From f260e858c0fe697098db7d5714656073757a35df Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Mon, 11 Apr 2016 15:39:22 -0400
Subject: [PATCH] [Numerics] Deprecate class SquareMatrix

---
 include/cantera/numerics.h              | 1 -
 include/cantera/numerics/ResidJacEval.h | 8 ++++----
 include/cantera/numerics/SquareMatrix.h | 1 +
 src/numerics/ResidJacEval.cpp           | 2 +-
 src/numerics/SquareMatrix.cpp           | 4 ++++
 5 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/include/cantera/numerics.h b/include/cantera/numerics.h
index 392f155f0..115c87581 100644
--- a/include/cantera/numerics.h
+++ b/include/cantera/numerics.h
@@ -10,6 +10,5 @@
 
 #include "numerics/DenseMatrix.h"
 #include "numerics/BandMatrix.h"
-#include "numerics/SquareMatrix.h"
 
 #endif
diff --git a/include/cantera/numerics/ResidJacEval.h b/include/cantera/numerics/ResidJacEval.h
index e78a4cb7a..0c548dd07 100644
--- a/include/cantera/numerics/ResidJacEval.h
+++ b/include/cantera/numerics/ResidJacEval.h
@@ -15,7 +15,7 @@
 #define CT_RESIDJACEVAL_H
 
 #include "ResidEval.h"
-#include "GeneralMatrix.h"
+#include "DenseMatrix.h"
 
 namespace Cantera
 {
@@ -271,7 +271,7 @@ public:
      * @param cj            Coefficient of yprime used in the evaluation of the Jacobian
      * @param y             Solution vector (input, do not modify)
      * @param ydot          Rate of change of solution vector. (input, do not modify)
-     * @param J             Reference to the SquareMatrix object to be calculated (output)
+     * @param J             Reference to the DenseMatrix object to be calculated (output)
      * @param resid         Value of the residual that is computed (output)
      * @returns a flag to indicate that operation is successful.
      *            1  Means a successful operation
@@ -279,7 +279,7 @@ public:
      */
     virtual int evalJacobian(const doublereal t, const doublereal delta_t, doublereal cj,
                              const doublereal* const y, const doublereal* const ydot,
-                             GeneralMatrix& J, doublereal* const resid);
+                             DenseMatrix& J, doublereal* const resid);
 
     //! Calculate an analytical Jacobian and the residual at the current time and values.
     /*!
@@ -290,7 +290,7 @@ public:
      * @param cj            Coefficient of yprime used in the evaluation of the Jacobian
      * @param y             Solution vector (input, do not modify)
      * @param ydot          Rate of change of solution vector. (input, do not modify)
-     * @param jacobianColPts   Pointer to the vector of pts to columns of the SquareMatrix
+     * @param jacobianColPts   Pointer to the vector of pts to columns of the DenseMatrix
      *                         object to be calculated (output)
      * @param resid         Value of the residual that is computed (output)
      * @returns a flag to indicate that operation is successful.
diff --git a/include/cantera/numerics/SquareMatrix.h b/include/cantera/numerics/SquareMatrix.h
index 18b0e4c90..1447cb070 100644
--- a/include/cantera/numerics/SquareMatrix.h
+++ b/include/cantera/numerics/SquareMatrix.h
@@ -19,6 +19,7 @@ namespace Cantera
 /**
  * A class for full (non-sparse) matrices with Fortran-compatible data storage.
  * Adds matrix inversion operations to this class from DenseMatrix.
+ * @deprecated Use class DenseMatrix instead. To be removed after Cantera 2.3.
  */
 class SquareMatrix: public DenseMatrix, public GeneralMatrix
 {
diff --git a/src/numerics/ResidJacEval.cpp b/src/numerics/ResidJacEval.cpp
index 5a5ce2ea9..a9ad2c8c3 100644
--- a/src/numerics/ResidJacEval.cpp
+++ b/src/numerics/ResidJacEval.cpp
@@ -164,7 +164,7 @@ int ResidJacEval::eval(const doublereal t, const doublereal* const y, const doub
 
 int ResidJacEval::evalJacobian(const doublereal t, const doublereal delta_t,
                                doublereal cj, const doublereal* const y,
-                               const doublereal* const ydot, GeneralMatrix& J,
+                               const doublereal* const ydot, DenseMatrix& J,
                                doublereal* const resid)
 {
     doublereal* const* jac_colPts = J.colPts();
diff --git a/src/numerics/SquareMatrix.cpp b/src/numerics/SquareMatrix.cpp
index 05669ab5c..9e595d0a7 100644
--- a/src/numerics/SquareMatrix.cpp
+++ b/src/numerics/SquareMatrix.cpp
@@ -21,6 +21,8 @@ SquareMatrix::SquareMatrix() :
     a1norm_(0.0),
     useQR_(0)
 {
+    warn_deprecated("class SquareMatrix",
+        "Use class DenseMatrix instead. To be removed after Cantera 2.3.");
 }
 
 SquareMatrix::SquareMatrix(size_t n, doublereal v)  :
@@ -29,6 +31,8 @@ SquareMatrix::SquareMatrix(size_t n, doublereal v)  :
     a1norm_(0.0),
     useQR_(0)
 {
+    warn_deprecated("class SquareMatrix",
+        "Use class DenseMatrix instead. To be removed after Cantera 2.3.");
 }
 
 SquareMatrix::SquareMatrix(const SquareMatrix& y) :