source: src/atom.cpp@ 10f641

/** \file atom.cpp
 * 
 * Function implementations for the class atom.
 * 
 */

#include "molecules.hpp"
 
/************************************* Functions for class atom *************************************/

/** Constructor of class atom.
 */
atom::atom() 
{
        Name = NULL;
  previous = NULL;
  next = NULL;
  father = this;  // generally, father is itself
  Ancestor = NULL;
  type = NULL;
  sort = NULL;
  FixedIon = 0;
  nr = -1;
  GraphNr = -1;
  ComponentNr = NULL;
  SeparationVertex = false;
  LowpointNr = -1;
};

/** Destructor of class atom.
 */
atom::~atom() 
{
        Free((void **)&Name, "atom::~atom: *Name");
  Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
};


/** Climbs up the father list until NULL, last is returned.
 * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
 */
atom *atom::GetTrueFather()
{
  atom *walker = this;
  do {
    if (walker == walker->father) // top most father is the one that points on itself
      break;
    walker = walker->father;
  } while (walker != NULL);
  return walker;
};

/** Output of a single atom.
 * \param ElementNo cardinal number of the element
 * \param AtomNo cardinal number among these atoms of the same element
 * \param *out stream to output to
 */
bool atom::Output(int ElementNo, int AtomNo, ofstream *out) const
{
  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 << "\t" << FixedIon;
    if (v.Norm() > MYEPSILON)
      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
    *out << " # 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
 */
bool atom::OutputXYZLine(ofstream *out) const
{
  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;
};

ostream & operator << (ostream &ost, atom &a) 
{
  ost << "[" << a.Name << "|" << &a << "]";
  return ost;
};

/** Compares the indices of \a this atom with a given \a ptr.
 * \param ptr atom to compare index against
 * \return true - this one's is smaller, false - not
 */ 
bool atom::Compare(atom &ptr)
{
  if (nr < ptr.nr)
    return true;
  else
    return false;
};

bool operator < (atom &a, atom &b) 
{
  return a.Compare(b);
};

/******************************** Functions for class AtomStackClass ********************************/

/** Constructor of class AtomStackClass.
 */
AtomStackClass::AtomStackClass(int dimension)
{
  CurrentLastEntry = 0;
  CurrentFirstEntry = 0;
  NextFreeField = 0;
  EntryCount = dimension;
  StackList = (atom **) Malloc(sizeof(atom *)*EntryCount, "AtomStackClass::AtomStackClass: **StackList");
};

/** Destructor of class AtomStackClass.
 */
AtomStackClass::~AtomStackClass()
{
  Free((void **)&StackList, "AtomStackClass::AtomStackClass: **StackList");
};

/** Pushes an object onto the stack.
 * \param *object atom to be pushed on stack
 * \return true - sucess, false - failure, meaning stack field was occupied
 */
bool AtomStackClass::Push(atom *object)
{
  if (!IsFull()) {    // check whether free field is really not occupied
    StackList[NextFreeField] = object;
    CurrentLastEntry = NextFreeField;
    NextFreeField = (NextFreeField + 1) % EntryCount; // step on to next free field
    return true;
  } else {
    cerr << "ERROR: Stack is full, " << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tNextFreeField " << NextFreeField << "\tEntryCount " << EntryCount << "!" << endl;
    return false;
  }
};

/** Pops first/oldest atom from stack.
 * First in, last out.
 * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
 */
atom *AtomStackClass::PopFirst()
{
  atom *Walker = NULL;
  if (!IsEmpty()) {
    Walker = StackList[CurrentFirstEntry];
    if (Walker == NULL)
      cerr << "ERROR: Stack's field is empty!" << endl;
    StackList[CurrentFirstEntry] = NULL;
    if (CurrentFirstEntry != CurrentLastEntry) { // hasn't last item been popped as well?
      CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
    } else {
      CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
      CurrentLastEntry = CurrentFirstEntry;
    }
  } else
    cerr << "ERROR: Stack is empty!" << endl; 
  return Walker;
};

/** Pops last atom from stack.
 * First in, first out.
 * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
 */
atom *AtomStackClass::PopLast()
{
  atom *Walker = NULL;
  if (!IsEmpty()) {
    Walker = StackList[CurrentLastEntry];
    StackList[CurrentLastEntry] = NULL;
    if (Walker == NULL)
      cerr << "ERROR: Stack's field is empty!" << endl;
    NextFreeField = CurrentLastEntry;
    if (CurrentLastEntry != CurrentFirstEntry)  // has there been more than one item on stack
      CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount; // step back from current free field to last (modulo does not work in -1, thus go EntryCount-1 instead)
  } else {
    cerr << "ERROR: Stack is empty!" << endl;
  } 
  return Walker;
};

