Aligning the code with contributing guidelines

examples/Grid3Bus/README.md

@@ -22,13 +22,13 @@ Problem variables are voltage magnitudes and phases; they are stored in bus obje
 
 **Bus 1**: Slack bus, does not store variables no residuals. Voltage and phase are set to $`V_1 \equiv 1`$p.u. and $`\theta_1 \equiv 0`$, respectively.
 
-**Bus 2**: PQ bus, stores variables $`V_2, \theta_2`$ and residuals $`P_2, Q_2`$. Load $`P_{L2} = 2.5`$p.u., $`Q_{L2} = -j0.8`$p.u. is attached to it. From the equations for [branch](../../src/Model/PowerFlow/Branch/README.md) and [load](../../src/Model/PowerFlow/Load/README.md) components, we assemble Bus 2 residuals as:
+**Bus 2**: PQ bus, stores variables $`V_2, \theta_2`$ and residuals $`P_2, Q_2`$. Load $`P_{L1} = 2.5`$p.u., $`Q_{L1} = -j0.8`$p.u. is attached to it. From the equations for [branch](../../src/Model/PowerFlow/Branch/README.md) and [load](../../src/Model/PowerFlow/Load/README.md) components, we assemble Bus 2 residuals as:
 ```math
 \begin{array}{rcll}
-P_2 & = &-P_{L2} &~~~\mathrm{(load ~2)} \\
+P_2 & = &-P_{L1} &~~~\mathrm{(load ~2)} \\
       &&+ b_{12}|V_1||V_2|\sin(\theta_2-\theta_1) &~~~\mathrm{(branch ~12)} \\
       &&+ b_{23}|V_2||V_3|\sin(\theta_2-\theta_3) &~~~\mathrm{(branch ~23)} \\
-Q_2 & = & -Q_{L2} &~~~\mathrm{(load ~2)} \\
+Q_2 & = & -Q_{L1} &~~~\mathrm{(load ~2)} \\
       &&+ b_{12}|V_2|^2 - b_{12}|V_1||V_2|\cos(\theta_2-\theta_1) &~~~\mathrm{(branch ~12)} \\
       &&+ b_{23}|V_2|^2 - b_{23}|V_2||V_3|\cos(\theta_2-\theta_3) &~~~\mathrm{(branch ~23)}
 \end{array}
@@ -57,7 +57,7 @@ with variables $`\theta_2, |V_2|`$ and $`\theta_3`$.
 
 Nonlinear solver can approximate Jacobian numerically, however this is computationaly expensive and scales poorly with the size of the problem. Typically, one needs to provide Jacobian in addition to residual to the nonlinear solver. For nonlinear problem defined by (vector) function $`\mathbf{f}(\mathbf{x})=0`$, Jacobian matrix is defined as
 ```math
-J_{i,j}=\frac{\partial f_i}{\partial x_j}, ~~~ i,j=1,\ldots,N
+jac_{i,j}=\frac{\partial f_i}{\partial x_j}, ~~~ i,j=1,\ldots,N
 ```
 where $`N`$ is the size of vectors $`\mathbf{f}`$ and $`\mathbf{x}`$. Jacobian for our model is evaluated as
 ```math

examples/Microgrid/Microgrid.cpp

@@ -21,13 +21,13 @@
 int main(int argc, char const *argv[])
 {
 	///@todo Needs to be modified. Some components are small relative to others thus there error is high (or could be matlab vector issue)
-    double abstol = 1.0e-8;
-    double reltol = 1.0e-8;
+    double abs_tol = 1.0e-8;
+    double rel_tol = 1.0e-8;
     size_t max_step_amount = 3000;
-    bool usejac = true;
+    bool use_jac = true;
 
     //Create model
-    GridKit::PowerElectronicsModel<double, size_t>* sysmodel = new GridKit::PowerElectronicsModel<double, size_t>(reltol, abstol, usejac, max_step_amount);
+    GridKit::PowerElectronicsModel<double, size_t>* sysmodel = new GridKit::PowerElectronicsModel<double, size_t>(rel_tol, abs_tol, use_jac, max_step_amount);
 
