -42,7 +42,7 @@ Because of translational invariance, we need to impose another constraint on the
 ## Numerical algorithm
 
 ### Newton–Raphson iteration scheme
-The nonlinear boundary value problem is solved numerically on a finite interval $I = [l, r]$ $\left(|l|, |r| \gg 1 \right)$, using a Newton–Raphson iteration scheme, similar to one, described in deal.II tutorial [step-15](https://www.dealii.org/current/doxygen/deal.II/step_15.html). The main difference from step-15 is that we have an additional scalar unknown, the front velocity $c$. So the algorithm has to be modified to take this feature into account.
+The nonlinear boundary value problem is solved numerically on a finite interval $I = [l, r]$ $\left(|l|, |r| \gg 1 \right)$, using a Newton–Raphson iteration scheme, similar to one, described in deal.II tutorial step-15. The main difference from step-15 is that we have an additional scalar unknown, the front velocity $c$. So the algorithm has to be modified to take this feature into account.
 
 Rewriting the system in a vector form
 @f{align*}{
@@ -159,7 +159,7 @@ for $i, j < 3N + 1$.
 In order for the system to have a unique solution, we need to supplement it with one more equation, corresponding to the constraint $T(0) = T_{\text{ign}}$. The initial approximation to the solution is set so as to satisfy this condition, so we just need the computed increment function $dT$ to be zero at the specified point. Thus, we add a row of zeros with a value of 1 in the position corresponding to $dT(0)$ to the matrix $J$ and set $b_{3N + 1} = 0$.
 
 The resulting sparsity pattern structure has the form shown in the figure below.
-![Sparsity pattern corresponding to basis polynomial degree $p=1$.](doc/pics/sparsity-pattern_p1.png)
+![Sparsity pattern corresponding to basis polynomial degree $p=1$.](./doc/pics/sparsity-pattern_p1.png)
 
 The integration of the terms with $\kappa_1$ need special attention because of the Dirac delta function. If $U_n$ and $U_m$ are the degrees of freedom, associated with the vertex $\xi = 0$ (i.e., $\phi_n^2(0) = 1$ and $\phi_m^3(0) = 1$), we get
 @f{align*}{
@@ -207,12 +207,12 @@ The calculation parameters are set in the `ParametersList.prm` file. To reproduc
 ### Class `TravelingWaveSolver`
 `TravelingWaveSolver` is the main class for computation of the traveling-wave profiles.
 
-The implementation of Newton's method is based on that described in [step-77](https://www.dealii.org/current/doxygen/deal.II/step_77.html) and relies on SUNDIALS' [KINSOL](https://computing.llnl.gov/projects/sundials/kinsol) package. Because of the additional unknown, the front velocity, we expand the Jacobi matrix by one column and one row (`jacobian_matrix_extended`), and add one more element to the solution vector (`current_solution_extended`). After completing the Newton iterations, we split the resulting extended solution vector `current_solution_extended` into two parts: the solution vector `current_solution`, corresponding to $(u, T, \lambda)$, and the front velocity `current_wave_speed`. After that the adaptive mesh refinement is performed using the `current_solution` vector, which is very important for resolving a narrow transition layer with a large solution gradient in the vicinity of zero. The [KellyErrorEstimator](https://www.dealii.org/current/doxygen/deal.II/classKellyErrorEstimator.html) is used as a refinement indicator.
+The implementation of Newton's method is based on that described in step-77 and relies on SUNDIALS' [KINSOL](https://computing.llnl.gov/projects/sundials/kinsol) package. Because of the additional unknown, the front velocity, we expand the Jacobi matrix by one column and one row (`jacobian_matrix_extended`), and add one more element to the solution vector (`current_solution_extended`). After completing the Newton iterations, we split the resulting extended solution vector `current_solution_extended` into two parts: the solution vector `current_solution`, corresponding to $(u, T, \lambda)$, and the front velocity `current_wave_speed`. After that the adaptive mesh refinement is performed using the `current_solution` vector, which is very important for resolving a narrow transition layer with a large solution gradient in the vicinity of zero. The [KellyErrorEstimator](https://www.dealii.org/current/doxygen/deal.II/classKellyErrorEstimator.html) is used as a refinement indicator.
 
 ### Function `calculate_profile`
 The full calculation cycle is done in the `calculate_profile` function. First, we construct an initial guess to the solution depending on the selected wave type and store the result as an object of type `SolutionStruct`. This object, along with the problem parameters, is then passed to the constructor of the `TravelingWaveSolver` class to calculate the traveling wave.
 
-Decreasing the dissipation parameter $\delta$ leads to the appearance of large gradients in solutions in the neighborhood of zero. As a consequence, Newton's method becomes more sensitive to the initial data and ceases to converge. To solve this problem, the `calculate_profile` function implements the method of continuation by the $\delta$ parameter (for an example, see [step-57](https://www.dealii.org/current/doxygen/deal.II/step_57.html)). The solution and the refined triangulation are saved after each step of the method using the `get_solution` and `get_triangulation` functions and then passed to the next step.
+Decreasing the dissipation parameter $\delta$ leads to the appearance of large gradients in solutions in the neighborhood of zero. As a consequence, Newton's method becomes more sensitive to the initial data and ceases to converge. To solve this problem, the `calculate_profile` function implements the method of continuation by the $\delta$ parameter (for an example, see step-57). The solution and the refined triangulation are saved after each step of the method using the `get_solution` and `get_triangulation` functions and then passed to the next step.
 
 
 ### Error estimation
@@ -247,20 +247,20 @@ or execute the python script `plot.py`
 
 ### Slow deflagration for $\delta = 0.01$
 The calculated wave speed is $c = 0.0909$.
-![Slow deflagration, $\delta = 0.01$, $c = 0.0909$](doc/pics/slow_deflagration_delta_0.01.png)
+![Slow deflagration, $\delta = 0.01$, $c = 0.0909$](./doc/pics/slow_deflagration_delta_0.01.png)
 
 
 ### Fast deflagration for $\delta = 0.01$
 The calculated wave speed is $c = 0.8252$.
-![Fast deflagration, $\delta = 0.01$, $0.8252$](doc/pics/fast_deflagration_delta_0.01.png)
+![Fast deflagration, $\delta = 0.01$, $0.8252$](./doc/pics/fast_deflagration_delta_0.01.png)
 
 
 ### Detonation for $\delta = 0.01$ and $\delta = 0.001$
 The calculated wave speed in both cases is the same $c = 1.216481$, as expected. Solid lines represent the detonation profile for the ideal case, when $\delta=0$. 
 
-![Detonation, $\delta = 0.01$, $c = 1.216481$.](doc/pics/detonation_delta_0.01.png)
+![Detonation, $\delta = 0.01$, $c = 1.216481$.](./doc/pics/detonation_delta_0.01.png)
 
-![Detonation, $\delta = 0.001$, $c = 1.216481$](doc/pics/detonation_delta_0.001.png)
+![Detonation, $\delta = 0.001$, $c = 1.216481$](./doc/pics/detonation_delta_0.001.png)
 
 
 ## Acknowledgments