Changeset 0a4f7f for src/molecule.cpp

Timestamp:

Apr 7, 2010, 3:45:38 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:

72e7fa

Parents:

f9352d

Message:

Made data internal data-structure of vector class private

• Replaced occurences of access to internals with operator
• moved Vector-class into LinAlg-Module
• Reworked Vector to allow clean modularization
• Added Plane class to describe arbitrary planes in 3d space

File:

• src/molecule.cpp (modified) (11 diffs)

src/molecule.cpp

@@ -25 +25 @@
 #include "tesselation.hpp"
 #include "vector.hpp"
+#include "Plane.hpp"
+#include "Exceptions/LinearDependenceException.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -231 +233 @@
     Orthovector1.Zero();
     for (int i=NDIM;i--;) {
-      l = TopReplacement->x.x[i] - TopOrigin->x.x[i];
+      l = TopReplacement->x[i] - TopOrigin->x[i];
       if (fabs(l) > BondDistance) { // is component greater than bond distance
-        Orthovector1.x[i] = (l < 0) ? -1. : +1.;
+        Orthovector1[i] = (l < 0) ? -1. : +1.;
       } // (signs are correct, was tested!)
     }
@@ -305 +307 @@
 
         // determine the plane of these two with the *origin
-        AllWentWell = AllWentWell && Orthovector1.MakeNormalVector(&TopOrigin->x, &FirstOtherAtom->x, &SecondOtherAtom->x);
+        try {
+          Orthovector1 =Plane(TopOrigin->x, FirstOtherAtom->x, SecondOtherAtom->x).getNormal();
+        }
+        catch(LinearDependenceException &excp){
+          Log() << Verbose(0) << excp;
+          // TODO: figure out what to do with the Orthovector in this case
+          AllWentWell = false;
+        }
       } else {
         Orthovector1.GetOneNormalVector(&InBondvector);
@@ -313 +322 @@
       //Log() << Verbose(0) << endl;
       // orthogonal vector and bond vector between origin and replacement form the new plane
-      Orthovector1.MakeNormalVector(&InBondvector);
+      Orthovector1.MakeNormalTo(InBondvector);
       Orthovector1.Normalize();
       //Log() << Verbose(3) << "ReScaleCheck: " << Orthovector1.Norm() << " and " << InBondvector.Norm() << "." << endl;
@@ -345 +354 @@
       SecondOtherAtom->x.Zero();
       for(int i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondvector is bondangle = 0 direction)
-        FirstOtherAtom->x.x[i] = InBondvector.x[i] * cos(bondangle) + Orthovector1.x[i] * (sin(bondangle));
-        SecondOtherAtom->x.x[i] = InBondvector.x[i] * cos(bondangle) + Orthovector1.x[i] * (-sin(bondangle));
+        FirstOtherAtom->x[i] = InBondvector[i] * cos(bondangle) + Orthovector1[i] * (sin(bondangle));
+        SecondOtherAtom->x[i] = InBondvector[i] * cos(bondangle) + Orthovector1[i] * (-sin(bondangle));
       }
       FirstOtherAtom->x.Scale(&BondRescale);  // rescale by correct BondDistance
@@ -352 +361 @@
       //Log() << Verbose(3) << "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << "." << endl;
       for(int i=NDIM;i--;) { // and make relative to origin atom
-        FirstOtherAtom->x.x[i] += TopOrigin->x.x[i];
-        SecondOtherAtom->x.x[i] += TopOrigin->x.x[i];
+        FirstOtherAtom->x[i] += TopOrigin->x[i];
+        SecondOtherAtom->x[i] += TopOrigin->x[i];
       }
       // ... and add to molecule
@@ -394 +403 @@
 //      Orthovector1.Output(out);
 //      Log() << Verbose(0) << endl;
-      AllWentWell = AllWentWell && Orthovector2.MakeNormalVector(&InBondvector, &Orthovector1);
+      try{
+        Orthovector2 = Plane(InBondvector, Orthovector1,0).getNormal();
+      }
+      catch(LinearDependenceException &excp) {
+        Log() << Verbose(0) << excp;
+        AllWentWell = false;
+      }
 //      Log() << Verbose(3) << "Orthovector2: ";
 //      Orthovector2.Output(out);
@@ -514 +529 @@
     }
     for(j=NDIM;j--;) {
-      Walker->x.x[j] = x[j];
-      Walker->Trajectory.R.at(MDSteps-1).x[j] = x[j];
-      Walker->Trajectory.U.at(MDSteps-1).x[j] = 0;
-      Walker->Trajectory.F.at(MDSteps-1).x[j] = 0;
+      Walker->x[j] = x[j];
+      Walker->Trajectory.R.at(MDSteps-1)[j] = x[j];
+      Walker->Trajectory.U.at(MDSteps-1)[j] = 0;
+      Walker->Trajectory.F.at(MDSteps-1)[j] = 0;
     }
     AddAtom(Walker);  // add to molecule
@@ -661 +676 @@
 void molecule::SetBoxDimension(Vector *dim)
 {
-  cell_size[0] = dim->x[0];
+  cell_size[0] = dim->at(0);
   cell_size[1] = 0.;
-  cell_size[2] = dim->x[1];
+  cell_size[2] = dim->at(1);
   cell_size[3] = 0.;
   cell_size[4] = 0.;
-  cell_size[5] = dim->x[2];
+  cell_size[5] = dim->at(2);
 };
 
@@ -755 +770 @@
   for (int i=0;i<NDIM;i++) {
     j += i+1;
-    result = result && ((x->x[i] >= 0) && (x->x[i] < cell_size[j]));
+    result = result && ((x->at(i) >= 0) && (x->at(i) < cell_size[j]));
   }
   //return result;
@@ -1005 +1020 @@
     DeterminePeriodicCenter(CenterOfGravity);
     OtherMolecule->DeterminePeriodicCenter(OtherCenterOfGravity);
-    Log() << Verbose(5) << "Center of Gravity: ";
-    CenterOfGravity.Output();
-    Log() << Verbose(0) << endl << Verbose(5) << "Other Center of Gravity: ";
-    OtherCenterOfGravity.Output();
-    Log() << Verbose(0) << endl;
+    Log() << Verbose(5) << "Center of Gravity: " << CenterOfGravity << endl;
+    Log() << Verbose(5) << "Other Center of Gravity: " << OtherCenterOfGravity << endl;
     if (CenterOfGravity.DistanceSquared(&OtherCenterOfGravity) > threshold*threshold) {
       Log() << Verbose(4) << "Centers of gravity don't match." << endl;