Changeset 056e70 for src/atom.cpp

Timestamp:

Feb 24, 2011, 5:56:03 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, Candidate_v1.7.0, 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:

6b020f

Parents:

6625c3

Message:

Suffixed getters and setters for AtomInfo trajecories with AtStep.

• AtomInfo:: getters are now const members
• added lots of ASSERTS to getters with time step to assure no out-of-bounds access.

File:

• src/atom.cpp (modified) (2 diffs)

src/atom.cpp

@@ -218 +218 @@
     ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
     *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[getType()->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << getPosition(step)[0] << "\t" << getPosition(step)[1] << "\t" << getPosition(step)[2];
+    *out << getPositionAtStep(step)[0] << "\t" << getPositionAtStep(step)[1] << "\t" << getPositionAtStep(step)[2];
     *out << "\t" << (int)(getFixedIon());
-    if (getAtomicVelocity(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << getAtomicVelocity(step)[0] << "\t" << getAtomicVelocity(step)[1] << "\t" << getAtomicVelocity(step)[2] << "\t";
-    if (getAtomicForce(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << getAtomicForce(step)[0] << "\t" << getAtomicForce(step)[1] << "\t" << getAtomicForce(step)[2] << "\t";
+    if (getAtomicVelocityAtStep(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicVelocityAtStep(step)[0] << "\t" << getAtomicVelocityAtStep(step)[1] << "\t" << getAtomicVelocityAtStep(step)[2] << "\t";
+    if (getAtomicForceAtStep(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicForceAtStep(step)[0] << "\t" << getAtomicForceAtStep(step)[1] << "\t" << getAtomicForceAtStep(step)[2] << "\t";
     *out << "\t# Number in molecule " << nr << endl;
     return true;
@@ -239 +239 @@
   if (out != NULL) {
     *out << getType()->getSymbol() << "\t";
-    *out << getPosition(step)[0] << "\t";
-    *out << getPosition(step)[1] << "\t";
-    *out << getPosition(step)[2] << endl;
+    *out << getPositionAtStep(step)[0] << "\t";
+    *out << getPositionAtStep(step)[1] << "\t";
+    *out << getPositionAtStep(step)[2] << endl;
     return true;
   } else