fixing some typos and missing list prunes

Typos in grad2DPeriodic and grad3DPeriodic fixed bfore removing those files. Just a sanity check. In addition, removing repeated rows in addBC2D and addScalar2D to speed up these codes. addBC2D will be removed. Again, having a better code before removing it just in case we need to get back to it in the future.

Author: mdumett

src/matlab/addBC2D.m

@@ -82,10 +82,15 @@
     [rr,~,~] = find(Abcr);
     [rb,~,~] = find(Abcb);
     [rt,~,~] = find(Abct);
+    rl = unique(rl);
+    rr = unique(rr);
+    rb = unique(rb);
+    rt = unique(rt);
 
     % remove rows of A associated to boundary
     Abc = Abcl + Abcr + Abct + Abcb;
     [rowsbc,~,~] = find(Abc);
+    rowsbc = unique(rowsbc);
     [rows,cols,s] = find(A(rowsbc,:));
     A = A - sparse(rows, cols, s, size(A,1), size(A,2));
     % update matrix A with boundary information

src/matlab/addScalarBC2D.m

@@ -106,6 +106,8 @@
     if ~isempty(qrl)    
         [rl,~,~] = find(Abcl);
         [rr,~,~] = find(Abcr);
+        rl = unique(rl);
+        rr = unique(rr);
         % remove rows of A associated to boundary
         Abc1 = Abcl + Abcr;
         [rowsbc1,~,~] = find(Abc1);
@@ -120,6 +122,8 @@
     if ~isempty(qbt)
         [rb,~,~] = find(Abcb);
         [rt,~,~] = find(Abct);
+        rb = unique(rb);
+        rt = unique(rt);
         % remove rows of A associated to boundary
         Abc2 = Abct + Abcb;
         [rowsbc2,~,~] = find(Abc2);

src/matlab/grad2DPeriodic.m

@@ -16,8 +16,8 @@
 % ----------------------------------------------------------------------------
 %
 
-    Gx = gradPer(k, m, dx);
-    Gy = gradPer(k, n, dy);
+    Gx = gradPeriodic(k, m, dx);
+    Gy = gradPeriodic(k, n, dy);
 
     Im = speye(m, m);
     In = speye(n, n);

src/matlab/grad3DPeriodic.m

@@ -22,9 +22,9 @@
     In = speye(n, n);
     Io = speye(o, o);
 
-    Gx = gradPer(k, m, dx);   
-    Gy = gradPer(k, n, dy);
-    Gz = gradPer(k, o, dz);
+    Gx = gradPeriodic(k, m, dx);   
+    Gy = gradPeriodic(k, n, dy);
+    Gz = gradPeriodic(k, o, dz);
 
     Sx = kron(kron(Io, In), Gx);
     Sy = kron(kron(Io, Gy), Im);