Changes in src/molecule_geometry.cpp [3930eb:a67d19]

File:

• src/molecule_geometry.cpp (modified) (14 diffs)

src/molecule_geometry.cpp

@@ -15 +15 @@
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
+#include "World.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -26 +27 @@
   bool status = true;
   const Vector *Center = DetermineCenterOfAll();
+  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -46 +48 @@
 {
   bool status = true;
+  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -226 +229 @@
 void molecule::TranslatePeriodically(const Vector *trans)
 {
+  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -252 +256 @@
 {
   atom *Walker = start;
+  double * const cell_size = World::get()->cell_size;
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
   double *inversematrix = InverseMatrix(cell_size);
@@ -275 +280 @@
               if ((fabs(tmp)) > BondDistance) {
                 flag = false;
-                Log() << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl;
+                DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
                 if (tmp > 0)
                   Translationvector.x[j] -= 1.;
@@ -286 +291 @@
         Testvector.MatrixMultiplication(matrix);
         Center.AddVector(&Testvector);
-        Log() << Verbose(1) << "vector is: ";
+        DoLog(1) && (Log() << Verbose(1) << "vector is: ");
         Testvector.Output();
-        Log() << Verbose(0) << endl;
+        DoLog(0) && (Log() << Verbose(0) << endl);
 #ifdef ADDHYDROGEN
         // now also change all hydrogens
@@ -298 +303 @@
             Testvector.MatrixMultiplication(matrix);
             Center.AddVector(&Testvector);
-            Log() << Verbose(1) << "Hydrogen vector is: ";
+            DoLog(1) && (Log() << Verbose(1) << "Hydrogen vector is: ");
             Testvector.Output();
-            Log() << Verbose(0) << endl;
+            DoLog(0) && (Log() << Verbose(0) << endl);
           }
         }
@@ -347 +352 @@
   }
   // print InertiaTensor for debugging
-  Log() << Verbose(0) << "The inertia tensor is:" << endl;
+  DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
   for(int i=0;i<NDIM;i++) {
     for(int j=0;j<NDIM;j++)
-      Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
-    Log() << Verbose(0) << endl;
-  }
-  Log() << Verbose(0) << endl;
+      DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
+    DoLog(0) && (Log() << Verbose(0) << endl);
+  }
+  DoLog(0) && (Log() << Verbose(0) << endl);
 
   // diagonalize to determine principal axis system
@@ -365 +370 @@
 
   for(int i=0;i<NDIM;i++) {
-    Log() << Verbose(1) << "eigenvalue = " << gsl_vector_get(eval, i);
-    Log() << Verbose(0) << ", eigenvector = (" << evec->data[i * evec->tda + 0] << "," << evec->data[i * evec->tda + 1] << "," << evec->data[i * evec->tda + 2] << ")" << endl;
+    DoLog(1) && (Log() << Verbose(1) << "eigenvalue = " << gsl_vector_get(eval, i));
+    DoLog(0) && (Log() << Verbose(0) << ", eigenvector = (" << evec->data[i * evec->tda + 0] << "," << evec->data[i * evec->tda + 1] << "," << evec->data[i * evec->tda + 2] << ")" << endl);
   }
 
   // check whether we rotate or not
   if (DoRotate) {
-    Log() << Verbose(1) << "Transforming molecule into PAS ... ";
+    DoLog(1) && (Log() << Verbose(1) << "Transforming molecule into PAS ... ");
     // the eigenvectors specify the transformation matrix
     ActOnAllVectors( &Vector::MatrixMultiplication, (const double *) evec->data );
-    Log() << Verbose(0) << "done." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
 
     // summing anew for debugging (resulting matrix has to be diagonal!)
@@ -399 +404 @@
     }
     // print InertiaTensor for debugging
-    Log() << Verbose(0) << "The inertia tensor is:" << endl;
+    DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
     for(int i=0;i<NDIM;i++) {
       for(int j=0;j<NDIM;j++)
-        Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
-      Log() << Verbose(0) << endl;
-    }
-    Log() << Verbose(0) << endl;
+        DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
+      DoLog(0) && (Log() << Verbose(0) << endl);
+    }
+    DoLog(0) && (Log() << Verbose(0) << endl);
   }
 
@@ -428 +433 @@
 
   // rotate on z-x plane
-  Log() << Verbose(0) << "Begin of Aligning all atoms." << endl;
+  DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
   alpha = atan(-n->x[0]/n->x[2]);
-  Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ";
+  DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -446 +451 @@
   n->x[0] =  cos(alpha) * tmp +  sin(alpha) * n->x[2];
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
-  Log() << Verbose(1) << "alignment vector after first rotation: ";
+  DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: ");
   n->Output();
-  Log() << Verbose(0) << endl;
+  DoLog(0) && (Log() << Verbose(0) << endl);
 
   // rotate on z-y plane
   ptr = start;
   alpha = atan(-n->x[1]/n->x[2]);
-  Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ";
+  DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -470 +475 @@
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
 
-  Log() << Verbose(1) << "alignment vector after second rotation: ";
+  DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: ");
   n->Output();
-  Log() << Verbose(1) << endl;
-  Log() << Verbose(0) << "End of Aligning all atoms." << endl;
+  DoLog(1) && (Log() << Verbose(1) << endl);
+  DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
 };