Changes in src/atom.cpp [97b825:83f176]

File:

• src/atom.cpp (modified) (9 diffs)

src/atom.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /** \file atom.cpp
  *
@@ -4 +11 @@
  *
  */
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
 
 #include "Helpers/MemDebug.hpp"
@@ -168 +180 @@
 bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
 {
-  AtomNo[getType()->Z]++;  // increment number
+  AtomNo[getType()->getAtomicNumber()]++;  // 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 << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
@@ -194 +206 @@
 {
   if (out != NULL) {
-    *out << getType()->symbol << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
+    *out << getType()->getSymbol() << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
     return true;
   } else
@@ -209 +221 @@
 bool atom::OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const
 {
-  AtomNo[getType()->Z]++;
-  if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[getType()->Z] << "_" << AtomNo[getType()->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+  AtomNo[getType()->getAtomicNumber()]++;
+  if (out != NULL) {
+    *out << "Ion_Type" << ElementNo[getType()->getAtomicNumber()] << "_" << AtomNo[getType()->getAtomicNumber()] << "\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;
@@ -232 +244 @@
 {
   if (out != NULL) {
-    *out << getType()->symbol << "\t";
+    *out << getType()->getSymbol() << "\t";
     *out << Trajectory.R.at(step)[0] << "\t";
     *out << Trajectory.R.at(step)[1] << "\t";
@@ -250 +262 @@
   Vector recentered(getPosition());
   recentered -= *center;
-  *out << "\t\t" << getType()->symbol << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
+  *out << "\t\t" << getType()->getSymbol() << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
   if (AtomNo != NULL)
     *AtomNo++;
@@ -344 +356 @@
 }
 
+/** Makes the atom be contained in the new molecule \a *_mol.
+ * Uses atom::removeFromMolecule() to delist from old molecule.
+ * \param *_mol pointer to new molecule
+ */
 void atom::setMolecule(molecule *_mol){
   // take this atom from the old molecule
@@ -353 +369 @@
 }
 
-molecule* atom::getMolecule(){
+/** Returns pointer to the molecule which atom belongs to.
+ * \return containing molecule
+ */
+molecule* atom::getMolecule() const {
   return mol;
 }
 
+/** Erases the atom in atom::mol's list of atoms and sets it to zero.
+ */
 void atom::removeFromMolecule(){
   if(mol){