Changes in src/atom_trajectoryparticle.cpp [952f38:83f176]

File:

• src/atom_trajectoryparticle.cpp (modified) (14 diffs)

src/atom_trajectoryparticle.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * atom_trajectoryparticle.cpp
@@ -5 +12 @@
  *      Author: heber
  */
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
 
 #include "Helpers/MemDebug.hpp"
@@ -38 +50 @@
 {
   for (int i=NDIM;i--;)
-    *temperature += type->mass * Trajectory.U.at(step)[i]* Trajectory.U.at(step)[i];
+    *temperature += getType()->getMass() * Trajectory.U.at(step)[i]* Trajectory.U.at(step)[i];
 };
 
@@ -65 +77 @@
   for(int d=0;d<NDIM;d++) {
     Trajectory.U.at(Step)[d] -= CoGVelocity->at(d);
-    *ActualTemp += 0.5 * type->mass * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
+    *ActualTemp += 0.5 * getType()->getMass() * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
   }
 };
@@ -113 +125 @@
     Trajectory.R.at(NextStep)[d] = Trajectory.R.at(NextStep-1)[d];
     Trajectory.R.at(NextStep)[d] += configuration->Deltat*(Trajectory.U.at(NextStep-1)[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
-    Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/type->mass);     // F = m * a and s =
+    Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/getType()->getMass());     // F = m * a and s =
   }
   // Update U
   for (int d=0; d<NDIM; d++) {
     Trajectory.U.at(NextStep)[d] = Trajectory.U.at(NextStep-1)[d];
-    Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/type->mass); // v = F/m * t
+    Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/getType()->getMass()); // v = F/m * t
   }
   // Update R (and F)
@@ -137 +149 @@
 void TrajectoryParticle::SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const
 {
-  *TotalMass += type->mass;  // sum up total mass
+  *TotalMass += getType()->getMass();  // sum up total mass
   for(int d=0;d<NDIM;d++) {
-    TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*type->mass;
+    TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*getType()->getMass();
   }
 };
@@ -154 +166 @@
     for (int d=0; d<NDIM; d++) {
       U[d] *= ScaleTempFactor;
-      *ekin += 0.5*type->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
     }
 };
@@ -170 +182 @@
     for (int d=0; d<NDIM; d++) {
       *G += U[d] * F[d];
-      *E += U[d]*U[d]*type->mass;
+      *E += U[d]*U[d]*getType()->getMass();
     }
 };
@@ -185 +197 @@
   if (FixedIon == 0) // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-      U[d] += configuration->Deltat/type->mass * ( (G_over_E) * (U[d]*type->mass) );
-      *ekin += type->mass * U[d]*U[d];
+      U[d] += configuration->Deltat/getType()->getMass() * ( (G_over_E) * (U[d]*getType()->getMass()) );
+      *ekin += getType()->getMass() * U[d]*U[d];
     }
 };
@@ -198 +210 @@
 void TrajectoryParticle::Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration)
 {
-  double sigma  = sqrt(configuration->Thermostats->TargetTemp/type->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
+  double sigma  = sqrt(configuration->Thermostats->TargetTemp/getType()->getMass()); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
   Vector &U = Trajectory.U.at(Step);
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
@@ -211 +223 @@
     }
     for (int d=0; d<NDIM; d++)
-      *ekin += 0.5*type->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
   }
 };
@@ -227 +239 @@
     for (int d=0; d<NDIM; d++) {
       U[d] *= sqrt(1+(configuration->Deltat/configuration->Thermostats->TempFrequency)*(ScaleTempFactor-1));
-      *ekin += 0.5*type->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
     }
   }
@@ -241 +253 @@
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-      *delta_alpha += U[d]*U[d]*type->mass;
+      *delta_alpha += U[d]*U[d]*getType()->getMass();
     }
   }
@@ -256 +268 @@
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-        U[d] += configuration->Deltat/type->mass * (configuration->Thermostats->alpha * (U[d] * type->mass));
-        *ekin += (0.5*type->mass) * U[d]*U[d];
+        U[d] += configuration->Deltat/getType()->getMass() * (configuration->Thermostats->alpha * (U[d] * getType()->getMass()));
+        *ekin += (0.5*getType()->getMass()) * U[d]*U[d];
       }
   }
 };
+
+
+std::ostream & TrajectoryParticle::operator << (std::ostream &ost) const
+{
+  ParticleInfo::operator<<(ost);
+  ost << "," << getPosition();
+  return ost;
+}
+
+std::ostream & operator << (std::ostream &ost, const TrajectoryParticle &a)
+{
+  a.ParticleInfo::operator<<(ost);
+  ost << "," << a.getPosition();
+  return ost;
+}
+