Changeset be97a8 for src/Actions/WorldAction

Timestamp:

Jul 20, 2010, 1:01:11 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:

3d078d, 4b6777, c644a5

Parents:

ba9f5b (diff), 818eda (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 'StructureRefactoring' into stable

Conflicts:

test_all.sh

• test_all.sh was modified by Till in StructureRefactoring (these changes taken over).
• World::setDomain() was missing OBSERVE macro.
• MapOfActions: "molecule-by-name" needs String not Molecule.
• TESTFIX: Tesselations/defs.in - paths changed such that @srcdir@ may be absolute.
• TESTFIX: Tesselations/heptan/1.5/NonConvexEnvelope.dat - exchanged due to same surface but different polygon triangulation.
• TESTFIX: Domain/4 molecule-by-id changed from 208 to 207 due to different handling of molecule ids.

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) (6 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));
 
   if(dialog->display()) {
-    World::getInstance().setDomain(cell_size);
     // center
     vector<molecule *> AllMolecules = World::getInstance().getAllMolecules();

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;
     }
-    World::getInstance().setDomain(cell_size);
+    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 "Matrix.hpp"
 
 #include <iostream>
@@ -34 +36 @@
   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);
-    World::getInstance().setDomain(cell_size);
+    DoLog(0) && (Log() << Verbose(0) << "Setting box domain to " << cell_size.getM() << endl);
+    World::getInstance().setDomain(cell_size.getM());
     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

@@ -13 +13 @@
 #include "molecule.hpp"
 #include "vector.hpp"
+#include "Matrix.hpp"
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 
 #include <iostream>
@@ -46 +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;
@@ -59 +61 @@
   if(dialog->display()) {
     (cout << "Repeating box " << Repeater << " times for (x,y,z) axis." << endl);
-    double * const cell_size = World::getInstance().getDomain();
-    double *M = ReturnFullMatrixforSymmetric(cell_size);
+    Matrix M = World::getInstance().getDomain().getM();
+    Matrix newM = M;
     Vector x,y;
     int n[NDIM];
+    Matrix repMat;
     for (int axis = 0; axis < NDIM; axis++) {
       Repeater[axis] = floor(Repeater[axis]);
@@ -69 +72 @@
         Repeater[axis] = 1;
       }
-      cell_size[ ((axis == 1) ? 2 : (axis == 2) ? 5 : 0) ] *= Repeater[axis];
+      repMat.at(axis,axis) = Repeater[axis];
     }
+    newM *= repMat;
+    World::getInstance().setDomain(newM);
 
-    World::getInstance().setDomain(cell_size);
     molecule *newmol = NULL;
     Vector ** vectors = NULL;
@@ -99 +103 @@
                 DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
               x = y;
-              x.MatrixMultiplication(M);
+              x *= M;
               newmol = World::getInstance().createMolecule();
               molecules->insert(newmol);
@@ -119 +123 @@
       }
     }
-    delete(M);
     delete dialog;
     return Action::success;

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -14 +14 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
+#include "Matrix.hpp"
 
 #include <iostream>
@@ -37 +39 @@
   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 +50 @@
       (*AtomRunner)->x.ScaleAll(x);
     }
-    j = -1;
-    double * const cell_size = World::getInstance().getDomain();
+
+    Matrix M = World::getInstance().getDomain().getM();
+    Matrix scale;
+
     for (int i=0;i<NDIM;i++) {
-      j += i+1;
-      cell_size[j]*=x[i];
+      scale.at(i,i) = x[i];
     }
-    World::getInstance().setDomain(cell_size);
+    M *= scale;
+    World::getInstance().setDomain(M);
 
     delete dialog;