Changes in src/molecule_geometry.cpp [a67d19:1614174]

File:

• src/molecule_geometry.cpp (modified) (15 diffs)

src/molecule_geometry.cpp

@@ -15 +15 @@
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
-#include "World.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -27 +26 @@
   bool status = true;
   const Vector *Center = DetermineCenterOfAll();
-  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -48 +46 @@
 {
   bool status = true;
-  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -104 +101 @@
 {
   int Num = 0;
-  atom *ptr = start;  // start at first in list
+  atom *ptr = start->next;  // start at first in list
 
   Center.Zero();
 
-  if (ptr->next != end) {   //list not empty?
+  if (ptr != end) {   //list not empty?
     while (ptr->next != end) {  // continue with second if present
       ptr = ptr->next;
@@ -229 +226 @@
 void molecule::TranslatePeriodically(const Vector *trans)
 {
-  double * const cell_size = World::get()->cell_size;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -256 +252 @@
 {
   atom *Walker = start;
-  double * const cell_size = World::get()->cell_size;
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
   double *inversematrix = InverseMatrix(cell_size);
@@ -280 +275 @@
               if ((fabs(tmp)) > BondDistance) {
                 flag = false;
-                DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
+                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.;
@@ -291 +286 @@
         Testvector.MatrixMultiplication(matrix);
         Center.AddVector(&Testvector);
-        DoLog(1) && (Log() << Verbose(1) << "vector is: ");
+        Log() << Verbose(1) << "vector is: ";
         Testvector.Output();
-        DoLog(0) && (Log() << Verbose(0) << endl);
+        Log() << Verbose(0) << endl;
 #ifdef ADDHYDROGEN
         // now also change all hydrogens
@@ -303 +298 @@
             Testvector.MatrixMultiplication(matrix);
             Center.AddVector(&Testvector);
-            DoLog(1) && (Log() << Verbose(1) << "Hydrogen vector is: ");
+            Log() << Verbose(1) << "Hydrogen vector is: ";
             Testvector.Output();
-            DoLog(0) && (Log() << Verbose(0) << endl);
+            Log() << Verbose(0) << endl;
           }
         }
@@ -352 +347 @@
   }
   // print InertiaTensor for debugging
-  DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
+  Log() << Verbose(0) << "The inertia tensor is:" << endl;
   for(int i=0;i<NDIM;i++) {
     for(int j=0;j<NDIM;j++)
-      DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
-    DoLog(0) && (Log() << Verbose(0) << endl);
-  }
-  DoLog(0) && (Log() << Verbose(0) << endl);
+      Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
+    Log() << Verbose(0) << endl;
+  }
+  Log() << Verbose(0) << endl;
 
   // diagonalize to determine principal axis system
@@ -370 +365 @@
 
   for(int i=0;i<NDIM;i++) {
-    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);
+    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;
   }
 
   // check whether we rotate or not
   if (DoRotate) {
-    DoLog(1) && (Log() << Verbose(1) << "Transforming molecule into PAS ... ");
+    Log() << Verbose(1) << "Transforming molecule into PAS ... ";
     // the eigenvectors specify the transformation matrix
     ActOnAllVectors( &Vector::MatrixMultiplication, (const double *) evec->data );
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+    Log() << Verbose(0) << "done." << endl;
 
     // summing anew for debugging (resulting matrix has to be diagonal!)
@@ -404 +399 @@
     }
     // print InertiaTensor for debugging
-    DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
+    Log() << Verbose(0) << "The inertia tensor is:" << endl;
     for(int i=0;i<NDIM;i++) {
       for(int j=0;j<NDIM;j++)
-        DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
-      DoLog(0) && (Log() << Verbose(0) << endl);
-    }
-    DoLog(0) && (Log() << Verbose(0) << endl);
+        Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
+      Log() << Verbose(0) << endl;
+    }
+    Log() << Verbose(0) << endl;
   }
 
@@ -433 +428 @@
 
   // rotate on z-x plane
-  DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
+  Log() << Verbose(0) << "Begin of Aligning all atoms." << endl;
   alpha = atan(-n->x[0]/n->x[2]);
-  DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
+  Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ";
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -451 +446 @@
   n->x[0] =  cos(alpha) * tmp +  sin(alpha) * n->x[2];
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
-  DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: ");
+  Log() << Verbose(1) << "alignment vector after first rotation: ";
   n->Output();
-  DoLog(0) && (Log() << Verbose(0) << endl);
+  Log() << Verbose(0) << endl;
 
   // rotate on z-y plane
   ptr = start;
   alpha = atan(-n->x[1]/n->x[2]);
-  DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
+  Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ";
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -475 +470 @@
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
 
-  DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: ");
+  Log() << Verbose(1) << "alignment vector after second rotation: ";
   n->Output();
-  DoLog(1) && (Log() << Verbose(1) << endl);
-  DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
+  Log() << Verbose(1) << endl;
+  Log() << Verbose(0) << "End of Aligning all atoms." << endl;
 };