Changes in src/atom.cpp [2fe971:57f243]

File:

• src/atom.cpp (modified) (7 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"
@@ -19 +19 @@
 
 #include <iomanip>
-#include <iostream>
 
 /************************************* Functions for class atom *************************************/
@@ -110 +109 @@
 };
 
-bool atom::isFather(const atom *ptr){
-  return ptr==father;
-}
-
 /** Checks whether atom is within the given box.
  * \param offset offset to box origin
@@ -166 +161 @@
   * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
+bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, 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 << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;
@@ -193 +186 @@
 {
   if (out != NULL) {
-    *out << type->getSymbol() << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
+    *out << type->symbol << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
     return true;
   } else
@@ -231 +224 @@
 {
   if (out != NULL) {
-    *out << type->getSymbol() << "\t";
+    *out << type->symbol << "\t";
     *out << Trajectory.R.at(step)[0] << "\t";
     *out << Trajectory.R.at(step)[1] << "\t";
@@ -247 +240 @@
 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;
+  *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++;