correcting a bug related to initializing (using command line parameters)

when branch lengths are not set to fixed 

BranchSiteModel.cpp

@@ -352,10 +352,9 @@ void BranchSiteModel::initFromParams(void) {
       throw FastCodeMLFatal("Invalid p0 and p1 values"); //
     if (p0 + p1 > 1)
       throw FastCodeMLFatal("Invalid p0 and p1 values");
-    mVar[0] = log((p0) / (1 - p0 - p1)); // log(p0);		// p0 -> x0
+    mVar[mNumTimes + 0] = log((p0) / (1 - p0 - p1)); // log(p0);		// p0 -> x0
 
-    mVar[1] =
-        log((p1) / (1 - p0 - p1)); // log(p1);			// p1 -> x1
+    mVar[mNumTimes + 1] =  log((p1) / (1 - p0 - p1)); // log(p1);			// p1 -> x1
 #else
     if (p0 < 0 || p1 < 0 || (p0 + p1) < 1e-15)
       throw FastCodeMLFatal("Invalid p0 and p1 values");