Changeset 4455f4 for src/atom.cpp

Timestamp:

Oct 19, 2009, 1:09:29 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

c75de1

Parents:

9eefda

Message:

Huge Refactoring: class atom split up into several inherited classes.

• There are now two parts: classes containing data (called ...Info) and classes containing associated functions:
  • new data classes: ParticleInfo (id and name), AtomInfo (element, position, velocity, force), TrajectoryParticleInfo, GraphNodeInfo (all graph variables), BondedParticleInfo (AdaptiveOrder, MaxOrder, ListOfBonds)
  • new associated function classes: TrajectoryParticle, GraphNode, BondedParticle

• template functions ActOnAllAtoms(), SumPerAtom() were adapted with another template type for the class of the member function
• template functions SetIndexedArrayForEachAtomTo() have their index as ParticleInfo::*index

File:

• src/atom.cpp (modified) (22 diffs)

src/atom.cpp

@@ -16 +16 @@
 /************************************* Functions for class atom *************************************/
 
+/** Constructor of class AtomInfo.
+ */
+AtomInfo::AtomInfo() : type(NULL) {};
+
+/** Destructor of class AtomInfo.
+ */
+AtomInfo::~AtomInfo()
+{
+};
+
+/** Constructor of class TrajectoryParticleInfo.
+ */
+TrajectoryParticleInfo::TrajectoryParticleInfo() : FixedIon(0) {};
+
+/** Destructor of class TrajectoryParticleInfo.
+ */
+TrajectoryParticleInfo::~TrajectoryParticleInfo()
+{
+  Trajectory.R.clear();
+  Trajectory.U.clear();
+  Trajectory.F.clear();
+};
+
+/** Constructor of class TrajectoryParticle.
+ */
+TrajectoryParticle::TrajectoryParticle()
+{
+};
+
+/** Destructor of class TrajectoryParticle.
+ */
+TrajectoryParticle::~TrajectoryParticle()
+{
+};
+
+/** Constructor of class GraphNodeInfo.
+ */
+GraphNodeInfo::GraphNodeInfo() : GraphNr(-1), ComponentNr(NULL), LowpointNr(-1), SeparationVertex(false), IsCyclic(false), Ancestor(NULL) {};
+
+/** Destructor of class GraphNodeInfo.
+ */
+GraphNodeInfo::~GraphNodeInfo()
+{
+  Free<int>(&ComponentNr, "atom::~atom: *ComponentNr");
+};
+
+/** Constructor of class GraphNode.
+ */
+GraphNode::GraphNode()
+{
+};
+
+/** Destructor of class GraphNode.
+ */
+GraphNode::~GraphNode()
+{
+};
+
+/** Constructor of class BondedParticleInfo.
+ */
+BondedParticleInfo::BondedParticleInfo() : AdaptiveOrder(0), MaxOrder(false) {};
+
+/** Destructor of class BondedParticleInfo.
+ */
+BondedParticleInfo::~BondedParticleInfo()
+{
+};
+
+/** Constructor of class BondedParticle.
+ */
+BondedParticle::BondedParticle(){};
+
+/** Destructor of class BondedParticle.
+ */
+BondedParticle::~BondedParticle()
+{
+  BondList::const_iterator Runner;
+  while (!ListOfBonds.empty()) {
+    Runner = ListOfBonds.begin();
+    removewithoutcheck(*Runner);
+  }
+};
+
 /** Constructor of class atom.
  */
@@ -23 +106 @@
   previous = NULL;
   next = NULL;
-  Ancestor = NULL;
-  type = NULL;
-  sort = NULL;
-  FixedIon = 0;
-  GraphNr = -1;
-  ComponentNr = NULL;
-  IsCyclic = false;
-  SeparationVertex = false;
-  LowpointNr = -1;
-  AdaptiveOrder = 0;
-  MaxOrder = false;
+  sort = &nr;
+
   // set LCNode::Vector to our Vector
   node = &x;
@@ -42 +116 @@
 atom::atom(atom *pointer)
 {
-  Name = NULL;
   previous = NULL;
   next = NULL;
   father = pointer;  // generally, father is itself
-  Ancestor = NULL;
-  GraphNr = -1;
-  ComponentNr = NULL;
-  IsCyclic = false;
-  SeparationVertex = false;
-  LowpointNr = -1;
-  AdaptiveOrder = 0;
-  MaxOrder = false;
+
   type = pointer->type;  // copy element of atom
   x.CopyVector(&pointer->x); // copy coordination
   v.CopyVector(&pointer->v); // copy velocity
   FixedIon = pointer->FixedIon;
-  nr = -1;
   sort = &nr;
   node = &x;
@@ -68 +133 @@
 atom::~atom()
 {
-  BondList::const_iterator Runner;
-  while (!ListOfBonds.empty()) {
-    Runner = ListOfBonds.begin();
-    removewithoutcheck(*Runner);
-  }
   unlink(this);
-  Free<int>(&ComponentNr, "atom::~atom: *ComponentNr");
-  Free<char>(&Name, "atom::~atom: *Name");
-  Trajectory.R.clear();
-  Trajectory.U.clear();
-  Trajectory.F.clear();
 };
 
