Changeset 3b470f for molecuilder/src/molecules.hpp

Timestamp:

Jul 23, 2009, 11:23:59 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

59a745

Parents:

09f4dc (diff), 14178b (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.

Message:

Merge branch 'Thermostat'

Conflicts:

.gitignore
Makefile.am
molecuilder/src/analyzer.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp

• config::SaveMPQC() has different call parameters
• analyzer and joiner had conflicts due to Chi and ChiPAS values
• molecule::VerletForceIntegration() is slightly different too, but Thermostat supposedly is old version

File:

• molecuilder/src/molecules.hpp (modified) (8 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
@@ -152 +154 @@
 };
 
-ostream & operator << (ostream &ost, atom &a);
+ostream & operator << (ostream &ost, const atom &a);
 
 /** Bonds between atoms.
@@ -191 +193 @@
 };
 
-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.
@@ -259 +267 @@
         void PrincipalAxisSystem(ofstream *out, bool DoRotate);
         double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
-        bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
-
+        
+  bool VerletForceIntegration(ofstream *out, char *file, config &configuration);
+  void Thermostats(config &configuration, double ActualTemp, int Thermostat);
+
+  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;
@@ -339 +354 @@
   bool AddHydrogenCorrection(ofstream *out, char *path);
   bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
-  bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
+  bool OutputConfigForListOfFragments(ofstream *out, const char *fragmentprefix, config *configuration, int *SortIndex, bool DoPeriodic, bool DoCentering);
   void Output(ofstream *out);
 
@@ -389 +404 @@
     string basis;
 
+    int DoConstrainedMD;
+    int MaxOuterStep;
+    int Thermostat;
+    int *ThermostatImplemented;
+    char **ThermostatNames;
+    double TempFrequency;
+    double alpha;
+    double HooverMass;
+    double TargetTemp;
+    int ScaleTempStep;
+    
     private:
     char *mainname;
@@ -409 +435 @@
     int Seed;
 
-    int MaxOuterStep;
     int OutVisStep;
     int OutSrcStep;
-    double TargetTemp;
-    int ScaleTempStep;
     int MaxPsiStep;
     double EpsWannier;
@@ -460 +483 @@
   char *GetDefaultPath() const;
   void SetDefaultPath(const char *path);
+  void InitThermostats(ifstream *source);
 };