| 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 "atom.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 | father = this; // generally, father is itself
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| 16 | previous = NULL;
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| 17 | next = NULL;
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| 18 | Ancestor = NULL;
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| 19 | type = NULL;
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| 20 | sort = NULL;
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| 21 | FixedIon = 0;
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| 22 | GraphNr = -1;
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| 23 | ComponentNr = NULL;
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| 24 | IsCyclic = false;
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| 25 | SeparationVertex = false;
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| 26 | LowpointNr = -1;
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| 27 | AdaptiveOrder = 0;
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| 28 | MaxOrder = false;
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| 29 | // set LCNode::Vector to our Vector
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| 30 | node = &x;
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| 31 | };
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| 32 |
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| 33 | /** Constructor of class atom.
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| 34 | */
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| 35 | atom::atom(atom *pointer)
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| 36 | {
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| 37 | Name = NULL;
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| 38 | previous = NULL;
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| 39 | next = NULL;
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| 40 | father = pointer; // generally, father is itself
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| 41 | Ancestor = NULL;
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| 42 | GraphNr = -1;
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| 43 | ComponentNr = NULL;
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| 44 | IsCyclic = false;
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| 45 | SeparationVertex = false;
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| 46 | LowpointNr = -1;
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| 47 | AdaptiveOrder = 0;
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| 48 | MaxOrder = false;
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| 49 | type = pointer->type; // copy element of atom
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| 50 | x.CopyVector(&pointer->x); // copy coordination
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| 51 | v.CopyVector(&pointer->v); // copy velocity
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| 52 | FixedIon = pointer->FixedIon;
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| 53 | nr = -1;
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| 54 | sort = &nr;
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| 55 | node = &x;
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| 56 | }
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| 57 |
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| 58 |
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| 59 | /** Destructor of class atom.
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| 60 | */
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| 61 | atom::~atom()
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| 62 | {
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| 63 | Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
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| 64 | };
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| 65 |
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| 66 |
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| 67 | /** Climbs up the father list until NULL, last is returned.
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| 68 | * \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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| 69 | */
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| 70 | atom *atom::GetTrueFather()
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| 71 | {
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| 72 | atom *walker = this;
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| 73 | do {
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| 74 | if (walker == walker->father) // top most father is the one that points on itself
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| 75 | break;
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| 76 | walker = walker->father;
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| 77 | } while (walker != NULL);
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| 78 | return walker;
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| 79 | };
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| 80 |
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| 81 | /** Output of a single atom.
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| 82 | * \param ElementNo cardinal number of the element
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| 83 | * \param AtomNo cardinal number among these atoms of the same element
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| 84 | * \param *out stream to output to
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| 85 | * \param *comment commentary after '#' sign
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| 86 | */
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| 87 | bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
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| 88 | {
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| 89 | if (out != NULL) {
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| 90 | *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t" << fixed << setprecision(9) << showpoint;
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| 91 | *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
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| 92 | *out << "\t" << FixedIon;
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| 93 | if (v.Norm() > MYEPSILON)
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| 94 | *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
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| 95 | if (comment != NULL)
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| 96 | *out << " # " << comment << endl;
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| 97 | else
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| 98 | *out << " # molecule nr " << nr << endl;
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| 99 | return true;
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| 100 | } else
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| 101 | return false;
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| 102 | };
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| 103 |
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| 104 | /** Output of a single atom as one lin in xyz file.
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| 105 | * \param *out stream to output to
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| 106 | */
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| 107 | bool atom::OutputXYZLine(ofstream *out) const
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| 108 | {
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| 109 | if (out != NULL) {
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| 110 | *out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
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| 111 | return true;
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| 112 | } else
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| 113 | return false;
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| 114 | };
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| 115 |
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| 116 | ostream & operator << (ostream &ost, const atom &a)
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| 117 | {
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| 118 | ost << "[" << a.Name << "|" << &a << "]";
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| 119 | return ost;
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| 120 | };
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| 121 |
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| 122 | ostream & atom::operator << (ostream &ost)
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| 123 | {
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| 124 | ost << "[" << Name << "|" << this << "]";
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| 125 | return ost;
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| 126 | };
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| 127 |
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| 128 | /** Compares the indices of \a this atom with a given \a ptr.
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| 129 | * \param ptr atom to compare index against
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| 130 | * \return true - this one's is smaller, false - not
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| 131 | */
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| 132 | bool atom::Compare(const atom &ptr)
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| 133 | {
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| 134 | if (nr < ptr.nr)
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| 135 | return true;
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| 136 | else
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| 137 | return false;
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| 138 | };
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| 139 |
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| 140 | bool operator < (atom &a, atom &b)
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| 141 | {
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| 142 | return a.Compare(b);
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| 143 | };
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| 144 |
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