Changeset 056e70 for src/atom_atominfo.cpp

Timestamp:

Feb 24, 2011, 5:56:03 PM (14 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:

6b020f

Parents:

6625c3

Message:

Suffixed getters and setters for AtomInfo trajecories with AtStep.

• AtomInfo:: getters are now const members
• added lots of ASSERTS to getters with time step to assure no out-of-bounds access.

File:

• src/atom_atominfo.cpp (modified) (25 diffs)

src/atom_atominfo.cpp

@@ -80 +80 @@
 const double& AtomInfo::operator[](size_t i) const
 {
+  ASSERT(AtomicPosition.size() > 0,
+      "AtomInfo::operator[]() - Access out of range.");
   return AtomicPosition[0][i];
 }
@@ -85 +87 @@
 const double& AtomInfo::at(size_t i) const
 {
+  ASSERT(AtomicPosition.size() > 0,
+      "AtomInfo::at() - Access out of range.");
   return AtomicPosition[0].at(i);
 }
 
+const double& AtomInfo::atStep(size_t i, int _step) const
+{
+  ASSERT(AtomicPosition.size() > _step,
+      "AtomInfo::atStep() - Access out of range.");
+  return AtomicPosition[_step].at(i);
+}
+
 void AtomInfo::set(size_t i, const double value)
 {
+  ASSERT(AtomicPosition.size() > 0,
+      "AtomInfo::set() - Access out of range.");
   AtomicPosition[0].at(i) = value;
 }
@@ -95 +108 @@
 const Vector& AtomInfo::getPosition() const
 {
+  ASSERT(AtomicPosition.size() > 0,
+      "AtomInfo::getPosition() - Access out of range.");
   return AtomicPosition[0];
 }
 
-const Vector& AtomInfo::getPosition(const int _step) const
+const Vector& AtomInfo::getPositionAtStep(const int _step) const
 {
   ASSERT(_step < AtomicPosition.size(),
-      "AtomInfo::getPosition() - Access out of range.");
+      "AtomInfo::getPositionAtStep() - Access out of range.");
   return AtomicPosition[_step];
 }
@@ -114 +129 @@
 }
 
-Vector& AtomInfo::getAtomicVelocity()
-{
+//Vector& AtomInfo::getAtomicVelocity()
+//{
+//  return AtomicVelocity[0];
+//}
+
+//Vector& AtomInfo::getAtomicVelocity(const int _step)
+//{
+//  ASSERT(_step < AtomicVelocity.size(),
+//      "AtomInfo::getAtomicVelocity() - Access out of range.");
+//  return AtomicVelocity[_step];
+//}
+
+const Vector& AtomInfo::getAtomicVelocity() const
+{
+  ASSERT(AtomicVelocity.size() > 0,
+      "AtomInfo::getAtomicVelocity() - Access out of range.");
   return AtomicVelocity[0];
 }
 
-Vector& AtomInfo::getAtomicVelocity(const int _step)
+const Vector& AtomInfo::getAtomicVelocityAtStep(const int _step) const
 {
   ASSERT(_step < AtomicVelocity.size(),
@@ -126 +155 @@
 }
 
-const Vector& AtomInfo::getAtomicVelocity() const
-{
-  return AtomicVelocity[0];
-}
-
-const Vector& AtomInfo::getAtomicVelocity(const int _step) const
-{
-  ASSERT(_step < AtomicVelocity.size(),
-      "AtomInfo::getAtomicVelocity() - Access out of range.");
-  return AtomicVelocity[_step];
-}
-
 void AtomInfo::setAtomicVelocity(const Vector &_newvelocity)
 {
+  ASSERT(0 < AtomicVelocity.size(),
+      "AtomInfo::setAtomicVelocity() - Access out of range.");
   AtomicVelocity[0] = _newvelocity;
 }
 
-void AtomInfo::setAtomicVelocity(const int _step, const Vector &_newvelocity)
+void AtomInfo::setAtomicVelocityAtStep(const int _step, const Vector &_newvelocity)
 {
   ASSERT(_step <= AtomicVelocity.size(),
-      "AtomInfo::setAtomicVelocity() - Access out of range.");
+      "AtomInfo::setAtomicVelocityAtStep() - Access out of range.");
   if(_step < (int)AtomicVelocity.size()) {
     AtomicVelocity[_step] = _newvelocity;
@@ -156 +175 @@
 const Vector& AtomInfo::getAtomicForce() const
 {
+  ASSERT(0 < AtomicForce.size(),
+      "AtomInfo::getAtomicForce() - Access out of range.");
   return AtomicForce[0];
 }
 
