Changeset 84c494 for src/Actions/WorldAction

Timestamp:

Jun 30, 2010, 1:55:42 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

4907a3

Parents:

9df5c6

Message:

Made the world store the cell_size within a Box object.

Location:

src/Actions/WorldAction

Files:

• AddEmptyBoundaryAction.cpp (modified) (3 diffs)
• CenterInBoxAction.cpp (modified) (1 diff)
• CenterOnEdgeAction.cpp (modified) (3 diffs)
• ChangeBoxAction.cpp (modified) (2 diffs)
• RemoveSphereOfAtomsAction.cpp (modified) (1 diff)
• RepeatBoxAction.cpp (modified) (4 diffs)
• ScaleBoxAction.cpp (modified) (3 diffs)

src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

@@ -41 +41 @@
   int j=0;
 
-  dialog->queryVector(NAME, &boundary, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryVector(NAME, &boundary, false, MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {
@@ -59 +59 @@
     }
     // set new box size
-    double * const cell_size = World::getInstance().getDomain();
+    double * const cell_size = new double[6];
     for (j=0;j<6;j++)
       cell_size[j] = 0.;
@@ -67 +67 @@
       cell_size[j] = (Max[i]-Min[i]+2.*boundary[i]);
     }
+    World::getInstance().setDomain(cell_size);
+    delete[] cell_size;
     // translate all atoms, such that Min is aty (0,0,0)
     AtomRunner = AllAtoms.begin();

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -34 +34 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  double * cell_size = World::getInstance().getDomain();
+  Box& cell_size = World::getInstance().getDomain();
   dialog->queryBox(NAME, &cell_size, MapOfActions::getInstance().getDescription(NAME));
 

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -13 +13 @@
 #include "vector.hpp"
 #include "World.hpp"
+#include "Matrix.hpp"
 
 #include <iostream>
@@ -37 +38 @@
   Vector Min;
   Vector Max;
-  int j=0;
 
   dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
@@ -57 +57 @@
     }
     // set new box size
-    double * const cell_size = World::getInstance().getDomain();
-    for (j=0;j<6;j++)
-      cell_size[j] = 0.;
-    j=-1;
+    Matrix domain;
     for (int i=0;i<NDIM;i++) {
-      j += i+1;
-      cell_size[j] = (Max[i]-Min[i]);
+      double tmp = Max[i]-Min[i];
+      tmp = fabs(tmp)>=1. ? tmp : 1.0;
+      domain.at(i,i) = tmp;
     }
+    cout << "new domain is: " << domain << endl;
+    World::getInstance().setDomain(domain);
     // translate all atoms, such that Min is aty (0,0,0)
     for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner)

src/Actions/WorldAction/ChangeBoxAction.cpp

@@ -12 +12 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 
 #include <iostream>
@@ -34 +35 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  double * cell_size = World::getInstance().getDomain();
+  Box& cell_size = World::getInstance().getDomain();
   dialog->queryBox(NAME, &cell_size, MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {
-    DoLog(0) && (Log() << Verbose(0) << "Setting box domain to " << cell_size[0] << "," << cell_size[1] << "," << cell_size[2] << "," << cell_size[3] << "," << cell_size[4] << "," << cell_size[5] << "," << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Setting box domain to " << cell_size.getM() << endl);
     delete dialog;
     return Action::success;

src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

@@ -41 +41 @@
 
   dialog->queryDouble(NAME, &radius, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryVector("position", &point, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription("position"));
+  dialog->queryVector("position", &point, false, MapOfActions::getInstance().getDescription("position"));
 
   if(dialog->display()) {

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -16 +16 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 
 #include <iostream>
@@ -47 +48 @@
   MoleculeListClass *molecules = World::getInstance().getMolecules();
 
-  dialog->queryVector(NAME, &Repeater, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryVector(NAME, &Repeater, false, MapOfActions::getInstance().getDescription(NAME));
   //dialog->queryMolecule("molecule-by-id", &mol,MapOfActions::getInstance().getDescription("molecule-by-id"));
   vector<molecule *> AllMolecules;
@@ -60 +61 @@
   if(dialog->display()) {
     (cout << "Repeating box " << Repeater << " times for (x,y,z) axis." << endl);
-    double * const cell_size = World::getInstance().getDomain();
-    Matrix M = ReturnFullMatrixforSymmetric(cell_size);
+    const Matrix &M = World::getInstance().getDomain().getM();
+    Matrix newM = M;
     Vector x,y;
     int n[NDIM];
@@ -70 +71 @@
         Repeater[axis] = 1;
       }
-      cell_size[(abs(axis+1) == 2) ? 2 : ((abs(axis+2) == 3) ? 5 : 0)] *= Repeater[axis];
+      newM.at(axis,axis) *= Repeater[axis];
     }
+    World::getInstance().getDomain().setM(newM);
 
     molecule *newmol = NULL;

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -14 +14 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 
 #include <iostream>
@@ -37 +38 @@
   Vector Scaler;
   double x[NDIM];
-  int j=0;
 
-  dialog->queryVector(NAME, &Scaler, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryVector(NAME, &Scaler, false, MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {
@@ -49 +49 @@
       (*AtomRunner)->x.ScaleAll(x);
     }
-    j = -1;
-    double * const cell_size = World::getInstance().getDomain();
+
+    Matrix M = World::getInstance().getDomain().getM();
     for (int i=0;i<NDIM;i++) {
-      j += i+1;
-      cell_size[j]*=x[i];
+      M.at(i,i) *= x[i];
     }