@@ -130 +185 @@
  * \param bonds times bond::BondDegree
  */
-int atom::CountBonds() const
+int BondedParticle::CountBonds() const
 {
   int NoBonds = 0;
@@ -233 +288 @@
 };
 
-/** Output graph info of this atom.
+/** Outputs the MPQC configuration line for this atom.
  * \param *out output stream
- */
-void atom::OutputGraphInfo(ofstream *out) const
-{
-  *out << Verbose(2) << "Atom " << Name << " is " << ((SeparationVertex) ? "a" : "not a") << " separation vertex, components are ";
-  OutputComponentNumber(out);
-  *out << " with Lowpoint " << LowpointNr << " and Graph Nr. " << GraphNr << "." << endl;
-};
-
-/** Output a list of flags, stating whether the bond was visited or not.
- * Note, we make use of the last entry of the ComponentNr always being -1 if allocated.
- * \param *out output stream for debugging
- */
-void atom::OutputComponentNumber(ofstream *out) const
-{
-  if (ComponentNr != NULL) {
-    for (int i=0; ComponentNr[i] != -1; i++)
-      *out << ComponentNr[i] << " ";
-  }
-};
-
-
-/** Prints all bonds of this atom with total degree.
- * \param *out stream to output to
- * \return true - \a *out present, false - \a *out is NULL
- */
-bool atom::OutputBondOfAtom(ofstream *out) const
-{
-  if (out != NULL) {
-#ifdef ADDHYDROGEN
-    if (type->Z != 1) {   // regard only non-hydrogen
-#endif
-      *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: ";
-      int TotalDegree = 0;
-      for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
-        *out << **Runner << "\t";
-        TotalDegree += (*Runner)->BondDegree;
-      }
-      *out << " -- TotalDegree: " << TotalDegree << endl;
-#ifdef ADDHYDROGEN
-    }
-#endif
+ * \param *center center of molecule subtracted from position
+ * \param *AtomNo pointer to atom counter that is increased by one
+ */
+void atom::OutputMPQCLine(ofstream *out, Vector *center, int *AtomNo = NULL) const
+{
+  *out << "\t\t" << type->symbol << " [ " << x.x[0]-center->x[0] << "\t" << x.x[1]-center->x[1] << "\t" << x.x[2]-center->x[2] << " ]" << endl;
+  if (AtomNo != NULL)
+    *AtomNo++;
+};
+
+ostream & operator << (ostream &ost, const ParticleInfo &a)
+{
+  ost << "[" << a.Name << "|" << &a << "]";
+  return ost;
+};
+
+ostream & ParticleInfo::operator << (ostream &ost)
+{
+  ost << "[" << Name << "|" << this << "]";
+  return ost;
+};
+
+/** Compares the indices of \a this atom with a given \a ptr.
+ * \param ptr atom to compare index against
+ * \return true - this one's is smaller, false - not
+ */
+bool atom::Compare(const atom &ptr)
+{
+  if (nr < ptr.nr)
     return true;
-  } else
+  else
     return false;
 };
 
