Small restructuring and cleaning up spurious includes and and namespaces.

include/SM_Helpers.hpp

@@ -1,43 +1,42 @@
-// Helpers.hpp
+// SM_Helpers.hpp
 // Some usefull helper functions to support the Maponi algorithm.
 #include <iostream>
-#include <cmath>
 #include <string>
 #include <cstring>
-using namespace std;
+#include <cmath>
 
 template<typename T>
-void showScalar(T scalar, string name) {
-    cout << name << " = " << scalar << endl << endl;
+void showScalar(T scalar, std::string name) {
+    std::cout << name << " = " << scalar << std::endl << std::endl;
 }
 
 template<typename T>
-void showVector(T *vector, unsigned int size, string name) {
-    cout << name << " = " << endl;
+void showVector(T *vector, unsigned int size, std::string name) {
+    std::cout << name << " = " << std::endl;
     for (unsigned int i = 0; i < size; i++) {
-        cout << "[ " << vector[i] << " ]" << endl;
+        std::cout << "[ " << vector[i] << " ]" << std::endl;
     }
-    cout << endl;
+    std::cout << std::endl;
 }
 
 template<typename T>
-void showMatrix(T *matrix, unsigned int M, string name) {
-    cout.precision(17);
-    cout << name << " = [" << endl;
+void showMatrix(T *matrix, unsigned int M, std::string name) {
+    std::cout.precision(17);
+    std::cout << name << " = [" << std::endl;
     for (unsigned int i = 0; i < M; i++) {
-        cout << "[";
+        std::cout << "[";
         for (unsigned int j = 0; j < M; j++) {
             if (matrix[i*M + j] >= 0) {
-                cout << "  " << matrix[i*M + j] << ",";
+                std::cout << "  " << matrix[i*M + j] << ",";
             }
             else {
-                cout << " " << matrix[i*M + j] << "," ;
+                std::cout << " " << matrix[i*M + j] << "," ;
             }
         }
-        cout << " ]," << endl;
+        std::cout << " ]," << std::endl;
     }
-    cout << "]" << endl;
-    cout << endl;
+    std::cout << "]" << std::endl;
+    std::cout << std::endl;
 }
 
 template<typename T>

smvars.sh

@@ -43,7 +43,7 @@ case $ENV in
 	;;
   *)
     echo "Unknown environment descriptor given."
-	echo "Usage: source smvars.sh {intel | llvm | gnu}"
+	echo "Usage: source smvars.sh {intel | llvm | vfc | gnu}"
 	return 1
 	;;
 esac

src/SM_MaponiA3.cpp

@@ -2,9 +2,17 @@
 // Algorithm 3 from P. Maponi,
 // p. 283, doi:10.1016/j.laa.2006.07.007
 #include "SM_MaponiA3.hpp"
-#include "Helpers.hpp"
+#include "SM_Helpers.hpp"
 
-void selectBestUpdate(unsigned int l, unsigned int N_updates, 
+// #define DEBUG
+
+void Switch(unsigned int *p, unsigned int l, unsigned int lbar) {
+  unsigned int tmp = p[l+1];
+  p[l+1] = p[lbar];
+  p[lbar] = tmp;
+}
+
+void selectLargestDenominator(unsigned int l, unsigned int N_updates, 
                       unsigned int *Updates_index, unsigned int *p, 
                       double ***ylk) {
   unsigned int lbar = l+1, max =0;
@@ -16,18 +24,16 @@ void selectBestUpdate(unsigned int l, unsigned int N_updates,
     component = Updates_index[index - 1];
     breakdown = abs(1 + ylk[l][index][component]);
     #ifdef DEBUG
-    cout << "Inside selectBestUpdate()" << endl;
-    cout << "breakdown = abs(1 + ylk[" << l << "][" << index << "][" << component << "]) = " << breakdown << endl;
-    cout << endl;
+    std::cout << "Inside selectLargestDenominator()" << std::endl;
+    std::cout << "breakdown = abs(1 + ylk[" << l << "][" << index << "][" << component << "]) = " << breakdown << std::endl;
+    std::cout << std::endl;
     #endif
     if (breakdown > max) {
       max = breakdown;
       lbar = j;
     }
   }
-  tmp = p[l+1];
-  p[l+1] = p[lbar];
-  p[lbar] = tmp; 
+  Switch(p, l, lbar);
 }
 
