Changeset f39735 for molecuilder/src/boundary.hpp

Timestamp:

Jul 23, 2009, 1:45:24 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

47548d

Parents:

560995 (diff), 1b2aa1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• molecuilder/src/boundary.hpp (modified) (3 diffs)

molecuilder/src/boundary.hpp

@@ -17 +17 @@
 
 #include <gsl/gsl_poly.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_multimin.h>
+#include <gsl/gsl_permutation.h>
 
+#include "linkedcell.hpp"
 #include "molecules.hpp"
 
@@ -85 +90 @@
     void AddTriangleLine(class BoundaryPointSet *a, class BoundaryPointSet *b, int n);
     void AddTriangleToLines();
-    void Find_starting_triangle(molecule* mol, const double RADIUS);
-    bool Find_next_suitable_triangle(ofstream *out, ofstream *tecplot, molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, int N, const char *filename);
+    void Find_starting_triangle(ofstream *out, molecule* mol, const double RADIUS, LinkedCell *LC);
+    bool Find_next_suitable_triangle(ofstream *out, molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, int N, const char *filename, LinkedCell *LC);
     bool CheckPresenceOfTriangle(ofstream *out, atom *a, atom *b, atom *c);
     void Find_next_suitable_point_via_Angle_of_Sphere(atom* a, atom* b, atom* c, atom* Candidate, atom* Parent, int RecursionLevel, Vector *Chord, Vector *direction1, Vector *OldNormal, Vector ReferencePoint, atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule* mol);
@@ -109 +114 @@
 
 
-double VolumeOfConvexEnvelope(ofstream *out, ofstream *tecplot, config *configuration, Boundaries *BoundaryPoints, molecule *mol);
+double VolumeOfConvexEnvelope(ofstream *out, const char *filename, config *configuration, Boundaries *BoundaryPoints, molecule *mol);
 double * GetDiametersOfCluster(ofstream *out, Boundaries *BoundaryPtr, molecule *mol, bool IsAngstroem);
 void PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol, double ClusterVolume, double celldensity);
-void Find_non_convex_border(ofstream *out, ofstream *tecplot, molecule* mol, const char *tempbasename, const double RADIUS);
-void Find_next_suitable_point(atom a, atom b, atom Candidate, int n, Vector *d1, Vector *d2, atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule *mol, bool problem);
-
+void Find_non_convex_border(ofstream *out, molecule* mol, class Tesselation *T, class LinkedCell *LCList, const char *tempbasename, const double RADIUS);
+void Find_next_suitable_point(class BoundaryTriangleSet *BaseTriangle, class BoundaryLineSet *BaseLine, atom*& OptCandidate, Vector *OptCandidateCenter, double *ShortestAngle, const double RADIUS, LinkedCell *LC);
 
 #endif /*BOUNDARY_HPP_*/