Changeset 543ce4 for molecuilder/src/molecule_geometry.cpp

Timestamp:

Nov 4, 2009, 7:56:04 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

4ef101, aa8542

Parents:

ec70ec

Message:

Huge change from ofstream * (const) out --> Log().

• first shift was done via regular expressions
• then via error messages from the code
• note that class atom, class element and class molecule kept in parts their output stream, was they print to file.
• make check runs fine
• MISSING: Verbosity is not fixed for everything (i.e. if no endl; is present and next has Verbose(0) ...)

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/molecule_geometry.cpp (modified) (23 diffs)

molecuilder/src/molecule_geometry.cpp

@@ -12 +12 @@
 #include "helpers.hpp"
 #include "leastsquaremin.hpp"
+#include "log.hpp"
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
@@ -21 +22 @@
  * \param *out output stream for debugging
  */
-bool molecule::CenterInBox(ofstream *out)
+bool molecule::CenterInBox()
 {
   bool status = true;
-  const Vector *Center = DetermineCenterOfAll(out);
+  const Vector *Center = DetermineCenterOfAll();
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = InverseMatrix(M);
@@ -42 +43 @@
  * \param *out output stream for debugging
  */
-bool molecule::BoundInBox(ofstream *out)
+bool molecule::BoundInBox()
 {
   bool status = true;
@@ -60 +61 @@
  * \param *max coordinates of other edge, specifying box dimensions.
  */
-void molecule::CenterEdge(ofstream *out, Vector *max)
+void molecule::CenterEdge(Vector *max)
 {
   Vector *min = new Vector;
 
-//  *out << Verbose(3) << "Begin of CenterEdge." << endl;
+//  Log() << Verbose(3) << "Begin of CenterEdge." << endl;
   atom *ptr = start->next;  // start at first in list
   if (ptr != end) {   //list not empty?
@@ -79 +80 @@
       }
     }
-//    *out << Verbose(4) << "Maximum is ";
+//    Log() << Verbose(4) << "Maximum is ";
 //    max->Output(out);
-//    *out << ", Minimum is ";
+//    Log() << Verbose(0) << ", Minimum is ";
 //    min->Output(out);
-//    *out << endl;
+//    Log() << Verbose(0) << endl;
     min->Scale(-1.);
     max->AddVector(min);
@@ -90 +91 @@
   }
   delete(min);
-//  *out << Verbose(3) << "End of CenterEdge." << endl;
+//  Log() << Verbose(3) << "End of CenterEdge." << endl;
 };
 
@@ -97 +98 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterOrigin(ofstream *out)
+void molecule::CenterOrigin()
 {
   int Num = 0;
@@ -117 +118 @@
 
