Changeset ccd9f5 for src/atom.cpp

Timestamp:

Oct 9, 2009, 2:35:14 PM (16 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:

4a7776a

Parents:

c111db

Message:

First half of molecule_dynamics.cpp is refactored into smaller parts.

• new function atom::EvaluateConstrainedForce() evaluating a constraint force
• molecule::EvaluateConstrainedForces() uses the above with ActOnAllatoms()
• new helper functions in molecule_dynamics.cpp: SumDistanceOfTrajectories(), SumDistanceOfTrajectories(), FillDistanceList(), CreateInitialLists(), TryNextNearestNeighbourForInjectivePermutation(), MakeInjectivePermutation()
• new struct EvaluatePotential in molecules.hpp to contain most of the values for the above functions

File:

• src/atom.cpp (modified) (2 diffs)

src/atom.cpp

@@ -9 +9 @@
 #include "element.hpp"
 #include "memoryallocator.hpp"
+#include "parser.hpp"
 #include "vector.hpp"
 
@@ -297 +298 @@
 };
 
+/** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
+ * \param startstep trajectory begins at
+ * \param endstep trajectory ends at
+ * \param **PermutationMap if atom switches places with some other atom, there is no translation but a permutaton noted here (not in the trajectories of each).
+ * \param *Force Force matrix to store result in
+ */
+void atom::EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force)
+{
+  double constant = 10.;
+  atom *Sprinter = PermutationMap[nr];
+  // set forces
+  for (int i=NDIM;i++;)
+    Force->Matrix[0][nr][5+i] += 2.*constant*sqrt(Trajectory.R.at(startstep).Distance(&Sprinter->Trajectory.R.at(endstep)));
+};