refactor checkpoint

analysis/runAnalysis.cpp

@@ -44,17 +44,15 @@ public:
         filename(filename_), phase(phase_), dist(dist_), N(N_) {}
     virtual void run() {
         PROFILE_START("Save Checkpoint",1);
-
-        int q,n;
         double value;
         ofstream File(filename,ios::binary);
         for (int n=0; n<N; n++){
             // Write the two density values
-            value = cPhi[n];
+	  value = phase.data()[n];
             File.write((char*) &value, sizeof(value));
             // Write the distributions
             for (int q=0; q<19; q++){
-                value = cfq[q*N+n];
+	      value = dist.data()[q*N+n];
                 File.write((char*) &value, sizeof(value));
             }
         }

models/ColorModel.cpp

@@ -404,11 +404,12 @@ void ScaLBL_ColorModel::Initialize(){
 		double *cPhi = new double[Np];
 		double *cDist = new double[19*Np];
 	    ifstream File(LocalRestartFile,ios::binary);
-	    for (n=0; n<Np; n++){
+	    double value;
+	    for (int n=0; n<Np; n++){
 	        File.read((char*) &value, sizeof(value));
 	        cPhi[n] = value;
 	        // Read the distributions
-	        for (q=0; q<19; q++){
+	        for (int q=0; q<19; q++){
 	            File.read((char*) &value, sizeof(value));
 	            cDist[q*Np+n] = value;
 	        }