Changeset 8ffe32 for molecuilder/src/atom.cpp

Timestamp:

Oct 6, 2009, 5:57:01 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

567b7f

Parents:

a4644b

Message:

More functions of molecule now use templated iterators.

• the following template functions are defined in molecule.hpp and implemented in molecule_template.hpp
  • ActOnAllVectors() - Vector of current atom is object to member function pointer
  • ActOnAllAtoms() - current atom is object to member function pointer
  • ActWithEachAtom() - current atom is parameter to molecule member function not object
  • ActOnCopyWithEachAtom() - Same as ActWithEachAtom() but object is not this but an extra pointer to a copy
  • ActOnCopyWithEachAtomIfTrue() - Same as ActWithEachAtom() but with additional condition (bool member function of atom) that has to be true
  • SetIndexedArrayForEachAtomTo() - current atom's index or its element's Z acts as index to a given array in conjunction with a setor function
• the following functions were converted in molecule: molecule::CopyMolecule(), molecule::CopyMoleculeFromSubRegion(), molecule::Output(), molecule::OutputTrajectories(), molecule::OutputXYZ()
• atom.cpp: new functions IsInParallelepiped(), overloaded Output()
• helper.cpp: new template functions Increment() and AbsolutValue acting as wrapper to operator+=() and operator=()

File:

• molecuilder/src/atom.cpp (modified) (2 diffs)

molecuilder/src/atom.cpp

@@ -102 +102 @@
 };
 
+/** 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
@@ -112 +122 @@
   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;
+};
+bool atom::Output(int *ElementNo, int *AtomNo, ofstream *out, 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;