Changeset 567b7f for molecuilder/src/molecule.hpp

Timestamp:

Oct 7, 2009, 1:11:28 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

0cd3b2

Parents:

8ffe32

git-author:

Frederik Heber <heber@…> (10/07/09 12:14:15)

git-committer:

Frederik Heber <heber@…> (10/07/09 13:11:28)

Message:

In molecule::OutputTrajectories() ActOnAllAtoms() with new function atom::OutputTrajectory() is used.

For this to work, I had to change the Trajectory struct that was so far included in molecule.hpp to be incorporated directly into the class atom.
NOTE: This incorporation is incomplete and a ticket (#34) has been filed to remind of this issue.
However, the trajectory is better suited to reside in atom anyway and was probably just put in molecule due to memory prejudices against STL vector<>.
Functions in molecule.cpp, config.cpp, molecule_geometry.cpp and molecule_dynamics.cpp were adapted (changed from Trajectories[atom *] to atom *->Trajectory).
And the atom pointer in the Trajectory structure was removed.

File:

• molecuilder/src/molecule.hpp (modified) (2 diffs)

molecuilder/src/molecule.hpp

@@ -65 +65 @@
 {
   bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
-};
-
-struct Trajectory
-{
-  vector<Vector> R;  //!< position vector
-  vector<Vector> U;  //!< velocity vector
-  vector<Vector> F;  //!< last force vector
-  atom *ptr;         //!< pointer to atom whose trajectory we contain
 };
 
@@ -101 +93 @@
     bond *last;         //!< end of bond list
     bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
-    map<atom *, struct Trajectory> Trajectories; //!< contains old trajectory points
     int MDSteps;        //!< The number of MD steps in Trajectories
     int *NumberOfBondsPerAtom;  //!< Number of Bonds each atom has