Changes in src/atom.cpp [49f802c:d3dfe18]

File:

• src/atom.cpp (modified) (7 diffs, 1 prop)

src/atom.cpp

@@ -6 +6 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "element.hpp"
 #include "memoryallocator.hpp"
-#include "vector.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -65 +62 @@
 atom::~atom()
 {
-  Free<int>(&ComponentNr, "atom::~atom: *ComponentNr");
-  Free<char>(&Name, "atom::~atom: *Name");
-  Trajectory.R.clear();
-  Trajectory.U.clear();
-  Trajectory.F.clear();
+  Free(&ComponentNr);
 };
 
@@ -87 +80 @@
 };
 
-/** Sets father to itself or its father in case of copying a molecule.
- */
-void atom::CorrectFather()
-{
-  if (father->father == father)   // same atom in copy's father points to itself
-    father = this;  // set father to itself (copy of a whole molecule)
-  else
-   father = father->father;  // set father to original's father
-
-};
-
-/** Check whether father is equal to given atom.
- * \param *ptr atom to compare father to
- * \param **res return value (only set if atom::father is equal to \a *ptr)
- */
-void atom::EqualsFather ( atom *ptr, atom **res )
-{
-  if ( ptr == father )
-    *res = this;
-};
-
-/** Checks whether atom is within the given box.
- * \param offset offset to box origin
- * \param *parallelepiped box matrix
- * \return true - is inside, false - is not
- */
-bool atom::IsInParallelepiped(Vector offset, double *parallelepiped)
-{
-  return (node->IsInParallelepiped(offset, parallelepiped));
-};
-
 /** Output of a single atom.
  * \param ElementNo cardinal number of the element
@@ -123 +85 @@
  * \param *out stream to output to
  * \param *comment commentary after '#' sign
-  * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::Output(ofstream *out, int ElementNo, int AtomNo, const char *comment) const
+bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
 {
   if (out != NULL) {
@@ -141 +102 @@
     return false;
 };
-bool atom::Output(ofstream *out, int *ElementNo, int *AtomNo, const char *comment)
-{
-  AtomNo[type->Z]++;  // increment number
-  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 << "\t" << FixedIon;
-    if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
-    if (comment != NULL)
-      *out << " # " << comment << endl;
-    else
-      *out << " # molecule nr " << nr << endl;
-    return true;
-  } else
-    return false;
-};
 
 /** Output of a single atom as one lin in xyz file.
  * \param *out stream to output to
-  * \return true - \a *out present, false - \a *out is NULL
  */
 bool atom::OutputXYZLine(ofstream *out) const
@@ -167 +110 @@
   if (out != NULL) {
     *out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
-    return true;
-  } else
-    return false;
-};
-
-/** Output of a single atom as one lin in xyz file.
- * \param *out stream to output to
- * \param *ElementNo array with ion type number in the config file this atom's element shall have
- * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
- * \param step Trajectory time step to output
-  * \return true - \a *out present, false - \a *out is NULL
- */
-bool atom::OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const
-{
-  AtomNo[type->Z]++;
-  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 << "\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";
-    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# Number in molecule " << nr << endl;
-    return true;
-  } else
-    return false;
-};
-
-/** Output of a single atom as one lin in xyz file.
- * \param *out stream to output to
- * \param step Trajectory time step to output
- * \return true - \a *out present, false - \a *out is NULL
- */
-bool atom::OutputTrajectoryXYZ(ofstream *out, int step) const
-{
-  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;
-    return true;
-  } else
-    return false;
-};
-
-/** Prints all bonds of this atom from given global lists.
- * \param *out stream to output to
- * \param *NumberOfBondsPerAtom array with number of bonds per atomic index
- * \param ***ListOfBondsPerAtom array per atomic index of array with pointer to bond
- * \return true - \a *out present, false - \a *out is NULL
- */
-bool atom::OutputBondOfAtom(ofstream *out, int *NumberOfBondsPerAtom, bond ***ListOfBondsPerAtom) const
-{
-  if (out != NULL) {
-#ifdef ADDHYDROGEN
-    if (type->Z != 1) {   // regard only non-hydrogen
-#endif
-      *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << NumberOfBondsPerAtom[nr] << " bonds: ";
-      int TotalDegree = 0;
-      for (int j=0;j<NumberOfBondsPerAtom[nr];j++) {
-        *out << *ListOfBondsPerAtom[nr][j] << "\t";
-        TotalDegree += ListOfBondsPerAtom[nr][j]->BondDegree;
-      }
-      *out << " -- TotalDegree: " << TotalDegree << endl;
-#ifdef ADDHYDROGEN
-    }
-#endif
     return true;
   } else
@@ -264 +139 @@
 };
 
-/** Returns squared distance to a given vector.
- * \param origin vector to calculate distance to
- * \return distance squared
- */
-double atom::DistanceSquaredToVector(Vector &origin)
-{
-  return origin.DistanceSquared(&x);
-};
-
-/** Adds kinetic energy of this atom to given temperature value.
- * \param *temperature add on this value
- * \param step given step of trajectory to add
- */
-void atom::AddKineticToTemperature(double *temperature, int step) const
-{
-  for (int i=NDIM;i--;)
-    *temperature += type->mass * Trajectory.U.at(step).x[i]* Trajectory.U.at(step).x[i];
-};
-
-/** Returns distance to a given vector.
- * \param origin vector to calculate distance to
- * \return distance
- */
-double atom::DistanceToVector(Vector &origin)
-{
-  return origin.Distance(&x);
-};
-
 bool operator < (atom &a, atom &b)
 {