Changeset 54b42e

Timestamp:

Feb 24, 2011, 4:35:59 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:

6625c3

Parents:

bce72c

git-author:

Frederik Heber <heber@…> (02/07/11 18:56:11)

git-committer:

Frederik Heber <heber@…> (02/24/11 16:35:59)

Message:

AtomInfo::AtomicPosition, ::AtomicVelocity, ::AtomicForce are now a std:vector.

• This is preparatory for trajectories.

Location:

src

Files:

• atom_atominfo.cpp (modified) (10 diffs)
• atom_atominfo.hpp (modified) (2 diffs)

src/atom_atominfo.cpp

@@ -29 +29 @@
 AtomInfo::AtomInfo() :
   AtomicElement(NULL)
-{};
+{
+  AtomicPosition.reserve(1);
+  AtomicPosition.push_back(zeroVec);
+  AtomicVelocity.reserve(1);
+  AtomicVelocity.push_back(zeroVec);
+  AtomicForce.reserve(1);
+  AtomicForce.push_back(zeroVec);
+};
 
 /** Copy constructor of class AtomInfo.
@@ -39 +46 @@
 
 AtomInfo::AtomInfo(const VectorInterface &_v) :
-    AtomicPosition(_v.getPosition()),
     AtomicElement(NULL)
-{};
+{
+  AtomicPosition[0] = _v.getPosition();
+};
 
 /** Destructor of class AtomInfo.
@@ -56 +64 @@
 const double& AtomInfo::operator[](size_t i) const
 {
-  return AtomicPosition[i];
+  return AtomicPosition[0][i];
 }
 
 const double& AtomInfo::at(size_t i) const
 {
-  return AtomicPosition.at(i);
+  return AtomicPosition[0].at(i);
 }
 
 void AtomInfo::set(size_t i, const double value)
 {
-  AtomicPosition.at(i) = value;
+  AtomicPosition[0].at(i) = value;
 }
 
 const Vector& AtomInfo::getPosition() const
 {
-  return AtomicPosition;
+  return AtomicPosition[0];
 }
 
@@ -85 +93 @@
 Vector& AtomInfo::getAtomicVelocity()
 {
-  return AtomicVelocity;
+  return AtomicVelocity[0];
 }
 
 const Vector& AtomInfo::getAtomicVelocity() const
 {
-  return AtomicVelocity;
+  return AtomicVelocity[0];
 }
 
 void AtomInfo::setAtomicVelocity(const Vector &_newvelocity)
 {
-  AtomicVelocity = _newvelocity;
+  AtomicVelocity[0] = _newvelocity;
 }
 
 const Vector& AtomInfo::getAtomicForce() const
 {
-  return AtomicForce;
+  return AtomicForce[0];
 }
 
 void AtomInfo::setAtomicForce(const Vector &_newforce)
 {
-  AtomicForce = _newforce;
+  AtomicForce[0] = _newforce;
 }
 
 void AtomInfo::setPosition(const Vector& _vector)
 {
-  AtomicPosition = _vector;
+  AtomicPosition[0] = _vector;
   //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
 }
@@ -116 +124 @@
 const VectorInterface& AtomInfo::operator+=(const Vector& b)
 {
-  AtomicPosition += b;
+  AtomicPosition[0] += b;
   return *this;
 }
@@ -122 +130 @@
 const VectorInterface& AtomInfo::operator-=(const Vector& b)
 {
-  AtomicPosition -= b;
+  AtomicPosition[0] -= b;
   return *this;
 }
@@ -128 +136 @@
 Vector const AtomInfo::operator+(const Vector& b) const
 {
-  Vector a(AtomicPosition);
+  Vector a(AtomicPosition[0]);
   a += b;
   return a;
@@ -135 +143 @@
 Vector const AtomInfo::operator-(const Vector& b) const
 {
-  Vector a(AtomicPosition);
+  Vector a(AtomicPosition[0]);
   a -= b;
   return a;
@@ -142 +150 @@
 double AtomInfo::distance(const Vector &point) const
 {
-  return AtomicPosition.distance(point);
+  return AtomicPosition[0].distance(point);
 }
 
 double AtomInfo::DistanceSquared(const Vector &y) const
 {
-  return AtomicPosition.DistanceSquared(y);
+  return AtomicPosition[0].DistanceSquared(y);
 }
 
 double AtomInfo::distance(const VectorInterface &_atom) const
 {
-  return _atom.distance(AtomicPosition);
+  return _atom.distance(AtomicPosition[0]);
 }
 
 double AtomInfo::DistanceSquared(const VectorInterface &_atom) const
 {
-  return _atom.DistanceSquared(AtomicPosition);
+  return _atom.DistanceSquared(AtomicPosition[0]);
 }
 
 VectorInterface &AtomInfo::operator=(const Vector& _vector)
 {
-  AtomicPosition = _vector;
+  AtomicPosition[0] = _vector;
   return *this;
 }
@@ -168 +176 @@
 void AtomInfo::ScaleAll(const double *factor)
 {
-  AtomicPosition.ScaleAll(factor);
+  AtomicPosition[0].ScaleAll(factor);
 }
 
 void AtomInfo::ScaleAll(const Vector &factor)
 {
-  AtomicPosition.ScaleAll(factor);
+  AtomicPosition[0].ScaleAll(factor);
 }
 
 void AtomInfo::Scale(const double factor)
 {
-  AtomicPosition.Scale(factor);
+  AtomicPosition[0].Scale(factor);
 }
 
 void AtomInfo::Zero()
 {
-  AtomicPosition.Zero();
+  AtomicPosition[0].Zero();
 }
 
 void AtomInfo::One(const double one)
 {
-  AtomicPosition.One(one);
+  AtomicPosition[0].One(one);
 }
 
 void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors)
 {
-  AtomicPosition.LinearCombinationOfVectors(x1,x2,x3,factors);
+  AtomicPosition[0].LinearCombinationOfVectors(x1,x2,x3,factors);
 }
 

src/atom_atominfo.hpp

@@ -18 +18 @@
 #include <config.h>
 #endif
+
+#include <vector>
 
 #include "LinearAlgebra/Vector.hpp"
@@ -115 +117 @@
 
 private:
-  Vector AtomicPosition;       //!< coordinate vector of atom, giving last position within cell
-  Vector AtomicVelocity;       //!< velocity vector of atom, giving last velocity within cell
-  Vector AtomicForce;       //!< Force vector of atom, giving last force within cell
+  std::vector<Vector> AtomicPosition;       //!< coordinate vector of atom, giving last position within cell
+  std::vector<Vector> AtomicVelocity;       //!< velocity vector of atom, giving last velocity within cell
+  std::vector<Vector> AtomicForce;       //!< Force vector of atom, giving last force within cell
 
   const element *AtomicElement;  //!< pointing to element