Changes in src/atom.cpp [2fe971:97b825]

File:

• src/atom.cpp (modified) (14 diffs)

src/atom.cpp

@@ -13 +13 @@
 #include "lists.hpp"
 #include "parser.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
 #include "molecule.hpp"
@@ -27 +27 @@
  */
 atom::atom() :
-  father(this), sort(&nr), mol(0)
-{
-  node = &x;  // TesselPoint::x can only be referenced from here
-};
+  father(this),
+  sort(&nr),
+  mol(0)
+{};
 
 /** Constructor of class atom.
  */
 atom::atom(atom *pointer) :
-    ParticleInfo(pointer),father(pointer), sort(&nr)
-{
-  type = pointer->type;  // copy element of atom
-  x = pointer->x; // copy coordination
-  v = pointer->v; // copy velocity
+    ParticleInfo(pointer),
+    father(pointer),
+    sort(&nr)
+{
+  setType(pointer->getType());  // copy element of atom
+  setPosition(pointer->getPosition()); // copy coordination
+  AtomicVelocity = pointer->AtomicVelocity; // copy velocity
   FixedIon = pointer->FixedIon;
-  node = &x;
   mol = 0;
 };
@@ -49 +50 @@
   res->father = this;
   res->sort = &res->nr;
-  res->type = type;
-  res->x = this->x;
-  res->v = this->v;
+  res->setType(getType());
+  res->setPosition(this->getPosition());
+  res->AtomicVelocity = this->AtomicVelocity;
   res->FixedIon = FixedIon;
-  res->node = &x;
   res->mol = 0;
   World::getInstance().registerAtom(res);
@@ -121 +121 @@
 bool atom::IsInShape(const Shape& shape) const
 {
-  return shape.isInside(*node);
+  return shape.isInside(getPosition());
 };
 
@@ -146 +146 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x[0] << "\t" << x[1] << "\t" << x[2];
+    *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
+    if (AtomicVelocity.Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -168 +168 @@
 bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
 {
-  AtomNo[type->Z]++;  // increment number
-  if (out != NULL) {
-    cout << "Looking for atom with element " << *type << endl;
-    ASSERT(elementLookup.there.find(type)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
-    *out << "Ion_Type" << elementLookup.there.find(type)->second << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x[0] << "\t" << x[1] << "\t" << x[2];
+  AtomNo[getType()->Z]++;  // increment number
+  if (out != NULL) {
+    const element *elemental = getType();
+    cout << "Looking for atom with element " << *elemental << endl;
+    ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
+    *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+    *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
+    if (AtomicVelocity.Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -193 +194 @@
 {
   if (out != NULL) {
-    *out << type->getSymbol() << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
+    *out << getType()->symbol << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
     return true;
   } else
@@ -208 +209 @@
 bool atom::OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const
 {
-  AtomNo[type->Z]++;
-  if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+  AtomNo[getType()->Z]++;
+  if (out != NULL) {
+    *out << "Ion_Type" << ElementNo[getType()->Z] << "_" << AtomNo[getType()->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
     *out << "\t" << FixedIon;
@@ -231 +232 @@
 {
   if (out != NULL) {
-    *out << type->getSymbol() << "\t";
+    *out << getType()->symbol << "\t";
     *out << Trajectory.R.at(step)[0] << "\t";
     *out << Trajectory.R.at(step)[1] << "\t";
@@ -247 +248 @@
 void atom::OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo = NULL) const
 {
-  *out << "\t\t" << type->getSymbol() << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;
+  Vector recentered(getPosition());
+  recentered -= *center;
+  *out << "\t\t" << getType()->symbol << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
   if (AtomNo != NULL)
     *AtomNo++;
@@ -270 +273 @@
 double atom::DistanceSquaredToVector(const Vector &origin) const
 {
-  return origin.DistanceSquared(x);
+  return DistanceSquared(origin);
 };
 
@@ -279 +282 @@
 double atom::DistanceToVector(const Vector &origin) const
 {
-  return origin.distance(x);
+  return distance(origin);
 };
 
@@ -294 +297 @@
 };
 
+std::ostream & atom::operator << (std::ostream &ost) const
+{
+  ParticleInfo::operator<<(ost);
+  ost << "," << getPosition();
+  return ost;
+}
+
+std::ostream & operator << (std::ostream &ost, const atom &a)
+{
+  a.ParticleInfo::operator<<(ost);
+  ost << "," << a.getPosition();
+  return ost;
+}
 
 bool operator < (atom &a, atom &b)
@@ -333 +349 @@
   mol = _mol;
   if(!mol->containsAtom(this)){
-    mol->AddAtom(this);
+    mol->insert(this);
   }
 }