Changeset 0d111b for molecuilder/src/atom.cpp

Timestamp:

Apr 29, 2010, 1:55:21 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Children:

070651, 5d1a94

Parents:

90c4460 (diff), 32842d8 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp

File:

• molecuilder/src/atom.cpp (modified) (10 diffs)

molecuilder/src/atom.cpp

@@ -33 +33 @@
 {
   type = pointer->type;  // copy element of atom
-  x.CopyVector(&pointer->x); // copy coordination
-  v.CopyVector(&pointer->v); // copy velocity
+  x = pointer->x; // copy coordination
+  v = pointer->v; // copy velocity
   FixedIon = pointer->FixedIon;
   node = &x;
@@ -46 +46 @@
   res->sort = &res->nr;
   res->type = type;
-  res->x.CopyVector(&this->x);
-  res->v.CopyVector(&this->v);
+  res->x = this->x;
+  res->v = this->v;
   res->FixedIon = FixedIon;
   res->node = &x;
@@ -130 +130 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
+    *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;
     if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -155 +155 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
+    *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;
     if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -175 +175 @@
 {
   if (out != NULL) {
-    *out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
+    *out << type->symbol << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
     return true;
   } else
@@ -193 +193 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << Trajectory.R.at(step).x[0] << "\t" << Trajectory.R.at(step).x[1] << "\t" << Trajectory.R.at(step).x[2];
+    *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
     *out << "\t" << FixedIon;
     if (Trajectory.U.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step).x[0] << "\t" << Trajectory.U.at(step).x[1] << "\t" << Trajectory.U.at(step).x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step)[0] << "\t" << Trajectory.U.at(step)[1] << "\t" << Trajectory.U.at(step)[2] << "\t";
     if (Trajectory.F.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step).x[0] << "\t" << Trajectory.F.at(step).x[1] << "\t" << Trajectory.F.at(step).x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step)[0] << "\t" << Trajectory.F.at(step)[1] << "\t" << Trajectory.F.at(step)[2] << "\t";
     *out << "\t# Number in molecule " << nr << endl;
     return true;
@@ -214 +214 @@
   if (out != NULL) {
     *out << type->symbol << "\t";
-    *out << Trajectory.R.at(step).x[0] << "\t";
-    *out << Trajectory.R.at(step).x[1] << "\t";
-    *out << Trajectory.R.at(step).x[2] << endl;
+    *out << Trajectory.R.at(step)[0] << "\t";
+    *out << Trajectory.R.at(step)[1] << "\t";
+    *out << Trajectory.R.at(step)[2] << endl;
     return true;
   } else
@@ -229 +229 @@
 void atom::OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo = NULL) const
 {
-  *out << "\t\t" << type->symbol << " [ " << x.x[0]-center->x[0] << "\t" << x.x[1]-center->x[1] << "\t" << x.x[2]-center->x[2] << " ]" << endl;
+  *out << "\t\t" << type->symbol << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;
   if (AtomNo != NULL)
     *AtomNo++;
@@ -252 +252 @@
 double atom::DistanceSquaredToVector(const Vector &origin) const
 {
-  return origin.DistanceSquared(&x);
+  return origin.DistanceSquared(x);
 };
 
@@ -261 +261 @@
 double atom::DistanceToVector(const Vector &origin) const
 {
-  return origin.Distance(&x);
+  return origin.Distance(x);
 };