     //Modeled after the problem in the paper
     double RN = 1.0e4;
@@ -336,8 +336,6 @@ int main(int argc, char const *argv[])
     sysmodel->updateTime(0.0, 1.0e-8);
     sysmodel->evaluateJacobian();
     std::cout << "Intial Jacobian with alpha:\n";
-    // std::cout << sysmodel->getJacobian().frobnorm() << "\n";
-
 
     //Create numerical integrator and configure it for the generator model
     AnalysisManager::Sundials::Ida<double, size_t>* idas = new AnalysisManager::Sundials::Ida<double, size_t>(sysmodel);

examples/RLCircuit/RLCircuit.cpp

@@ -18,13 +18,13 @@
 
 int main(int argc, char const *argv[])
 {
-    double abstol = 1.0e-8;
-    double reltol = 1.0e-8;
-    bool usejac = true;
+    double abs_tol = 1.0e-8;
+    double rel_tol = 1.0e-8;
+    bool use_jac = true;
 
     //TODO:setup as named parameters
     //Create circuit model
-    GridKit::PowerElectronicsModel<double, size_t>* sysmodel = new GridKit::PowerElectronicsModel<double, size_t>(reltol, abstol, usejac);
+    auto* sysmodel = new GridKit::PowerElectronicsModel<double, size_t>(rel_tol, abs_tol, use_jac);
 
     size_t idoff = 0;
 

examples/ScaleMicrogrid/ScaleMicrogrid.cpp

@@ -66,18 +66,18 @@ int test(index_type Nsize, real_type error_tol, bool debug_output)
 {
     using namespace GridKit;
 
-    bool usejac = true;
+    bool use_jac = true;
 
     real_type t_init  = 0.0;
     real_type t_final = 1.0;
 
-    real_type reltol = SCALE_MICROGRID_REL_TOL;
-    real_type abstol = SCALE_MICROGRID_ABS_TOL;
+    real_type rel_tol = SCALE_MICROGRID_REL_TOL;
+    real_type abs_tol = SCALE_MICROGRID_ABS_TOL;
 
     // Create circuit model
-    auto* sysmodel = new PowerElectronicsModel<real_type, index_type>(reltol,
-                                                                      abstol,
-                                                                      usejac,
+    auto* sysmodel = new PowerElectronicsModel<real_type, index_type>(rel_tol,
+                                                                      abs_tol,
+                                                                      use_jac,
                                                                       SCALE_MICROGRID_MAX_STEPS);
 
     const std::vector<real_type>* true_vec = &answer_key_N8;

examples/ScaleMicrogrid/SolutionKeys.hpp

@@ -5,7 +5,7 @@
  * @brief Answer keys for Scaled Microgrid test with Nsize = 2, 4, 8
  * 
  * Data generated with Matlab ode23tb solver with tolerances set to
- * abstol = 1e-12 and reltol = 1e-12 for the ODE derivation of the model.
+ * abs_tol = 1e-12 and rel_tol = 1e-12 for the ODE derivation of the model.
  * No index reduction was preformed to get to the ODE model.
  * 
  * @note This file is only to be included in ScaleMicrogrid.cpp. It has no

examples/SparseTest/SparseTest.cpp

@@ -50,7 +50,7 @@ int main(int argc, char const *argv[])
     std::vector<size_t> r;
     std::vector<size_t> c;
     std::vector<double> v;
-    std::tie(r,c,v) = A.getDataToCSR();
+    std::tie(r,c,v) = A.setDataToCSR();
 
     for (size_t i = 0; i < r.size() - 1; i++)
     {

src/CircuitGraph.hpp

@@ -95,12 +95,13 @@ size_t CircuitGraph<N, E>::amountHyperEdges()
 }
 
 /**
- * @brief Printing
+ * @brief Print the bipartite graph
  *
  * @todo need to add verbose printing for connections display
  *
  * @tparam IdxT
- * @param verbose
+ * @param[in] verbose if true will print connections, 
+ * otherwise just the number of nodes and edges
  */
 
 template <typename N, typename E>