source: src/atom_trajectoryparticle.hpp@ 7aa3cf

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
Last change on this file since 7aa3cf was d74077, checked in by Frederik Heber <heber@…>, 15 years ago

Member variable Vector and element of class atom are now private.
  • Property mode set to 100644
File size: 2.3 KB
RevLine 
[6b919f8]1/*
2 * atom_trajectoryparticle.hpp
3 *
4 * Created on: Oct 19, 2009
5 * Author: heber
6 */
7
8#ifndef ATOM_TRAJECTORYPARTICLE_HPP_
9#define ATOM_TRAJECTORYPARTICLE_HPP_
10
11using namespace std;
12
13/*********************************************** includes ***********************************/
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <fstream>
21
[aafd77]22#include <gsl/gsl_inline.h>
[6b919f8]23#include <gsl/gsl_randist.h>
24
25#include "atom_atominfo.hpp"
26#include "atom_particleinfo.hpp"
27#include "atom_trajectoryparticleinfo.hpp"
28
29/****************************************** forward declarations *****************************/
30
31class atom;
32class config;
33class ForceMatrix;
34class Vector;
35
36/********************************************** declarations *******************************/
37
38
39class TrajectoryParticle : public TrajectoryParticleInfo, public virtual AtomInfo, public virtual ParticleInfo {
40public:
41
42 TrajectoryParticle();
43 virtual ~TrajectoryParticle();
44
45 // constraint potential and dynamics stuff
46 void AddKineticToTemperature(double *temperature, int step) const;
[b453f9]47 void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const;
[6b919f8]48 void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
49
50 // trajectory stuff
51 void ResizeTrajectory(int MaxSteps);
52 void CopyStepOnStep(int dest, int src);
[ef7d30]53 void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force, const size_t offset);
[b453f9]54 void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const;
[6b919f8]55
56 // thermostats
57 void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
58 void Thermostat_Gaussian_init(int Step, double *G, double *E);
59 void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
60 void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
61 void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
62 void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
63 void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
64
[d74077]65 std::ostream & operator << (std::ostream &ost) const;
[6b919f8]66
[d74077]67private:
[6b919f8]68};
69
[d74077]70ostream & operator << (ostream &ost, const TrajectoryParticle &a);
[6b919f8]71
72#endif /* ATOM_TRAJECTORYPARTICLE_HPP_ */
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