/** Removes a certain item from the stack.
 * Item is seeked between \a CurrentFirstEntry and \a CurrentLastEntry, if found, place in stack is NULL'd and
 * all subsequent items shifted by one position downward (with wrapping taken into account).
 * \param *ptr adress of item
 * \return true - item was removed, false - item was not found
 */
bool AtomStackClass::RemoveItem(atom *ptr)
{
  bool found = false;
  cout << Verbose(5) << "First " << CurrentFirstEntry<< "\tLast " << CurrentLastEntry<< "\tNext " << NextFreeField<< "\tCount " << EntryCount<< "." << endl;
  int i=CurrentFirstEntry;
  if (!IsEmpty())
    do {
      if (StackList[i] == ptr) {  // if item found, remove
        cout << Verbose(5) << "Item " << *ptr << " was number " << i << " on stack, removing it." << endl;
        found = true;
        StackList[i] = NULL;
      }
      if ((found) && (StackList[i] != NULL)) {  // means we have to shift (and not the removed item)
        if (i == 0) { // we are down to first item in stack, have to put onto last item
          cout << Verbose(5) << "Shifting item 0 to place " << EntryCount-1 << "." << endl;
          StackList[EntryCount-1] = StackList[0];
        } else {
          cout << Verbose(5) << "Shifting item " << i << " to place " << i-1 << "." << endl;
          StackList[i-1] = StackList[i];
        }
      }
      i=((i + 1) % EntryCount); // step on
    } while (i!=NextFreeField);
  else
    cerr << "ERROR: Stack is already empty!" << endl;
  if (found) {
    NextFreeField = CurrentLastEntry;
    if (CurrentLastEntry != CurrentFirstEntry)  // has there been more than one item on stack
      CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount;
  }
  return found;
};

/** Test the functionality of the stack.
 * \param *out ofstream for debugging
 * \param *test one item to put on stack  
 * \return true - all tests worked correctly
 */
void AtomStackClass::TestImplementation(ofstream *out, atom *test)
{
  atom *Walker = test;
  *out << Verbose(1) << "Testing the snake stack..." << endl;
  for (int i=0;i<EntryCount;i++) {
    *out << Verbose(2) << "Filling " << i << "th element of stack." << endl; 
    Push(Walker);
    Walker=Walker->next;
  }
  *out << endl;
  Output(out);
  if (IsFull())
    *out << "Stack is full as supposed to be!" << endl;
  else
    *out << "ERROR: Stack is not as full as supposed to be!" << endl;
  //if (StackList[(EntryCount+1)/2] != NULL) {
    *out << "Removing element in the middle ..." << endl;
    RemoveItem(StackList[(EntryCount+1)/2]);
    Output(out);
  //}
  //if (StackList[CurrentFirstEntry] != NULL) {
    *out << "Removing first element  ..." << endl;
    RemoveItem(StackList[CurrentFirstEntry]);
    Output(out);
  //}
  //if (StackList[CurrentLastEntry] != NULL) {
    *out << "Removing last element ..." << endl;
    RemoveItem(StackList[CurrentLastEntry]);
    Output(out);
  //}
  *out << "Clearing stack ... " << endl;  
  ClearStack();
  Output(out);
  if (IsEmpty())
    *out << "Stack is empty as supposed to be!" << endl;
  else
    *out << "ERROR: Stack is not as empty as supposed to be!" << endl;
  *out << "done." << endl;
};

/** Puts contents of stack into ofstream \a *out.
 * \param *out ofstream for output
 */
void AtomStackClass::Output(ofstream *out) const
{
  *out << "Contents of Stack: ";
  for(int i=0;i<EntryCount;i++) {
    *out << "\t";
    if (i == CurrentFirstEntry)
      *out << " 1";
    if  (i == CurrentLastEntry)
      *out << " "<< EntryCount;
    if (i ==  NextFreeField)
      *out << " F";
    *out << ": " << StackList[i];
  }
  *out << endl;
};

/** Checks whether stack is empty.
 * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
 * AtomStackClass::CurrentFirstEntry is equal to AtomStackClass::CurrentLastEntry.
 * \return true - empty, false - not
 */
bool AtomStackClass::IsEmpty()
{
  return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry == CurrentFirstEntry));
};

/** Checks whether stack is full.
 * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
 * AtomStackClass::CurrentFirstEntry is _not_ equal to AtomStackClass::CurrentLastEntry.
 * \return true - full, false - not
 */
bool AtomStackClass::IsFull()
{
  return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry != CurrentFirstEntry));
};

/** Returns number of items on stack.
 * Simply returns difference between AtomStackClass::Stacklist entry AtomStackClass::CurrentEntry-1.
 * \return number of items on stack
 * \warning will never return correct item count if stack is full, i.e. count would be AtomStackClass::EntryCount.
 */
int AtomStackClass::ItemCount()
{
  //cout << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tEntryCount " << EntryCount << "." << endl;
  return((NextFreeField + (EntryCount - CurrentFirstEntry)) % EntryCount);
};

/** Clears the stack from all atoms.
 * \return true - sucess, false - failure
 */
void AtomStackClass::ClearStack()
{
  for(int i=0;i<EntryCount; i++)
    StackList[i] = NULL;
  CurrentFirstEntry = 0;
  CurrentLastEntry = 0;
  NextFreeField = 0;
};