| 1 | /** \file atom.cpp
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| 2 | *
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| 3 | * Function implementations for the class atom.
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| 4 | *
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| 5 | */
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| 6 |
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| 7 | #include "molecules.hpp"
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| 8 |
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| 9 | /************************************* Functions for class atom *************************************/
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| 10 |
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| 11 | /** Constructor of class atom.
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| 12 | */
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| 13 | atom::atom()
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| 14 | {
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| 15 | Name = NULL;
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| 16 | previous = NULL;
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| 17 | next = NULL;
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| 18 | father = this; // generally, father is itself
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| 19 | Ancestor = NULL;
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| 20 | type = NULL;
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| 21 | sort = NULL;
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| 22 | nr = -1;
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| 23 | GraphNr = -1;
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| 24 | ComponentNr = NULL;
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| 25 | SeparationVertex = false;
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| 26 | LowpointNr = -1;
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| 27 | };
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| 28 |
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| 29 | /** Destructor of class atom.
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| 30 | */
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| 31 | atom::~atom()
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| 32 | {
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| 33 | Free((void **)&Name, "atom::~atom: *Name");
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| 34 | Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
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| 35 | };
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| 36 |
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| 37 |
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| 38 | /** Climbs up the father list until NULL, last is returned.
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| 39 | * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
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| 40 | */
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| 41 | atom *atom::GetTrueFather()
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| 42 | {
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| 43 | atom *walker = this;
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| 44 | do {
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| 45 | if (walker == walker->father) // top most father is the one that points on itself
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| 46 | break;
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| 47 | walker = walker->father;
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| 48 | } while (walker != NULL);
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| 49 | return walker;
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| 50 | };
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| 51 |
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| 52 | /** Output of a single atom.
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| 53 | * \param ElementNo cardinal number of the element
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| 54 | * \param AtomNo cardinal number among these atoms of the same element
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| 55 | * \param *out stream to output to
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| 56 | */
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| 57 | bool atom::Output(int ElementNo, int AtomNo, ofstream *out) const
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| 58 | {
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| 59 | if (out != NULL) {
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| 60 | *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t" << fixed << setprecision(9) << showpoint;
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| 61 | *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t";
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| 62 | *out << "\t" << "0\t# Number in molecule " << nr << endl;
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| 63 | return true;
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| 64 | } else
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| 65 | return false;
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| 66 | };
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| 67 |
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| 68 | /** Output of a single atom as one lin in xyz file.
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| 69 | * \param *out stream to output to
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| 70 | */
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| 71 | bool atom::OutputXYZLine(ofstream *out) const
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| 72 | {
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| 73 | if (out != NULL) {
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| 74 | *out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
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| 75 | return true;
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| 76 | } else
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| 77 | return false;
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| 78 | };
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| 79 |
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| 80 | ostream & operator << (ostream &ost, atom &a)
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| 81 | {
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| 82 | ost << "[" << a.Name << "|" << &a << "]";
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| 83 | return ost;
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| 84 | };
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| 85 |
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| 86 | /** Compares the indices of \a this atom with a given \a ptr.
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| 87 | * \param ptr atom to compare index against
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| 88 | * \return true - this one's is smaller, false - not
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| 89 | */
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| 90 | bool atom::Compare(atom &ptr)
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| 91 | {
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| 92 | if (nr < ptr.nr)
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| 93 | return true;
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| 94 | else
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| 95 | return false;
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| 96 | };
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| 97 |
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| 98 | bool operator < (atom &a, atom &b)
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| 99 | {
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| 100 | return a.Compare(b);
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| 101 | };
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| 102 |
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| 103 | /******************************** Functions for class AtomStackClass ********************************/
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| 104 |
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| 105 | /** Constructor of class AtomStackClass.
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| 106 | */
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| 107 | AtomStackClass::AtomStackClass(int dimension)
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| 108 | {
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| 109 | CurrentLastEntry = 0;
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| 110 | CurrentFirstEntry = 0;
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| 111 | NextFreeField = 0;
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| 112 | EntryCount = dimension;
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| 113 | StackList = (atom **) Malloc(sizeof(atom *)*EntryCount, "AtomStackClass::AtomStackClass: **StackList");
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| 114 | };
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| 115 |
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| 116 | /** Destructor of class AtomStackClass.
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| 117 | */
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| 118 | AtomStackClass::~AtomStackClass()
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| 119 | {
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| 120 | Free((void **)&StackList, "AtomStackClass::AtomStackClass: **StackList");
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| 121 | };
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| 122 |
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| 123 | /** Pushes an object onto the stack.