-/** Output of atom::nr along with all bond partners.
- * \param *AdjacencyFile output stream
- */
-void atom::OutputAdjacency(ofstream *AdjacencyFile) const
-{
-  *AdjacencyFile << nr << "\t";
-  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
-    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->nr << "\t";
-  *AdjacencyFile << endl;
-};
-
-/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
- * \param *file output stream
- */
-void atom::OutputOrder(ofstream *file)
-{
-  *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
-  //cout << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
+/** Returns squared distance to a given vector.
+ * \param origin vector to calculate distance to
+ * \return distance squared
+ */
+double atom::DistanceSquaredToVector(Vector &origin)
+{
+  return origin.DistanceSquared(&x);
+};
+
+/** Returns distance to a given vector.
+ * \param origin vector to calculate distance to
+ * \return distance
+ */
+double atom::DistanceToVector(Vector &origin)
+{
+  return origin.Distance(&x);
 };
 
@@ -313 +354 @@
 };
 
+
+bool operator < (atom &a, atom &b)
+{
+  return a.Compare(b);
+};
+
+/** Output graph info of this atom.
+ * \param *out output stream
+ */
+void GraphNode::OutputGraphInfo(ofstream *out) const
+{
+  *out << Verbose(2) << "Atom " << Name << " is " << ((SeparationVertex) ? "a" : "not a") << " separation vertex, components are ";
+  OutputComponentNumber(out);
+  *out << " with Lowpoint " << LowpointNr << " and Graph Nr. " << GraphNr << "." << endl;
+};
+
+/** Output a list of flags, stating whether the bond was visited or not.
+ * Note, we make use of the last entry of the ComponentNr always being -1 if allocated.
+ * \param *out output stream for debugging
+ */
+void GraphNode::OutputComponentNumber(ofstream *out) const
+{
+  if (ComponentNr != NULL) {
+    for (int i=0; ComponentNr[i] != -1; i++)
+      *out << ComponentNr[i] << " ";
+  }
+};
+
+/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
+ * \param *file output stream
+ */
+void BondedParticle::OutputOrder(ofstream *file)
+{
+  *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
+  //cout << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
+};
+
+/** Prints all bonds of this atom with total degree.
+ * \param *out stream to output to
+ * \return true - \a *out present, false - \a *out is NULL
+ */
+bool BondedParticle::OutputBondOfAtom(ofstream *out) const
+{
+  if (out != NULL) {
+    *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: ";
+    int TotalDegree = 0;
+    for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
+      *out << **Runner << "\t";
+      TotalDegree += (*Runner)->BondDegree;
+    }
+    *out << " -- TotalDegree: " << TotalDegree << endl;
+    return true;
+  } else
+    return false;
+};
+
+/** Output of atom::nr along with all bond partners.
+ * \param *AdjacencyFile output stream
+ */
+void BondedParticle::OutputAdjacency(ofstream *AdjacencyFile) const
+{
+  *AdjacencyFile << nr << "\t";
+  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
+    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->nr << "\t";
+  *AdjacencyFile << endl;
+};
+
 /** Puts a given bond into atom::ListOfBonds.
  * \param *Binder bond to insert
  */
-bool atom::RegisterBond(bond *Binder)
+bool BondedParticle::RegisterBond(bond *Binder)
 {
   bool status = false;
@@ -335 +443 @@
  * \param *Binder bond to remove
  */
-bool atom::UnregisterBond(bond *Binder)
+bool BondedParticle::UnregisterBond(bond *Binder)
 {
   bool status = false;
@@ -354 +462 @@
  * \note Does not do any memory de-allocation.
  */
-void atom::UnregisterAllBond()
+void BondedParticle::UnregisterAllBond()
 {
   ListOfBonds.clear();
@@ -362 +470 @@
  * \param *out output stream for debugging
  */
-int atom::CorrectBondDegree(ofstream *out)
+int BondedParticle::CorrectBondDegree(ofstream *out)
 {
   int NoBonds = 0;
@@ -395 +503 @@
 };
 
