Changeset d74077 for src/molecule_geometry.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/molecule_geometry.cpp (modified) (18 diffs)

src/molecule_geometry.cpp

@@ -45 +45 @@
 
   // go through all atoms
-  ActOnAllVectors( &Vector::SubtractVector, *Center);
-  ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
   BOOST_FOREACH(atom* iter, atoms){
-    *iter->node = domain.WrapPeriodically(*iter->node);
+    *iter -= *Center;
+    *iter -= *CenterBox;
+    iter->setPosition(domain.WrapPeriodically(iter->getPosition()));
   }
 
@@ -67 +67 @@
   // go through all atoms
   BOOST_FOREACH(atom* iter, atoms){
-    *iter->node = domain.WrapPeriodically(*iter->node);
+    iter->setPosition(domain.WrapPeriodically(iter->getPosition()));
   }
 
@@ -85 +85 @@
   if (iter != end()) { //list not empty?
     for (int i=NDIM;i--;) {
-      max->at(i) = (*iter)->x[i];
-      min->at(i) = (*iter)->x[i];
+      max->at(i) = (*iter)->at(i);
+      min->at(i) = (*iter)->at(i);
     }
     for (; iter != end(); ++iter) {// continue with second if present
       //(*iter)->Output(1,1,out);
       for (int i=NDIM;i--;) {
-        max->at(i) = (max->at(i) < (*iter)->x[i]) ? (*iter)->x[i] : max->at(i);
-        min->at(i) = (min->at(i) > (*iter)->x[i]) ? (*iter)->x[i] : min->at(i);
+        max->at(i) = (max->at(i) < (*iter)->at(i)) ? (*iter)->at(i) : max->at(i);
+        min->at(i) = (min->at(i) > (*iter)->at(i)) ? (*iter)->at(i) : min->at(i);
       }
     }
@@ -123 +123 @@
     for (; iter != end(); ++iter) {  // continue with second if present
       Num++;
-      Center += (*iter)->x;
+      Center += (*iter)->getPosition();
     }
     Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
@@ -145 +145 @@
     for (; iter != end(); ++iter) {  // continue with second if present
       Num++;
-      (*a) += (*iter)->x;
+      (*a) += (*iter)->getPosition();
     }
     a->Scale(1./(double)Num); // divide through total mass (and sign for direction)
@@ -178 +178 @@
   if (iter != end()) {   //list not empty?
     for (; iter != end(); ++iter) {  // continue with second if present
-      Num += (*iter)->type->mass;
-      tmp = (*iter)->type->mass * (*iter)->x;
+      Num += (*iter)->getType()->mass;
+      tmp = (*iter)->getType()->mass * (*iter)->getPosition();
       (*a) += tmp;
     }
@@ -223 +223 @@
     for (int j=0;j<MDSteps;j++)
       (*iter)->Trajectory.R.at(j).ScaleAll(*factor);
-    (*iter)->x.ScaleAll(*factor);
+    (*iter)->ScaleAll(*factor);
   }
 };
@@ -235 +235 @@
     for (int j=0;j<MDSteps;j++)
       (*iter)->Trajectory.R.at(j) += (*trans);
-    (*iter)->x += (*trans);
+    *(*iter) += (*trans);
   }
 };
@@ -248 +248 @@
 
   // go through all atoms
-  ActOnAllVectors( &Vector::AddVector, *trans);
   BOOST_FOREACH(atom* iter, atoms){
-    *iter->node = domain.WrapPeriodically(*iter->node);
+    *iter += *trans;
+    iter->setPosition(domain.WrapPeriodically(iter->getPosition()));
   }
 