-const Vector& AtomInfo::getAtomicForce(const int _step) const
+const Vector& AtomInfo::getAtomicForceAtStep(const int _step) const
 {
   ASSERT(_step < AtomicForce.size(),
@@ -168 +189 @@
 void AtomInfo::setAtomicForce(const Vector &_newforce)
 {
+  ASSERT(0 < AtomicForce.size(),
+      "AtomInfo::setAtomicForce() - Access out of range.");
   AtomicForce[0] = _newforce;
 }
 
-void AtomInfo::setAtomicForce(const int _step, const Vector &_newforce)
-{
-  ASSERT(_step <= AtomicForce.size(),
+void AtomInfo::setAtomicForceAtStep(const int _step, const Vector &_newforce)
+{
+  const int size = AtomicForce.size();
+  ASSERT(_step <= size,
       "AtomInfo::setAtomicForce() - Access out of range.");
-  if(_step < (int)AtomicForce.size()) {
+  if(_step < size) {
     AtomicForce[_step] = _newforce;
-  } else if (_step == (int)AtomicForce.size()) {
+  } else if (_step == size) {
     AtomicForce.push_back(_newforce);
   }
@@ -194 +218 @@
 void AtomInfo::setPosition(const Vector& _vector)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::setPosition() - Access out of range.");
   AtomicPosition[0] = _vector;
   //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
 }
 
-void AtomInfo::setPosition(int _step, const Vector& _vector)
+void AtomInfo::setPositionAtStep(int _step, const Vector& _vector)
 {
   ASSERT(_step <= AtomicPosition.size(),
@@ -212 +238 @@
 const VectorInterface& AtomInfo::operator+=(const Vector& b)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::operator+=() - Access out of range.");
   AtomicPosition[0] += b;
   return *this;
@@ -218 +246 @@
 const VectorInterface& AtomInfo::operator-=(const Vector& b)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::operator-=() - Access out of range.");
   AtomicPosition[0] -= b;
   return *this;
@@ -224 +254 @@
 Vector const AtomInfo::operator+(const Vector& b) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::operator+() - Access out of range.");
   Vector a(AtomicPosition[0]);
   a += b;
@@ -231 +263 @@
 Vector const AtomInfo::operator-(const Vector& b) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::operator-() - Access out of range.");
   Vector a(AtomicPosition[0]);
   a -= b;
@@ -238 +272 @@
 double AtomInfo::distance(const Vector &point) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::distance() - Access out of range.");
   return AtomicPosition[0].distance(point);
 }
@@ -243 +279 @@
 double AtomInfo::DistanceSquared(const Vector &y) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::DistanceSquared() - Access out of range.");
   return AtomicPosition[0].DistanceSquared(y);
 }
@@ -248 +286 @@
 double AtomInfo::distance(const VectorInterface &_atom) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::distance() - Access out of range.");
   return _atom.distance(AtomicPosition[0]);
 }
@@ -253 +293 @@
 double AtomInfo::DistanceSquared(const VectorInterface &_atom) const
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::DistanceSquared() - Access out of range.");
   return _atom.DistanceSquared(AtomicPosition[0]);
 }
@@ -258 +300 @@
 VectorInterface &AtomInfo::operator=(const Vector& _vector)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::operator=() - Access out of range.");
   AtomicPosition[0] = _vector;
   return *this;
@@ -264 +308 @@
 void AtomInfo::ScaleAll(const double *factor)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::ScaleAll() - Access out of range.");
   AtomicPosition[0].ScaleAll(factor);
 }
@@ -269 +315 @@
 void AtomInfo::ScaleAll(const Vector &factor)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::ScaleAll() - Access out of range.");
   AtomicPosition[0].ScaleAll(factor);
 }
@@ -274 +322 @@
 void AtomInfo::Scale(const double factor)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::Scale() - Access out of range.");
   AtomicPosition[0].Scale(factor);
 }
@@ -279 +329 @@
 void AtomInfo::Zero()
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::Zero() - Access out of range.");
   AtomicPosition[0].Zero();
 }
@@ -284 +336 @@
 void AtomInfo::One(const double one)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::One() - Access out of range.");
   AtomicPosition[0].One(one);
 }
@@ -289 +343 @@
 void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors)
 {
+  ASSERT(0 < AtomicPosition.size(),
+      "AtomInfo::LinearCombinationOfVectors() - Access out of range.");
   AtomicPosition[0].LinearCombinationOfVectors(x1,x2,x3,factors);
 }
@@ -295 +351 @@
  *  returns the kinetic energy of this atom at a given time step
  */
-double AtomInfo::getKineticEnergy(unsigned int step) const{
-  return getMass() * AtomicVelocity[step].NormSquared();
-}
-
-Vector AtomInfo::getMomentum(unsigned int step) const{
-  return getMass()*AtomicVelocity[step];
+double AtomInfo::getKineticEnergy(unsigned int _step) const{
+  ASSERT(_step < AtomicPosition.size(),
+      "AtomInfo::getKineticEnergy() - Access out of range.");
+  return getMass() * AtomicVelocity[_step].NormSquared();
+}
+
+Vector AtomInfo::getMomentum(unsigned int _step) const{
+  ASSERT(_step < AtomicPosition.size(),
+      "AtomInfo::getMomentum() - Access out of range.");
+  return getMass()*AtomicVelocity[_step];
 }
 
