Changeset 0a4f7f for src/atom.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/atom.cpp (modified) (6 diffs)

src/atom.cpp

@@ -130 +130 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
+    *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;
     if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -155 +155 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
+    *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;
     if (v.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << v[0] << "\t" << v[1] << "\t" << v[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -175 +175 @@
 {
   if (out != NULL) {
-    *out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
+    *out << type->symbol << "\t" << x[0] << "\t" << x[1] << "\t" << x[2] << "\t" << endl;
     return true;
   } else
@@ -193 +193 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << Trajectory.R.at(step).x[0] << "\t" << Trajectory.R.at(step).x[1] << "\t" << Trajectory.R.at(step).x[2];
+    *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
     *out << "\t" << FixedIon;
     if (Trajectory.U.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step).x[0] << "\t" << Trajectory.U.at(step).x[1] << "\t" << Trajectory.U.at(step).x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step)[0] << "\t" << Trajectory.U.at(step)[1] << "\t" << Trajectory.U.at(step)[2] << "\t";
     if (Trajectory.F.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step).x[0] << "\t" << Trajectory.F.at(step).x[1] << "\t" << Trajectory.F.at(step).x[2] << "\t";
+      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step)[0] << "\t" << Trajectory.F.at(step)[1] << "\t" << Trajectory.F.at(step)[2] << "\t";
     *out << "\t# Number in molecule " << nr << endl;
     return true;
@@ -214 +214 @@
   if (out != NULL) {
     *out << type->symbol << "\t";
-    *out << Trajectory.R.at(step).x[0] << "\t";
-    *out << Trajectory.R.at(step).x[1] << "\t";
-    *out << Trajectory.R.at(step).x[2] << endl;
+    *out << Trajectory.R.at(step)[0] << "\t";
+    *out << Trajectory.R.at(step)[1] << "\t";
+    *out << Trajectory.R.at(step)[2] << endl;
     return true;
   } else
@@ -229 +229 @@
 void atom::OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo = NULL) const
 {
-  *out << "\t\t" << type->symbol << " [ " << x.x[0]-center->x[0] << "\t" << x.x[1]-center->x[1] << "\t" << x.x[2]-center->x[2] << " ]" << endl;
+  *out << "\t\t" << type->symbol << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;
   if (AtomNo != NULL)
     *AtomNo++;