@@ -264 +264 @@
   Plane p(*n,0);
   BOOST_FOREACH(atom* iter, atoms ){
-    (*iter->node) = p.mirrorVector(*iter->node);
+    iter->setPosition(p.mirrorVector(iter->getPosition()));
   }
 };
@@ -284 +284 @@
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
 #ifdef ADDHYDROGEN
-      if ((*iter)->type->Z != 1) {
+      if ((*iter)->getType()->Z != 1) {
 #endif
-        Testvector = inversematrix * (*iter)->x;
+        Testvector = inversematrix * (*iter)->getPosition();
         Translationvector.Zero();
         for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
          if ((*iter)->nr < (*Runner)->GetOtherAtom((*iter))->nr) // otherwise we shift one to, the other fro and gain nothing
             for (int j=0;j<NDIM;j++) {
-              tmp = (*iter)->x[j] - (*Runner)->GetOtherAtom(*iter)->x[j];
+              tmp = (*iter)->at(j) - (*Runner)->GetOtherAtom(*iter)->at(j);
               if ((fabs(tmp)) > BondDistance) {
                 flag = false;
@@ -309 +309 @@
         // now also change all hydrogens
         for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
-          if ((*Runner)->GetOtherAtom((*iter))->type->Z == 1) {
-            Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->x;
+          if ((*Runner)->GetOtherAtom((*iter))->getType()->Z == 1) {
+            Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->getPosition();
             Testvector += Translationvector;
             Testvector *= matrix;
@@ -343 +343 @@
   // sum up inertia tensor
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    Vector x = (*iter)->x;
+    Vector x = (*iter)->getPosition();
     //x.SubtractVector(CenterOfGravity);
-    InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
-    InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
-    InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
-    InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
-    InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
-    InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
-    InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
-    InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
-    InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
+    InertiaTensor[0] += (*iter)->getType()->mass*(x[1]*x[1] + x[2]*x[2]);
+    InertiaTensor[1] += (*iter)->getType()->mass*(-x[0]*x[1]);
+    InertiaTensor[2] += (*iter)->getType()->mass*(-x[0]*x[2]);
+    InertiaTensor[3] += (*iter)->getType()->mass*(-x[1]*x[0]);
+    InertiaTensor[4] += (*iter)->getType()->mass*(x[0]*x[0] + x[2]*x[2]);
+    InertiaTensor[5] += (*iter)->getType()->mass*(-x[1]*x[2]);
+    InertiaTensor[6] += (*iter)->getType()->mass*(-x[2]*x[0]);
+    InertiaTensor[7] += (*iter)->getType()->mass*(-x[2]*x[1]);
+    InertiaTensor[8] += (*iter)->getType()->mass*(x[0]*x[0] + x[1]*x[1]);
   }
   // print InertiaTensor for debugging
@@ -383 +383 @@
     // the eigenvectors specify the transformation matrix
     Matrix M = Matrix(evec->data);
+    Vector tempVector;
     BOOST_FOREACH(atom* iter, atoms){
-      (*iter->node) *= M;
+      tempVector = iter->getPosition();
+      tempVector *= M;
+      iter->setPosition(tempVector);
     }
     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
@@ -395 +398 @@
     // sum up inertia tensor
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      Vector x = (*iter)->x;
-      InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
-      InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
-      InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
-      InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
-      InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
-      InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
-      InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
-      InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
-      InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
+      Vector x = (*iter)->getPosition();
+      InertiaTensor[0] += (*iter)->getType()->mass*(x[1]*x[1] + x[2]*x[2]);
+      InertiaTensor[1] += (*iter)->getType()->mass*(-x[0]*x[1]);
+      InertiaTensor[2] += (*iter)->getType()->mass*(-x[0]*x[2]);
+      InertiaTensor[3] += (*iter)->getType()->mass*(-x[1]*x[0]);
+      InertiaTensor[4] += (*iter)->getType()->mass*(x[0]*x[0] + x[2]*x[2]);
+      InertiaTensor[5] += (*iter)->getType()->mass*(-x[1]*x[2]);
+      InertiaTensor[6] += (*iter)->getType()->mass*(-x[2]*x[0]);
+      InertiaTensor[7] += (*iter)->getType()->mass*(-x[2]*x[1]);
+      InertiaTensor[8] += (*iter)->getType()->mass*(x[0]*x[0] + x[1]*x[1]);
     }
     // print InertiaTensor for debugging
@@ -439 +442 @@
   DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    tmp = (*iter)->x[0];
-    (*iter)->x[0] =  cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
-    (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
+    tmp = (*iter)->at(0);
+    (*iter)->set(0,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
+    (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
     for (int j=0;j<MDSteps;j++) {
       tmp = (*iter)->Trajectory.R.at(j)[0];
@@ -458 +461 @@
   DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    tmp = (*iter)->x[1];
-    (*iter)->x[1] =  cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
-    (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
+    tmp = (*iter)->at(1);
+    (*iter)->set(1,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
+    (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
     for (int j=0;j<MDSteps;j++) {
       tmp = (*iter)->Trajectory.R.at(j)[1];
@@ -498 +501 @@
   // go through all atoms
   for (molecule::const_iterator iter = par->mol->begin(); iter != par->mol->end(); ++iter) {
-    if ((*iter)->type == ((struct lsq_params *)params)->type) { // for specific type
-      c = (*iter)->x - a;
+    if ((*iter)->getType() == ((struct lsq_params *)params)->type) { // for specific type
+      c = (*iter)->getPosition() - a;
       t = c.ScalarProduct(b);           // get direction parameter
       d = t*b;       // and create vector