@@ -354 +414 @@
 void AtomInfo::VelocityVerletUpdate(int nr, int NextStep, config *configuration, ForceMatrix *Force, const size_t offset)
 {
-  //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
-  if ((int)AtomicPosition.size() <= NextStep)
-    ResizeTrajectory(NextStep+10);
-  for (int d=0; d<NDIM; d++) {
-    AtomicForce.at(NextStep)[d] = -Force->Matrix[0][nr][d+offset]*(configuration->GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
-    AtomicPosition.at(NextStep)[d] = AtomicPosition.at(NextStep-1)[d];
-    AtomicPosition.at(NextStep)[d] += configuration->Deltat*(AtomicVelocity.at(NextStep-1)[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
-    AtomicPosition.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(AtomicForce.at(NextStep)[d]/getMass());     // F = m * a and s =
-  }
+  // update force
+  // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
+  Vector tempVector;
+  for (int d=0; d<NDIM; d++)
+    tempVector[d] = -Force->Matrix[0][nr][d+offset]*(configuration->GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
+  setAtomicForceAtStep(NextStep, tempVector);
+
+  // update position
+  tempVector = getPositionAtStep(NextStep-1);
+  tempVector += configuration->Deltat*(getAtomicVelocityAtStep(NextStep-1));     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
+  tempVector += 0.5*configuration->Deltat*configuration->Deltat*(getAtomicForceAtStep(NextStep))*(1./getMass());     // F = m * a and s =
+  setPositionAtStep(NextStep, tempVector);
+
   // Update U
-  for (int d=0; d<NDIM; d++) {
-    AtomicVelocity.at(NextStep)[d] = AtomicVelocity.at(NextStep-1)[d];
-    AtomicVelocity.at(NextStep)[d] += configuration->Deltat * (AtomicForce.at(NextStep)[d]+AtomicForce.at(NextStep-1)[d]/getMass()); // v = F/m * t
-  }
-  // Update R (and F)
-//      out << "Integrated position&velocity of step " << (NextStep) << ": (";
-//      for (int d=0;d<NDIM;d++)
-//        out << AtomicPosition.at(NextStep).x[d] << " ";          // next step
-//      out << ")\t(";
-//      for (int d=0;d<NDIM;d++)
-//        Log() << Verbose(0) << AtomicVelocity.at(NextStep).x[d] << " ";          // next step
-//      out << ")" << endl;
+  tempVector = getAtomicVelocityAtStep(NextStep-1);
+  tempVector += configuration->Deltat * (getAtomicForceAtStep(NextStep)+getAtomicForceAtStep(NextStep-1))*(1./getMass()); // v = F/m * t
+  setAtomicVelocityAtStep(NextStep, tempVector);
+
+  // some info for debugging
+  DoLog(2) && (Log() << Verbose(2)
+      << "Integrated position&velocity of step " << (NextStep) << ": ("
+      << getPositionAtStep(NextStep) << ")\t("
+      << getAtomicVelocityAtStep(NextStep) << ")" << std::endl);
 };