Changeset 6625c3 for src/molecule.cpp

Timestamp:

Feb 24, 2011, 5:46:46 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:

056e70

Parents:

54b42e

git-author:

Frederik Heber <heber@…> (02/24/11 11:18:59)

git-committer:

Frederik Heber <heber@…> (02/24/11 17:46:46)

Message:

Removed atom_trajectoryparticle*, replaced by AtomInfo class now having std::vector<> for trajectories.

AtomInfo:

• AtomInfo stores position, velocity, and force in vectors.
• getter and setter implemented for velocity and force.
• all functions from TrajectoryParticle put into AtomInfo.
• Direct access to velocity and force exchanged by getter/setter everywhere.
• FIX: molecule::LinearInterpolationBetweenConfiguration() extends trajectory to MaxSteps+1 (for endstep).

Other changes:

• gsl_rng_gaussian() exchanged by boost::random specific type.

File:

• src/molecule.cpp (modified) (5 diffs)

src/molecule.cpp

@@ -365 +365 @@
       FirstOtherAtom->setType(1);  // element is Hydrogen
       FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
+      FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       if (TopReplacement->getType()->getAtomicNumber() == 1) { // neither rescale nor replace if it's already hydrogen
         FirstOtherAtom->father = TopReplacement;
@@ -430 +430 @@
       SecondOtherAtom->setType(1);
       FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
+      FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
+      SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
       SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
@@ -485 +485 @@
       ThirdOtherAtom->setType(1);
       FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
+      FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
+      SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       ThirdOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
-      ThirdOtherAtom->FixedIon = TopReplacement->FixedIon;
+      ThirdOtherAtom->setFixedIon(TopReplacement->getFixedIon());
       FirstOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
       SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
@@ -582 +582 @@
   istringstream *input = NULL;
   int NumberOfAtoms = 0; // atom number in xyz read
-  int i, j; // loop variables
+  int i; // loop variables
   atom *Walker = NULL;  // pointer to added atom
   char shorthand[3];  // shorthand for atom name
@@ -618 +618 @@
       Walker->setType(1);
     }
-    if (Walker->Trajectory.R.size() <= (unsigned int)MDSteps) {
-      Walker->Trajectory.R.resize(MDSteps+10);
-      Walker->Trajectory.U.resize(MDSteps+10);
-      Walker->Trajectory.F.resize(MDSteps+10);
+    if (Walker->getTrajectorySize() <= (unsigned int)MDSteps) {
+      Walker->ResizeTrajectory(MDSteps+10);
     }
     Walker->setPosition(Vector(x));
-    for(j=NDIM;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;
-    }
+    Walker->setPosition(MDSteps-1, Vector(x));
+    Walker->setAtomicVelocity(MDSteps-1, zeroVec);
+    Walker->setAtomicForce(MDSteps-1, zeroVec);
     AddAtom(Walker);  // add to molecule
     delete(item);