Changeset c830e8e for molecuilder/src/atom.cpp

Timestamp:

Apr 2, 2009, 4:12:54 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

3021d93

Parents:

451d7a

Message:

Basic implementation of Multiple molecules.

builder.cpp:

• MoleculeListClass *molecules instead of molecule *mol
• in menu replaced list of elements and atoms by list of molecules
• new option: SetActiveMolecule
• new submenus/functions that all work on MoleculeListClass:
  • EditMolecule()
  • ManipulateMolecules() (global operations on all atoms in a molecule)
  • MergeMolecules()
  • ManipulateAtoms() (local operations on single atoms)
• SaveConfig(): SimpleMultiAdd() of all molecules into a single new one that is stored with the present configuration.

molecules.hpp:

• new STL list MoleculeList
• new variables in MoleculeListClass: list of molecules as STL list
• new variables in molecule: ActiveFlag, name of molecule, Center of molecule (used on merging)

moleculelist.cpp:

• replaced listofmolecules array by STL list everywhere (only smaller changes necessary)
• new merging function: SimpleMerge, SimpleAdd, SimpleMultiMerge, SimpleMultiAdd, (EmbedMerge, ScatterMerge ... both not finished). Add does not while merge does delete the src molecules.
• new function: Enumerate(). Output of all molecules with number of atoms and chemical formula
• new function: NumberOfActiveMolecules(). Counts the number of molecules in the list with ActiveFlag set.
• new function: insert(). Inserts a molecule into the list with a unique index

molecules.cpp:

• new function: SetNameFromFilename. Takes basename of a filename and sets name accordingly.
• new function: UnlinkAtom. Only removes atom from list, does not delete it from memory.

atom.cpp:

• Output() also accepts specific comment instead of "# molecule nr ..."

File:

• molecuilder/src/atom.cpp (modified) (7 diffs)

molecuilder/src/atom.cpp

@@ -1 +1 @@
 /** \file atom.cpp
- * 
+ *
  * Function implementations for the class atom.
- * 
+ *
  */
 
 #include "molecules.hpp"
- 
+
 /************************************* Functions for class atom *************************************/
 
 /** Constructor of class atom.
  */
-atom::atom() 
+atom::atom()
 {
         Name = NULL;
@@ -33 +33 @@
 /** Destructor of class atom.
  */
-atom::~atom() 
+atom::~atom()
 {
         Free((void **)&Name, "atom::~atom: *Name");
@@ -58 +58 @@
  * \param AtomNo cardinal number among these atoms of the same element
  * \param *out stream to output to
+ * \param *comment commentary after '#' sign
  */
-bool atom::Output(int ElementNo, int AtomNo, ofstream *out) const
+bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
 {
         if (out != NULL) {
@@ -67 +68 @@
                 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;
+                if (comment != NULL)
+                  *out << " # " << comment << endl;
+                else
+                  *out << " # molecule nr " << nr << endl;
                 return true;
         } else
@@ -85 +89 @@
 };
 
-ostream & operator << (ostream &ost, atom &a) 
+ostream & operator << (ostream &ost, atom &a)
 {
         ost << "[" << a.Name << "|" << &a << "]";
@@ -94 +98 @@
  * \param ptr atom to compare index against
  * \return true - this one's is smaller, false - not
- */ 
+ */
 bool atom::Compare(atom &ptr)
 {
@@ -103 +107 @@
 };
 
-bool operator < (atom &a, atom &b) 
+bool operator < (atom &a, atom &b)
 {
         return a.Compare(b);