-ostream & operator << (ostream &ost, const atom &a)
-{
-  ost << "[" << a.Name << "|" << &a << "]";
-  return ost;
-};
-
-ostream & atom::operator << (ostream &ost)
-{
-  ost << "[" << Name << "|" << this << "]";
-  return ost;
-};
-
-/** Compares the indices of \a this atom with a given \a ptr.
- * \param ptr atom to compare index against
- * \return true - this one's is smaller, false - not
- */
-bool atom::Compare(const atom &ptr)
-{
-  if (nr < ptr.nr)
-    return true;
-  else
-    return false;
+/** Adds kinetic energy of this atom to given temperature value.
+ * \param *temperature add on this value
+ * \param step given step of trajectory to add
+ */
+void TrajectoryParticle::AddKineticToTemperature(double *temperature, int step) const
+{
+  for (int i=NDIM;i--;)
+    *temperature += type->mass * Trajectory.U.at(step).x[i]* Trajectory.U.at(step).x[i];
+};
+
+/** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
+ * \param startstep trajectory begins at
+ * \param endstep trajectory ends at
+ * \param **PermutationMap if atom switches places with some other atom, there is no translation but a permutaton noted here (not in the trajectories of each).
+ * \param *Force Force matrix to store result in
+ */
+void TrajectoryParticle::EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force)
+{
+  double constant = 10.;
+  TrajectoryParticle *Sprinter = PermutationMap[nr];
+  // set forces
+  for (int i=NDIM;i++;)
+    Force->Matrix[0][nr][5+i] += 2.*constant*sqrt(Trajectory.R.at(startstep).Distance(&Sprinter->Trajectory.R.at(endstep)));
+};
+
+/** Correct velocity against the summed \a CoGVelocity for \a step.
+ * \param *ActualTemp sum up actual temperature meanwhile
+ * \param Step MD step in atom::Tracjetory
+ * \param *CoGVelocity remnant velocity (i.e. vector sum of all atom velocities)
+ */
+void TrajectoryParticle::CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity)
+{
+  for(int d=0;d<NDIM;d++) {
+    Trajectory.U.at(Step).x[d] -= CoGVelocity->x[d];
+    *ActualTemp += 0.5 * type->mass * Trajectory.U.at(Step).x[d] * Trajectory.U.at(Step).x[d];
+  }
 };
 