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| 124 | * \param *object atom to be pushed on stack
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| 125 | * \return true - sucess, false - failure, meaning stack field was occupied
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| 126 | */
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| 127 | bool AtomStackClass::Push(atom *object)
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| 128 | {
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| 129 | if (!IsFull()) { // check whether free field is really not occupied
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| 130 | StackList[NextFreeField] = object;
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| 131 | CurrentLastEntry = NextFreeField;
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| 132 | NextFreeField = (NextFreeField + 1) % EntryCount; // step on to next free field
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| 133 | return true;
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| 134 | } else {
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| 135 | cerr << "ERROR: Stack is full, " << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tNextFreeField " << NextFreeField << "\tEntryCount " << EntryCount << "!" << endl;
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| 136 | return false;
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| 137 | }
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| 138 | };
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| 139 |
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| 140 | /** Pops first/oldest atom from stack.
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| 141 | * First in, last out.
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| 142 | * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
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| 143 | */
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| 144 | atom *AtomStackClass::PopFirst()
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| 145 | {
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| 146 | atom *Walker = NULL;
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| 147 | if (!IsEmpty()) {
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| 148 | Walker = StackList[CurrentFirstEntry];
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| 149 | if (Walker == NULL)
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| 150 | cerr << "ERROR: Stack's field is empty!" << endl;
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| 151 | StackList[CurrentFirstEntry] = NULL;
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| 152 | if (CurrentFirstEntry != CurrentLastEntry) { // hasn't last item been popped as well?
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| 153 | CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
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| 154 | } else {
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| 155 | CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
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| 156 | CurrentLastEntry = CurrentFirstEntry;
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| 157 | }
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| 158 | } else
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| 159 | cerr << "ERROR: Stack is empty!" << endl;
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| 160 | return Walker;
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| 161 | };
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| 162 |
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| 163 | /** Pops last atom from stack.
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| 164 | * First in, first out.
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| 165 | * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
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| 166 | */
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| 167 | atom *AtomStackClass::PopLast()
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| 168 | {
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| 169 | atom *Walker = NULL;
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| 170 | if (!IsEmpty()) {
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| 171 | Walker = StackList[CurrentLastEntry];
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| 172 | StackList[CurrentLastEntry] = NULL;
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| 173 | if (Walker == NULL)
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| 174 | cerr << "ERROR: Stack's field is empty!" << endl;
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| 175 | NextFreeField = CurrentLastEntry;
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| 176 | if (CurrentLastEntry != CurrentFirstEntry) // has there been more than one item on stack
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| 177 | CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount; // step back from current free field to last (modulo does not work in -1, thus go EntryCount-1 instead)
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| 178 | } else {
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| 179 | cerr << "ERROR: Stack is empty!" << endl;
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| 180 | }
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| 181 | return Walker;
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| 182 | };
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| 183 |
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| 184 | /** Removes a certain item from the stack.
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| 185 | * Item is seeked between \a CurrentFirstEntry and \a CurrentLastEntry, if found, place in stack is NULL'd and
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| 186 | * all subsequent items shifted by one position downward (with wrapping taken into account).
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| 187 | * \param *ptr adress of item
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| 188 | * \return true - item was removed, false - item was not found
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| 189 | */
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| 190 | bool AtomStackClass::RemoveItem(atom *ptr)
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| 191 | {
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| 192 | bool found = false;
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| 193 | cout << Verbose(5) << "First " << CurrentFirstEntry<< "\tLast " << CurrentLastEntry<< "\tNext " << NextFreeField<< "\tCount " << EntryCount<< "." << endl;
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| 194 | int i=CurrentFirstEntry;
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| 195 | if (!IsEmpty())
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| 196 | do {
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| 197 | if (StackList[i] == ptr) { // if item found, remove
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| 198 | cout << Verbose(5) << "Item " << *ptr << " was number " << i << " on stack, removing it." << endl;
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| 199 | found = true;
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| 200 | StackList[i] = NULL;
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| 201 | }
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| 202 | if ((found) && (StackList[i] != NULL)) { // means we have to shift (and not the removed item)
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| 203 | if (i == 0) { // we are down to first item in stack, have to put onto last item
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| 204 | cout << Verbose(5) << "Shifting item 0 to place " << EntryCount-1 << "." << endl;
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| 205 | StackList[EntryCount-1] = StackList[0];
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| 206 | } else {
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| 207 | cout << Verbose(5) << "Shifting item " << i << " to place " << i-1 << "." << endl;
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| 208 | StackList[i-1] = StackList[i];
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| 209 | }
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| 210 | }
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| 211 | i=((i + 1) % EntryCount); // step on
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| 212 | } while (i!=NextFreeField);
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| 213 | else
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| 214 | cerr << "ERROR: Stack is already empty!" << endl;
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| 215 | if (found) {
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| 216 | NextFreeField = CurrentLastEntry;
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| 217 | if (CurrentLastEntry != CurrentFirstEntry) // has there been more than one item on stack
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| 218 | CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount;
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| 219 | }
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| 220 | return found;
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| 221 | };
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| 222 |
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| 223 | /** Test the functionality of the stack.
