Changeset c3a303 for molecuilder/src/molecules.hpp

Timestamp:

Jul 24, 2009, 10:38:32 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

53d153

Parents:

a048fa (diff), 47548d (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 14:23:32)

git-committer:

Frederik Heber <heber@…> (07/24/09 10:38:32)

Message:

Merge branch 'master' into ConcaveHull

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/bond.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/defs.hpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/joiner.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp

merges:

• analyzer.cpp: all from master, due to Hessian; only Chi(PAS)Fragments from HEAD
• bond.cpp: bond::GetOtherAtom gives cerr output if neither atom matches from master
• boundary.cpp: all from HEAD, is tesselation stuff
• boundary.hpp: all from HEAD, is tesselation stuff
• builder.cpp: Center...(), RemoveAtoms(), SaveConfig() from master, is MultipleMolecules, rest from HEAD (Translation and ...)
• config.cpp: FileBuffer stuff from HEAD, only some taken over from HEAD
• datacreator.cpp: all from master, is Hessian
• datacreator.hpp: all from master, is Hessian
• defs.hpp: all from master, is Thermostat
• ellipsoid.cpp: all from HEAD, created during tesselation
• joiner.cpp: all from master, is Hessian
• molecules.cpp: molecule::molecule(), ConstrainedPotential() stuff, Thermostats(), RemoveAtom(),CreateAdjacencyList(), FragmentMolecule() from master, CenterInBox(), CenterEdge(), CenterOrigin(), CenterPeriodic() (instead of CenterAtVector()), TranslatePeriodically(), DeterminePeriodicCenter(), Output...(), ReturnFullForSymmnetricMatrix() from HEAD
• molecules.hpp: see above, ConfigfileBuffer struct from HEAD, class config joined
• parser.cpp: all from master, is Hessian
• parser.hpp: all from master, is Hessian

compilation fixes:

• molecules.cpp: PrincipalAxisSystem() - CenterGravity() -> CenterOrigin(), DetermineCenter() -> DeterminePeriodicCenter
• datacreator.cpp: all char * to const char *
• builder.cpp: ParseCommandLineOptions() - case 'c': had argptr++ and argptr+=3; case 'O' - x was not zero'd

File:

• molecuilder/src/molecules.hpp (modified) (9 diffs)

molecuilder/src/molecules.hpp

@@ -10 +10 @@
 
 // GSL headers
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_heapsort.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_matrix.h>
 #include <gsl/gsl_multimin.h>
 #include <gsl/gsl_vector.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_eigen.h>
-#include <gsl/gsl_heapsort.h>
+#include <gsl/gsl_randist.h>
 
 // STL headers
@@ -156 +158 @@
 };
 
-ostream & operator << (ostream &ost, atom &a);
+ostream & operator << (ostream &ost, const atom &a);
 
 /** Bonds between atoms.
@@ -195 +197 @@
 };
 
-ostream & operator << (ostream &ost, bond &b);
+
+ostream & operator << (ostream &ost, const bond &b);
 
 class MoleculeLeafClass;
+
+
+#define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
+enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover };   //!< Thermostat names for output
+
 
 /** The complete molecule.
@@ -254 +262 @@
   bool CenterInBox(ofstream *out);
   void CenterEdge(ofstream *out, Vector *max);
-  void CenterOrigin(ofstream *out, Vector *max);
-  void CenterGravity(ofstream *out, Vector *max);
+  void CenterOrigin(ofstream *out);
+  void CenterPeriodic(ofstream *out);
+  void CenterAtVector(ofstream *out, Vector *newcenter);
   void Translate(const Vector *x);
   void TranslatePeriodically(const Vector *trans);
@@ -261 +270 @@
   void Align(Vector *n);
   void Scale(double **factor);
-  void DetermineCenter(Vector &center);
+  void DeterminePeriodicCenter(Vector &center);
   Vector * DetermineCenterOfGravity(ofstream *out);
   Vector * DetermineCenterOfAll(ofstream *out);
-  void SetNameFromFilename(char *filename);
+  void SetNameFromFilename(const char *filename);
   void SetBoxDimension(Vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);
   void ScanForPeriodicCorrection(ofstream *out);
+  bool VerletForceIntegration(ofstream *out, char *file, config &configuration);
+  void Thermostats(config &configuration, double ActualTemp, int Thermostat);
   void PrincipalAxisSystem(ofstream *out, bool DoRotate);
   double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
   Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
 
-  bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
-
+
+  double ConstrainedPotential(ofstream *out, atom **permutation, int start, int end, double *constants, bool IsAngstroem);
+  double MinimiseConstrainedPotential(ofstream *out, atom **&permutation, int startstep, int endstep, bool IsAngstroem);
+  void EvaluateConstrainedForces(ofstream *out, int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
+  bool LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration); 
+        
   bool CheckBounds(const Vector *x) const;
   void GetAlignvector(struct lsq_params * par) const;
@@ -349 +364 @@
   bool AddHydrogenCorrection(ofstream *out, char *path);
   bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
-  bool insert(molecule *mol);
+  void insert(molecule *mol);
   molecule * ReturnIndex(int index);
   bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
@@ -429 +444 @@
     char *databasepath;
 
+    int DoConstrainedMD;
+    int MaxOuterStep;
+    int Thermostat;
+    int *ThermostatImplemented;
+    char **ThermostatNames;
+    double TempFrequency;
+    double alpha;
+    double HooverMass;
+    double TargetTemp;
+    int ScaleTempStep;
+    
   private:
     char *mainname;
@@ -449 +475 @@
     int Seed;
 
-    int MaxOuterStep;
     int OutVisStep;
     int OutSrcStep;
-    double TargetTemp;
-    int ScaleTempStep;
     int MaxPsiStep;
     double EpsWannier;
@@ -501 +524 @@
   char *GetDefaultPath() const;
   void SetDefaultPath(const char *path);
+  void InitThermostats(ifstream *source);
 };