Changeset 8f4df1 for src/Actions/WorldAction

Timestamp:

Aug 7, 2010, 12:07:04 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:

2d292d

Parents:

8d6d31 (diff), d74077 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'AtomicPositionEncapsulation' into stable

Conflicts:

src/Actions/AtomAction/ChangeElementAction.cpp
src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp
src/Makefile.am
src/UIElements/TextUI/TextDialog.cpp
src/analysis_correlation.hpp
src/atom.cpp
src/atom_atominfo.hpp
src/bond.cpp
src/boundary.cpp
src/molecule_geometry.cpp
src/tesselation.cpp
src/tesselationhelpers.cpp
src/triangleintersectionlist.cpp
src/unittests/Makefile.am

• fixed #includes due to moves to Helpers and LinearAlgebra
• moved VectorInterface.* and vector_ops.* to LinearAlgebra
• no more direct access of atom::node, remapped to set/getPosition()
• no more direct access to atom::type, remapped to set/getType() (also in atom due to derivation and atominfo::AtomicElement is private not protected).

Location:

src/Actions/WorldAction

Files:

• AddEmptyBoundaryAction.cpp (modified) (2 diffs)
• CenterOnEdgeAction.cpp (modified) (2 diffs)
• RemoveSphereOfAtomsAction.cpp (modified) (2 diffs)
• RepeatBoxAction.cpp (modified) (5 diffs)
• ScaleBoxAction.cpp (modified) (1 diff)

src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

@@ -60 +60 @@
   ASSERT(AllAtoms.size() > 0, "There must be atoms present for AddingEmptyBoundary.");
   vector<atom *>::iterator AtomRunner = AllAtoms.begin();
-  Min = (*AtomRunner)->x;
-  Max = (*AtomRunner)->x;
+  Min = (*AtomRunner)->getPosition();
+  Max = (*AtomRunner)->getPosition();
   for (; AtomRunner != AllAtoms.end(); ++AtomRunner) {
     for (int i=0;i<NDIM;i++) {
-      if ((*AtomRunner)->x[i] > Max[i])
-        Max[i] = (*AtomRunner)->x[i];
-      if ((*AtomRunner)->x[i] < Min[i])
-        Min[i] = (*AtomRunner)->x[i];
+      if ((*AtomRunner)->at(i) > Max[i])
+        Max[i] = (*AtomRunner)->at(i);
+      if ((*AtomRunner)->at(i) < Min[i])
+        Min[i] = (*AtomRunner)->at(i);
     }
   }
@@ -84 +84 @@
   AtomRunner = AllAtoms.begin();
   for (; AtomRunner != AllAtoms.end(); ++AtomRunner)
-    (*AtomRunner)->x -= Min - boundary;
+    *(*AtomRunner) -= Min - boundary;
   return Action::success;
 }

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -55 +55 @@
   ASSERT(AllAtoms.size() > 0, "For CenteronEdge atoms must be present.");
   vector<atom *>::iterator AtomRunner = AllAtoms.begin();
-  Min = (*AtomRunner)->x;
-  Max = (*AtomRunner)->x;
+  Min = (*AtomRunner)->getPosition();
+  Max = (*AtomRunner)->getPosition();
   for (; AtomRunner != AllAtoms.end(); ++AtomRunner) {
     for (int i=0;i<NDIM;i++) {
-      if ((*AtomRunner)->x[i] > Max[i])
-        Max[i] = (*AtomRunner)->x[i];
-      if ((*AtomRunner)->x[i] < Min[i])
-        Min[i] = (*AtomRunner)->x[i];
+      if ((*AtomRunner)->at(i) > Max[i])
+        Max[i] = (*AtomRunner)->at(i);
+      if ((*AtomRunner)->at(i) < Min[i])
+        Min[i] = (*AtomRunner)->at(i);
     }
   }
@@ -75 +75 @@
   // translate all atoms, such that Min is aty (0,0,0)
   for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner)
-    (*AtomRunner)->x -= Min;
+    *(*AtomRunner) -= Min;
 
   return Action::success;

src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

@@ -62 +62 @@
   vector<molecule *> molecules = World::getInstance().getAllMolecules();
   for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner) {
-    if (point.DistanceSquared((*AtomRunner)->x) > radius*radius) { // distance to first above radius ...
+    if ((*AtomRunner)->DistanceSquared(point) > radius*radius) { // distance to first above radius ...
+//      cout << "Removing " << (*AtomRunner)->getType()->symbol << (*AtomRunner)->getId() << " at " << (*AtomRunner)->getPosition() << " as distance is " << sqrt((*AtomRunner)->DistanceSquared(point)) << endl;
       // TODO: This is not necessary anymore when atoms are completely handled by World (create/destroy and load/save)
       for (vector<molecule *>::iterator iter = molecules.begin();iter != molecules.end();++iter)
@@ -68 +69 @@
       World::getInstance().destroyAtom(*AtomRunner);
     }
+//    else {
+//      cout << "Keeping" << (*AtomRunner)->getType()->symbol << (*AtomRunner)->getId() << " at " << (*AtomRunner)->getPosition() << " as distance is " << sqrt((*AtomRunner)->DistanceSquared(point)) << endl;
+//    }
   }
   return Action::success;

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -21 +21 @@
 #include <iostream>
 #include <string>
+#include <vector>
 
 using namespace std;
@@ -90 +91 @@
 
   molecule *newmol = NULL;
-  Vector ** vectors = NULL;
+  std::vector<Vector> vectors;
   for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
     y[0] = n[0];
@@ -105 +106 @@
           if (count != 0) {  // if there is more than none
             Elements = new const element *[count];
-            vectors = new Vector *[count];
+            vectors.resize(count);
             j = 0;
             for(molecule::iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
-              Elements[j] = (*AtomRunner)->type;
-              vectors[j] = &(*AtomRunner)->x;
+              Elements[j] = (*AtomRunner)->getType();
+              vectors[j] = (*AtomRunner)->getPosition();
               j++;
             }
@@ -120 +121 @@
             for (int k=count;k--;) { // go through every atom of the original cell
               Walker = World::getInstance().createAtom(); // create a new body
-              Walker->x = (*vectors[k]) + x;
-              Walker->type = Elements[k];  // insert original element
+              Walker->setPosition((vectors[k]) + x);
+              Walker->setType(Elements[k]);  // insert original element
               cout << "new atom is " << *Walker << endl;
               newmol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
@@ -127 +128 @@
             // free memory
             delete[](Elements);
-            delete[](vectors);
           } else {
             DoLog(1) && (Log() << Verbose(1) << "\t ... is empty." << endl);

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -60 +60 @@
   vector<atom*> AllAtoms = World::getInstance().getAllAtoms();
   for(vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner) {
-    (*AtomRunner)->x.ScaleAll(x);
+    (*AtomRunner)->ScaleAll(x);
   }