 void MaponiA3(double *Slater_inv, unsigned int Dim,
@@ -68,9 +74,9 @@ void MaponiA3(double *Slater_inv, unsigned int Dim,
   // Calculate the {y_{0,k}}
   for (k = 1; k < N_updates + 1; k++) {
     #ifdef DEBUG
-    cout << "Compute y0k: " << endl;
-    cout << "ylk[0][" << k << "][:]";
-    cout << endl;
+    std::cout << "Compute y0k: " << std::endl;
+    std::cout << "ylk[0][" << k << "][:]";
+    std::cout << std::endl;
     #endif
     for (i = 1; i < Dim + 1; i++) {
       for (j = 1; j < Dim + 1; j++) {
@@ -86,33 +92,33 @@ void MaponiA3(double *Slater_inv, unsigned int Dim,
   // Calculate the {y_{l,k}} from the {y_{0,k}}
   for (l = 0; l < N_updates; l++) {
     #ifdef DEBUG
-    cout << "In outer compute-ylk-loop: l = " << l << endl;
-    cout << endl;
+    std::cout << "In outer compute-ylk-loop: l = " << l << std::endl;
+    std::cout << std::endl;
     #endif
 
     // For given l select intermediate update with largest break-down val
-    selectBestUpdate(l, N_updates, Updates_index, p, ylk);
+    selectLargestDenominator(l, N_updates, Updates_index, p, ylk);
 
     // Select component and comp. bd-condition.
     component = Updates_index[p[l+1] - 1];
     beta = 1 + ylk[l][p[l+1]][component];
     #ifdef DEBUG
-    cout << "p[l+1] = " << p[l+1] << endl;
-    cout << "component = " << component << endl;
-    cout << "beta = 1 + ylk[" << l << "][" << p[l+1] << "][" << component << "] = " << beta << endl;
-    cout << endl;
+    std::cout << "p[l+1] = " << p[l+1] << std::endl;
+    std::cout << "component = " << component << std::endl;
+    std::cout << "beta = 1 + ylk[" << l << "][" << p[l+1] << "][" << component << "] = " << beta << std::endl;
+    std::cout << std::endl;
     #endif
     if (fabs(beta) < 1e-3) {
-      cerr << "Break-down occured." << endl;
+      std::cerr << "Break-down occured." << std::endl;
     }
 
     // Compute intermediate update to Slater_inv
     #ifdef DEBUG
-    cout << "Compute intermediate update to Slater_inv" << endl;
-    cout << "component = " << component << endl;
-    cout << "beta = 1 + ylk[" << l << "][" << p[l+1] << "][" << component << "]" << endl;
-    cout << "ylk[l][p[k]][:] = ylk[" << l << "][" << p[l+1] << "][:]" << endl;
-    cout << endl;
+    std::cout << "Compute intermediate update to Slater_inv" << std::endl;
+    std::cout << "component = " << component << std::endl;
+    std::cout << "beta = 1 + ylk[" << l << "][" << p[l+1] << "][" << component << "]" << std::endl;
+    std::cout << "ylk[l][p[k]][:] = ylk[" << l << "][" << p[l+1] << "][:]" << std::endl;
+    std::cout << std::endl;
     #endif
     for (i = 0; i < Dim; i++) {
       for (j = 0; j < Dim; j++) {
@@ -132,9 +138,9 @@ void MaponiA3(double *Slater_inv, unsigned int Dim,
     for (k = l+2; k < N_updates+1; k++) {
       alpha = ylk[l][p[k]][component] / beta;
       #ifdef DEBUG
-      cout << "Inside k-loop: k = " << k << endl;
-      cout << "ylk[" << l+1 << "][" << p[k] << "][:]" << endl;
-      cout << endl;
+      std::cout << "Inside k-loop: k = " << k << std::endl;
+      std::cout << "ylk[" << l+1 << "][" << p[k] << "][:]" << std::endl;
+      std::cout << std::endl;
       #endif
       for (i = 1; i < Dim + 1; i++) {
         ylk[l+1][p[k]][i] = ylk[l][p[k]][i]

src/SM_Standard.cpp

@@ -1,8 +1,7 @@
 // SM-Standard.cpp
 // Standard Sherman Morrison with multiple updates
 #include "SM_Standard.hpp"
-#include "Helpers.hpp"
-#include <iostream>
+#include "SM_Helpers.hpp"
 
 // Set common break-down threshold
 double threshold() {

tests/cMaponiA3_test_3x3_3.cpp

@@ -1,6 +1,6 @@
 // main.cpp
 #include "SM_MaponiA3.hpp"
-#include "Helpers.hpp"
+#include "SM_Helpers.hpp"
 
 int main() {
 

tests/test_h5.cpp

@@ -1,11 +1,9 @@
-#include <iostream>
-#include <string>
 #include "hdf5/serial/hdf5.h"
 #include "hdf5/serial/H5Cpp.h"
 
 #include "SM_MaponiA3.hpp"
 #include "SM_Standard.hpp"
-#include "Helpers.hpp"
+#include "SM_Helpers.hpp"
 
 using namespace H5;
 // #define DEBUG