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| 224 | * \param *out ofstream for debugging
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| 225 | * \param *test one item to put on stack
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| 226 | * \return true - all tests worked correctly
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| 227 | */
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| 228 | void AtomStackClass::TestImplementation(ofstream *out, atom *test)
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| 229 | {
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| 230 | atom *Walker = test;
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| 231 | *out << Verbose(1) << "Testing the snake stack..." << endl;
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| 232 | for (int i=0;i<EntryCount;i++) {
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| 233 | *out << Verbose(2) << "Filling " << i << "th element of stack." << endl;
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| 234 | Push(Walker);
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| 235 | Walker=Walker->next;
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| 236 | }
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| 237 | *out << endl;
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| 238 | Output(out);
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| 239 | if (IsFull())
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| 240 | *out << "Stack is full as supposed to be!" << endl;
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| 241 | else
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| 242 | *out << "ERROR: Stack is not as full as supposed to be!" << endl;
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| 243 | //if (StackList[(EntryCount+1)/2] != NULL) {
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| 244 | *out << "Removing element in the middle ..." << endl;
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| 245 | RemoveItem(StackList[(EntryCount+1)/2]);
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| 246 | Output(out);
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| 247 | //}
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| 248 | //if (StackList[CurrentFirstEntry] != NULL) {
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| 249 | *out << "Removing first element ..." << endl;
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| 250 | RemoveItem(StackList[CurrentFirstEntry]);
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| 251 | Output(out);
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| 252 | //}
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| 253 | //if (StackList[CurrentLastEntry] != NULL) {
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| 254 | *out << "Removing last element ..." << endl;
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| 255 | RemoveItem(StackList[CurrentLastEntry]);
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| 256 | Output(out);
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| 257 | //}
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| 258 | *out << "Clearing stack ... " << endl;
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| 259 | ClearStack();
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| 260 | Output(out);
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| 261 | if (IsEmpty())
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| 262 | *out << "Stack is empty as supposed to be!" << endl;
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| 263 | else
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| 264 | *out << "ERROR: Stack is not as empty as supposed to be!" << endl;
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| 265 | *out << "done." << endl;
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| 266 | };
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| 267 |
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| 268 | /** Puts contents of stack into ofstream \a *out.
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| 269 | * \param *out ofstream for output
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| 270 | */
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| 271 | void AtomStackClass::Output(ofstream *out) const
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| 272 | {
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| 273 | *out << "Contents of Stack: ";
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| 274 | for(int i=0;i<EntryCount;i++) {
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| 275 | *out << "\t";
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| 276 | if (i == CurrentFirstEntry)
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| 277 | *out << " 1";
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| 278 | if (i == CurrentLastEntry)
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| 279 | *out << " "<< EntryCount;
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| 280 | if (i == NextFreeField)
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| 281 | *out << " F";
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| 282 | *out << ": " << StackList[i];
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| 283 | }
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| 284 | *out << endl;
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| 285 | };
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| 286 |
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| 287 | /** Checks whether stack is empty.
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| 288 | * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
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| 289 | * AtomStackClass::CurrentFirstEntry is equal to AtomStackClass::CurrentLastEntry.
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| 290 | * \return true - empty, false - not
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| 291 | */
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| 292 | bool AtomStackClass::IsEmpty()
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| 293 | {
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| 294 | return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry == CurrentFirstEntry));
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| 295 | };
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| 296 |
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| 297 | /** Checks whether stack is full.
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| 298 | * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
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| 299 | * AtomStackClass::CurrentFirstEntry is _not_ equal to AtomStackClass::CurrentLastEntry.
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| 300 | * \return true - full, false - not
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| 301 | */
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| 302 | bool AtomStackClass::IsFull()
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| 303 | {
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| 304 | return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry != CurrentFirstEntry));
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| 305 | };
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| 306 |
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| 307 | /** Returns number of items on stack.
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| 308 | * Simply returns difference between AtomStackClass::Stacklist entry AtomStackClass::CurrentEntry-1.
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| 309 | * \return number of items on stack
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| 310 | * \warning will never return correct item count if stack is full, i.e. count would be AtomStackClass::EntryCount.
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| 311 | */
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| 312 | int AtomStackClass::ItemCount()
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| 313 | {
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| 314 | //cout << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tEntryCount " << EntryCount << "." << endl;
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| 315 | return((NextFreeField + (EntryCount - CurrentFirstEntry)) % EntryCount);
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| 316 | };
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| 317 |
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| 318 | /** Clears the stack from all atoms.
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| 319 | * \return true - sucess, false - failure
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| 320 | */
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| 321 | void AtomStackClass::ClearStack()
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| 322 | {
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| 323 | for(int i=0;i<EntryCount; i++)
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| 324 | StackList[i] = NULL;
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| 325 | CurrentFirstEntry = 0;
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| 326 | CurrentLastEntry = 0;
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| 327 | NextFreeField = 0;
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| 328 | };
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| 329 |
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