Changeset d74077 for src/atom.cpp

Timestamp:

Jul 31, 2010, 3:23:10 PM (15 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:

8f4df1

Parents:

5fbaeb

Message:

Member variable Vector and element of class atom are now private.

• renamed to AtomicPosition
• created interface class VectorInterface with alle functions from class Vector as virtual ones
• implemented in AtomInfo
• everywhere direct access to AtomicPosition has been replaced by get/setPosition() and others
• for element get/setType() have been present already, direct access has been replaced by calling of these.
• class TesselPoint now derives from AtomInfo and ParticleInfo
• tesselation.cpp split up
  • new files for the classes: BoundaryLineSet, BoundaryPointSet, BoundaryPolygonSet, BoundaryTriangleSet, CandidateForTesselation, PointCloud, TesselPoint
  • all defines are in BoundaryMaps.hpp

File:

• src/atom.cpp (modified) (13 diffs)

src/atom.cpp ¶

@@ -27 +27 @@
 atom::atom() :
   father(this), sort(&nr), mol(0)
-{
-  node = &x;  // TesselPoint::x can only be referenced from here
-};
+{};
 
 /** Constructor of class atom.
@@ -36 +34 @@
     ParticleInfo(pointer),father(pointer), sort(&nr)
 {
-  type = pointer->type;  // copy element of atom
-  x = pointer->x; // copy coordination
-  v = pointer->v; // copy velocity
+  setType(pointer->getType());  // copy element of atom
+  setPosition(pointer->getPosition()); // copy coordination
+  AtomicVelocity = pointer->AtomicVelocity; // copy velocity
   FixedIon = pointer->FixedIon;
-  node = &x;
   mol = 0;
 };
@@ -48 +45 @@
   res->father = this;
   res->sort = &res->nr;
-  res->type = type;
-  res->x = this->x;
-  res->v = this->v;
+  res->setType(getType());
+  res->setPosition(this->getPosition());
+  res->AtomicVelocity = this->AtomicVelocity;
   res->FixedIon = FixedIon;
-  res->node = &x;
   res->mol = 0;
   World::getInstance().registerAtom(res);
@@ -116 +112 @@
 bool atom::IsInShape(const Shape& shape) const
 {
-  return shape.isInside(*node);
+  return shape.isInside(getPosition());
 };
 
@@ -141 +137 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x[0] << "\t" << x[1] << "\t" << x[2];
+    *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
+    if (AtomicVelocity.Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -163 +159 @@
 bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
 {
-  AtomNo[type->Z]++;  // increment number
-  if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x[0] << "\t" << x[1] << "\t" << x[2];
+  AtomNo[getType()->Z]++;  // increment number
+  if (out != NULL) {
+    *out << "Ion_Type" << ElementNo[getType()->Z] << "_" << AtomNo[getType()->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+    *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
+    if (AtomicVelocity.Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -186 +182 @@
 {
   if (out != NULL) {
-    *out << type->symbol << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
+    *out << getType()->symbol << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
     return true;
   } else
@@ -201 +197 @@
 bool atom::OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const
 {
-  AtomNo[type->Z]++;
-  if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+  AtomNo[getType()->Z]++;
+  if (out != NULL) {
+    *out << "Ion_Type" << ElementNo[getType()->Z] << "_" << AtomNo[getType()->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
     *out << "\t" << FixedIon;
@@ -224 +220 @@
 {
   if (out != NULL) {
-    *out << type->symbol << "\t";
+    *out << getType()->symbol << "\t";
     *out << Trajectory.R.at(step)[0] << "\t";
     *out << Trajectory.R.at(step)[1] << "\t";
@@ -240 +236 @@
 void atom::OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo = NULL) const
 {
-  *out << "\t\t" << type->symbol << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;
+  Vector recentered(getPosition());
+  recentered -= *center;
+  *out << "\t\t" << getType()->symbol << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
   if (AtomNo != NULL)
     *AtomNo++;
@@ -263 +261 @@
 double atom::DistanceSquaredToVector(const Vector &origin) const
 {
-  return origin.DistanceSquared(x);
+  return DistanceSquared(origin);
 };
 
@@ -272 +270 @@
 double atom::DistanceToVector(const Vector &origin) const
 {
-  return origin.distance(x);
+  return distance(origin);
 };
 
@@ -287 +285 @@
 };
 
+std::ostream & atom::operator << (std::ostream &ost) const
+{
+  ParticleInfo::operator<<(ost);
+  ost << "," << getPosition();
+  return ost;
+}
+
+std::ostream & operator << (std::ostream &ost, const atom &a)
+{
+  a.ParticleInfo::operator<<(ost);
+  ost << "," << a.getPosition();
+  return ost;
+}
 
 bool operator < (atom &a, atom &b)