Changes in src/atom.cpp [357fba:321a11]

File:

• src/atom.cpp (modified) (7 diffs)

src/atom.cpp

@@ -5 +5 @@
  */
 
-#include "atom.hpp"
+#include "molecules.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -13 +13 @@
 atom::atom()
 {
-  father = this;  // generally, father is itself
-  previous = NULL;
-  next = NULL;
-  Ancestor = NULL;
-  type = NULL;
-  sort = NULL;
-  FixedIon = 0;
-  GraphNr = -1;
-  ComponentNr = NULL;
-  IsCyclic = false;
-  SeparationVertex = false;
-  LowpointNr = -1;
-  AdaptiveOrder = 0;
-  MaxOrder = false;
-  // set LCNode::Vector to our Vector
-  node = &x;
+        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;
+        IsCyclic = false;
+        SeparationVertex = false;
+        LowpointNr = -1;
+        AdaptiveOrder = 0;
+        MaxOrder = false;
 };
-
-/** Constructor of class atom.
- */
-atom::atom(atom *pointer)
-{
-  Name = NULL;
-  previous = NULL;
-  next = NULL;
-  father = this;  // generally, father is itself
-  Ancestor = NULL;
-  GraphNr = -1;
-  ComponentNr = NULL;
-  IsCyclic = false;
-  SeparationVertex = false;
-  LowpointNr = -1;
-  AdaptiveOrder = 0;
-  MaxOrder = false;
-  type = pointer->type;  // copy element of atom
-  x.CopyVector(&pointer->x); // copy coordination
-  v.CopyVector(&pointer->v); // copy velocity
-  FixedIon = pointer->FixedIon;
-  nr = -1;
-  sort = &nr;
-}
-
 
 /** Destructor of class atom.
@@ -60 +35 @@
 atom::~atom()
 {
-  Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
+        Free((void **)&Name, "atom::~atom: *Name");
+        Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
 };
 
@@ -69 +45 @@
 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;
+        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;
 };
 
@@ -86 +62 @@
 bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) 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";
-    if (comment != NULL)
-      *out << " # " << comment << endl;
-    else
-      *out << " # molecule nr " << nr << endl;
-    return true;
-  } else
-    return false;
+        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";
+                if (comment != NULL)
+                  *out << " # " << comment << endl;
+                else
+                  *out << " # molecule nr " << nr << endl;
+                return true;
+        } else
+                return false;
 };
 
@@ -106 +82 @@
 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;
+        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, const atom &a) 
+ostream & operator << (ostream &ost, const atom &a)
 {
-  ost << "[" << a.Name << "|" << &a << "]";
-  return ost;
+        ost << "[" << a.Name << "|" << &a << "]";
+        return ost;
 };
 
@@ -123 +99 @@
  * \return true - this one's is smaller, false - not
  */
-bool atom::Compare(atom &ptr)
+bool atom::Compare(const atom &ptr)
 {
-  if (nr < ptr.nr)
-    return true;
-  else
-    return false;
+        if (nr < ptr.nr)
+                return true;
+        else
+                return false;
 };
 
 bool operator < (atom &a, atom &b)
 {
-  return a.Compare(b);
+        return a.Compare(b);
 };