@@ -423 +545 @@
  * \param MaxSteps
  */
-void atom::ResizeTrajectory(int MaxSteps)
+void TrajectoryParticle::ResizeTrajectory(int MaxSteps)
 {
   if (Trajectory.R.size() <= (unsigned int)(MaxSteps)) {
@@ -437 +559 @@
  * \param src index of source step
  */
-void atom::CopyStepOnStep(int dest, int src)
+void TrajectoryParticle::CopyStepOnStep(int dest, int src)
 {
   if (dest == src)  // self assignment check
@@ -455 +577 @@
  * \param *Force matrix with forces
  */
-void atom::VelocityVerletUpdate(int NextStep, config *configuration, ForceMatrix *Force)
+void TrajectoryParticle::VelocityVerletUpdate(int NextStep, config *configuration, ForceMatrix *Force)
 {
   //a = configuration.Deltat*0.5/walker->type->mass;        // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
@@ -484 +606 @@
  * \param *TotalVelocity pointer to tota velocity sum
  */
-void atom::SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity )
+void TrajectoryParticle::SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity )
 {
   *TotalMass += type->mass;  // sum up total mass
   for(int d=0;d<NDIM;d++) {
     TotalVelocity->x[d] += Trajectory.U.at(Step).x[d]*type->mass;
-  }
-};
-
-/** Returns squared distance to a given vector.
- * \param origin vector to calculate distance to
- * \return distance squared
- */
-double atom::DistanceSquaredToVector(Vector &origin)
-{
-  return origin.DistanceSquared(&x);
-};
-
-/** Adds kinetic energy of this atom to given temperature value.
- * \param *temperature add on this value
- * \param step given step of trajectory to add
- */
-void atom::AddKineticToTemperature(double *temperature, int step) const
-{
-  for (int i=NDIM;i--;)
-    *temperature += type->mass * Trajectory.U.at(step).x[i]* Trajectory.U.at(step).x[i];
-};
-
-/** Returns distance to a given vector.
- * \param origin vector to calculate distance to
- * \return distance
- */
-double atom::DistanceToVector(Vector &origin)
-{
-  return origin.Distance(&x);
-};
-
-bool operator < (atom &a, atom &b)
-{
-  return a.Compare(b);
-};
-
-/** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
- * \param startstep trajectory begins at
- * \param endstep trajectory ends at
- * \param **PermutationMap if atom switches places with some other atom, there is no translation but a permutaton noted here (not in the trajectories of each).
- * \param *Force Force matrix to store result in
- */
-void atom::EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force)
-{
-  double constant = 10.;
-  atom *Sprinter = PermutationMap[nr];
-  // set forces
-  for (int i=NDIM;i++;)
-    Force->Matrix[0][nr][5+i] += 2.*constant*sqrt(Trajectory.R.at(startstep).Distance(&Sprinter->Trajectory.R.at(endstep)));
-};
-
-/** Correct velocity against the summed \a CoGVelocity for \a step.
- * \param *ActualTemp sum up actual temperature meanwhile
- * \param Step MD step in atom::Tracjetory
- * \param *CoGVelocity remnant velocity (i.e. vector sum of all atom velocities)
- */
-void atom::CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity)
-{
-  for(int d=0;d<NDIM;d++) {
-    Trajectory.U.at(Step).x[d] -= CoGVelocity->x[d];
-    *ActualTemp += 0.5 * type->mass * Trajectory.U.at(Step).x[d] * Trajectory.U.at(Step).x[d];
   }
 };
@@ -558 +619 @@
  * \param *ekin sum of kinetic energy
  */
-void atom::Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin)
+void TrajectoryParticle::Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin)
 {
   double *U = Trajectory.U.at(Step).x;
@@ -573 +634 @@
  * \param *E
  */
-void atom::Thermostat_Gaussian_init(int Step, double *G, double *E)
+void TrajectoryParticle::Thermostat_Gaussian_init(int Step, double *G, double *E)
 {
   double *U = Trajectory.U.at(Step).x;
@@ -590 +651 @@
  * \param *configuration configuration class with TempFrequency and TargetTemp
  */
-void atom::Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration)
+void TrajectoryParticle::Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration)
 {
   double *U = Trajectory.U.at(Step).x;
@@ -606 +667 @@
  * \param *configuration configuration class with TempFrequency and TargetTemp
  */
-void atom::Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration)
+void TrajectoryParticle::Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration)
 {
   double sigma  = sqrt(configuration->TargetTemp/type->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
@@ -631 +692 @@
  * \param *configuration configuration class with TempFrequency and Deltat
  */
-void atom::Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration)
+void TrajectoryParticle::Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration)
 {
   double *U = Trajectory.U.at(Step).x;
@@ -646 +707 @@
  * \param *delta_alpha additional sum of kinetic energy on return
  */
-void atom::Thermostat_NoseHoover_init(int Step, double *delta_alpha)
+void TrajectoryParticle::Thermostat_NoseHoover_init(int Step, double *delta_alpha)
 {
   double *U = Trajectory.U.at(Step).x;
@@ -661 +722 @@
  * \param *configuration configuration class with TempFrequency and Deltat
  */
-void atom::Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)
+void TrajectoryParticle::Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)
 {
   double *U = Trajectory.U.at(Step).x;