Changeset 8f4df1 for src/Parser

Timestamp:

Aug 7, 2010, 12:07:04 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:

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/Parser

Files:

• MpqcParser.cpp (modified) (2 diffs)
• PcpParser.cpp (modified) (3 diffs)
• TremoloParser.cpp (modified) (3 diffs)
• XyzParser.cpp (modified) (3 diffs)

src/Parser/MpqcParser.cpp

@@ -62 +62 @@
   // calculate center
   for (vector<atom *>::iterator runner = allatoms.begin();runner != allatoms.end(); ++runner)
-    center += (*runner)->x;
+    center += (*runner)->getPosition();
   center.Scale(1./allatoms.size());
 
@@ -110 +110 @@
   // calculate center
   for (vector<atom *>::iterator runner = allatoms.begin();runner != allatoms.end(); ++runner)
-    center += (*runner)->x;
+    center += (*runner)->getPosition();
   center.Scale(1./allatoms.size());
 

src/Parser/PcpParser.cpp

@@ -462 +462 @@
   PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
   for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
-    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->type->NoValenceOrbitals;
+    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->NoValenceOrbitals;
   }
   cout << PlaneWaveSpecifics.MaxPsiDouble << endl;
@@ -497 +497 @@
   // insert all found elements into the map
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->type->Z, 1));
+    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->Z, 1));
     if (!Inserter.second) // increase if present
       Inserter.first->second += 1;
@@ -528 +528 @@
   int nr = 0;
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->type->Z, 1) );
+    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->Z, 1) );
     if (!Inserter.second)
       Inserter.first->second += 1;
-    const int Z = (*AtomRunner)->type->Z;
+    const int Z = (*AtomRunner)->getType()->Z;
     *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << ZtoCountMap[Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *file << (*AtomRunner)->x[0] << "\t" << (*AtomRunner)->x[1] << "\t" << (*AtomRunner)->x[2];
+    *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);
     *file << "\t" << (*AtomRunner)->FixedIon;
-    if ((*AtomRunner)->v.Norm() > MYEPSILON)
-      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->v[0] << "\t" << (*AtomRunner)->v[1] << "\t" << (*AtomRunner)->v[2] << "\t";
+    if ((*AtomRunner)->AtomicVelocity.Norm() > MYEPSILON)
+      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->AtomicVelocity[0] << "\t" << (*AtomRunner)->AtomicVelocity[1] << "\t" << (*AtomRunner)->AtomicVelocity[2] << "\t";
     *file << " # molecule nr " << nr++ << endl;
   }

src/Parser/TremoloParser.cpp

@@ -143 +143 @@
       case TremoloKey::x :
         // for the moment, assume there are always three dimensions
-        *file << currentAtom->x[0] << "\t";
-        *file << currentAtom->x[1] << "\t";
-        *file << currentAtom->x[2] << "\t";
+        *file << currentAtom->at(0) << "\t";
+        *file << currentAtom->at(1) << "\t";
+        *file << currentAtom->at(2) << "\t";
         break;
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
-        *file << currentAtom->v[0] << "\t";
-        *file << currentAtom->v[1] << "\t";
-        *file << currentAtom->v[2] << "\t";
+        *file << currentAtom->AtomicVelocity[0] << "\t";
+        *file << currentAtom->AtomicVelocity[1] << "\t";
+        *file << currentAtom->AtomicVelocity[2] << "\t";
         break;
       case TremoloKey::Type :
@@ -228 +228 @@
   string word;
   int oldId;
+  double tmp;
 
   lineStream << line;
@@ -235 +236 @@
       case TremoloKey::x :
         // for the moment, assume there are always three dimensions
-        lineStream >> newAtom->x[0];
-        lineStream >> newAtom->x[1];
-        lineStream >> newAtom->x[2];
+        for (int i=0;i<NDIM;i++) {
+          lineStream >> tmp;
+          newAtom->set(i, tmp);
+        }
         break;
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
-        lineStream >> newAtom->v[0];
-        lineStream >> newAtom->v[1];
-        lineStream >> newAtom->v[2];
+        lineStream >> newAtom->AtomicVelocity[0];
+        lineStream >> newAtom->AtomicVelocity[1];
+        lineStream >> newAtom->AtomicVelocity[2];
         break;
       case TremoloKey::Type :

src/Parser/XyzParser.cpp

@@ -42 +42 @@
   int numberOfAtoms;
   char commentBuffer[512], type[3];
+  double tmp;
 
   // the first line tells number of atoms, the second line is always a comment
@@ -53 +54 @@
   for (int i = 0; i < numberOfAtoms; i++) {
     newAtom = World::getInstance().createAtom();
-    *file >> type >> ws >> newAtom->x[0] >> ws >> newAtom->x[1] >> ws >> newAtom->x[2];
+    *file >> type;
+    for (int j=0;j<NDIM;j++) {
+      *file >> tmp;
+      newAtom->set(j, tmp);
+    }
     newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
     newmol->AddAtom(newAtom);
@@ -81 +86 @@
   vector<atom*> atoms = World::getInstance().getAllAtoms();
   for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
-    *file << noshowpoint << (*it)->getType()->symbol << "\t" << (*it)->x[0] << "\t" << (*it)->x[1] << "\t" << (*it)->x[2] << endl;
+    *file << noshowpoint << (*it)->getType()->symbol << "\t" << (*it)->at(0) << "\t" << (*it)->at(1) << "\t" << (*it)->at(2) << endl;
   }
 }