Changeset 4a7776a for src/atom.hpp

Timestamp:

Oct 12, 2009, 10:30:02 AM (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, 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:

5034e1

Parents:

ccd9f5

Message:

Complete refactoring of molecule_dynamics.cpp

• new small functions: SumDistanceOfTrajectories(), PenalizeEqualTargets(), (), CreateInitialLists(), TryNextNearestNeighbourForInjectivePermutation(), MakeInjectivePermutation()
• Thermostat routines (case blocks) have been shifted to small functions in atom class (and soon to be extracted from there into its own class: ThermostatedParticle ?)
• old functions are a lot smaller now: MinimiseConstrainedPotential(), molecule::EvaluateConstrainedForces(), VerletForceIntegration(), also using ActOnAllAtoms
• atom class has a lot of new small functions:
  • trajectory: ResizeTrajectory(), CopyStepOnStep(), VelocityVerletUpdate(), VelocityVerletUpdate()
  • constraint potential: CorrectVelocity(), Thermostat_...()

File:

• src/atom.hpp (modified) (3 diffs)

src/atom.hpp

@@ -21 +21 @@
 #include <vector>
 
+#include <gsl/gsl_randist.h>
+
 #include "tesselation.hpp"
 
@@ -26 +28 @@
 
 class bond;
+class config;
 class element;
 class ForceMatrix;
@@ -80 +83 @@
   bool Compare(const atom &ptr);
 
+  // trajectory stuff
+  void ResizeTrajectory(int MaxSteps);
+  void CopyStepOnStep(int dest, int src);
+  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
+  void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity );
+
   double DistanceToVector(Vector &origin);
   double DistanceSquaredToVector(Vector &origin);
 
+  bool IsInParallelepiped(Vector offset, double *parallelepiped);
+
+  // constraint potential and dynamics stuff
   void AddKineticToTemperature(double *temperature, int step) const;
   void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
+  void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
 
-  bool IsInParallelepiped(Vector offset, double *parallelepiped);
+  // thermostats
+  void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
+  void Thermostat_Gaussian_init(int Step, double *G, double *E);
+  void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
+  void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
+  void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
+  void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
+  void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
+
 
   ostream & operator << (ostream &ost);