 /** Returns vector pointing to center of all atoms.
- * \param *out output stream for debugging
  * \return pointer to center of all vector
  */
-Vector * molecule::DetermineCenterOfAll(ofstream *out) const
+Vector * molecule::DetermineCenterOfAll() const
 {
   atom *ptr = start->next;  // start at first in list
@@ -138 +138 @@
     a->Scale(1./Num); // divide through total mass (and sign for direction)
   }
-  //cout << Verbose(1) << "Resulting center of gravity: ";
-  //a->Output(out);
-  //cout << endl;
   return a;
 };
@@ -148 +145 @@
  * \return pointer to center of gravity vector
  */
-Vector * molecule::DetermineCenterOfGravity(ofstream *out)
+Vector * molecule::DetermineCenterOfGravity()
 {
   atom *ptr = start->next;  // start at first in list
@@ -167 +164 @@
     a->Scale(-1./Num); // divide through total mass (and sign for direction)
   }
-//  *out << Verbose(1) << "Resulting center of gravity: ";
+//  Log() << Verbose(1) << "Resulting center of gravity: ";
 //  a->Output(out);
-//  *out << endl;
+//  Log() << Verbose(0) << endl;
   return a;
 };
@@ -177 +174 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterPeriodic(ofstream *out)
+void molecule::CenterPeriodic()
 {
   DeterminePeriodicCenter(Center);
@@ -187 +184 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterAtVector(ofstream *out, Vector *newcenter)
+void molecule::CenterAtVector(Vector *newcenter)
 {
   Center.CopyVector(newcenter);
@@ -277 +274 @@
               if ((fabs(tmp)) > BondDistance) {
                 flag = false;
-                cout << 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.;
@@ -288 +285 @@
         Testvector.MatrixMultiplication(matrix);
         Center.AddVector(&Testvector);
-        cout << Verbose(1) << "vector is: ";
-        Testvector.Output((ofstream *)&cout);
-        cout << endl;
+        Log() << Verbose(1) << "vector is: ";
+        Testvector.Output();
+        Log() << Verbose(0) << endl;
 #ifdef ADDHYDROGEN
         // now also change all hydrogens
@@ -300 +297 @@
             Testvector.MatrixMultiplication(matrix);
             Center.AddVector(&Testvector);
-            cout << Verbose(1) << "Hydrogen vector is: ";
-            Testvector.Output((ofstream *)&cout);
-            cout << endl;
+            Log() << Verbose(1) << "Hydrogen vector is: ";
+            Testvector.Output();
+            Log() << Verbose(0) << endl;
           }
         }
@@ -318 +315 @@
  * TODO treatment of trajetories missing
  */
-void molecule::PrincipalAxisSystem(ofstream *out, bool DoRotate)
+void molecule::PrincipalAxisSystem(bool DoRotate)
 {
   atom *ptr = start;  // start at first in list
   double InertiaTensor[NDIM*NDIM];
-  Vector *CenterOfGravity = DetermineCenterOfGravity(out);
-
-  CenterPeriodic(out);
+  Vector *CenterOfGravity = DetermineCenterOfGravity();
+
+  CenterPeriodic();
 
   // reset inertia tensor
@@ -347 +344 @@
   }
   // print InertiaTensor for debugging
-  *out << "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++)
-      *out << InertiaTensor[i*NDIM+j] << " ";
-    *out << endl;
-  }
-  *out << endl;
+      Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
+    Log() << Verbose(0) << endl;
+  }
+  Log() << Verbose(0) << endl;
 
   // diagonalize to determine principal axis system
@@ -365 +362 @@
 
   for(int i=0;i<NDIM;i++) {
-    *out << Verbose(1) << "eigenvalue = " << gsl_vector_get(eval, i);
-    *out << ", 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) {
-    *out << 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 );
-    *out << "done." << endl;
+    Log() << Verbose(0) << "done." << endl;
 
     // summing anew for debugging (resulting matrix has to be diagonal!)
@@ -399 +396 @@
     }
     // print InertiaTensor for debugging
-    *out << "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++)
-        *out << InertiaTensor[i*NDIM+j] << " ";
-      *out << endl;
-    }
-    *out << endl;
+        Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ";
+      Log() << Verbose(0) << endl;
+    }
+    Log() << Verbose(0) << endl;
   }
 
@@ -428 +425 @@
 
   // rotate on z-x plane
-  cout << 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]);
-  cout << Verbose(1) << "Z-X-angle: " << alpha << " ... ";
+  Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ";
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -446 +443 @@
   n->x[0] =  cos(alpha) * tmp +  sin(alpha) * n->x[2];
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
-  cout << Verbose(1) << "alignment vector after first rotation: ";
-  n->Output((ofstream *)&cout);
-  cout << endl;
+  Log() << Verbose(1) << "alignment vector after first rotation: ";
+  n->Output();
+  Log() << Verbose(0) << endl;
 
   // rotate on z-y plane
   ptr = start;
   alpha = atan(-n->x[1]/n->x[2]);
-  cout << Verbose(1) << "Z-Y-angle: " << alpha << " ... ";
+  Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ";
   while (ptr->next != end) {
     ptr = ptr->next;
@@ -470 +467 @@
   n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
 
-  cout << Verbose(1) << "alignment vector after second rotation: ";
-  n->Output((ofstream *)&cout);
-  cout << Verbose(1) << endl;
-  cout << Verbose(0) << "End of Aligning all atoms." << endl;
+  Log() << Verbose(1) << "alignment vector after second rotation: ";
+  n->Output();
+  Log() << Verbose(1) << endl;
+  Log() << Verbose(0) << "End of Aligning all atoms." << endl;
 };