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
Rev | Line | |
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[6b919f8] | 1 | /*
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| 2 | * atom_trajectoryparticle.hpp
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| 3 | *
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| 4 | * Created on: Oct 19, 2009
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef ATOM_TRAJECTORYPARTICLE_HPP_
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| 9 | #define ATOM_TRAJECTORYPARTICLE_HPP_
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| 10 |
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| 11 | using namespace std;
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| 12 |
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| 13 | /*********************************************** includes ***********************************/
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| 14 |
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| 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 |
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| 20 | #include <fstream>
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| 21 |
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| 22 | #include <gsl/gsl_randist.h>
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| 23 |
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| 24 | #include "atom_atominfo.hpp"
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| 25 | #include "atom_particleinfo.hpp"
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| 26 | #include "atom_trajectoryparticleinfo.hpp"
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| 27 |
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| 28 | /****************************************** forward declarations *****************************/
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| 29 |
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| 30 | class atom;
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| 31 | class config;
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| 32 | class ForceMatrix;
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| 33 | class Vector;
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| 34 |
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| 35 | /********************************************** declarations *******************************/
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| 36 |
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| 37 |
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| 38 | class TrajectoryParticle : public TrajectoryParticleInfo, public virtual AtomInfo, public virtual ParticleInfo {
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| 39 | public:
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| 40 |
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| 41 | TrajectoryParticle();
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| 42 | virtual ~TrajectoryParticle();
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| 43 |
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| 44 | // constraint potential and dynamics stuff
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[b453f9] | 45 | void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const;
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[6b919f8] | 46 |
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| 47 | // trajectory stuff
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| 48 | void ResizeTrajectory(int MaxSteps);
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| 49 | void CopyStepOnStep(int dest, int src);
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[ef7d30] | 50 | void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force, const size_t offset);
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[7329c3] | 51 | double getKineticEnergy(unsigned int step) const;
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[e95a59] | 52 | Vector getMomentum(unsigned int step) const;
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[6b919f8] | 53 |
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[d74077] | 54 | std::ostream & operator << (std::ostream &ost) const;
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[6b919f8] | 55 |
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[d74077] | 56 | private:
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[6b919f8] | 57 | };
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| 58 |
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[d74077] | 59 | ostream & operator << (ostream &ost, const TrajectoryParticle &a);
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[6b919f8] | 60 |
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| 61 | #endif /* ATOM_TRAJECTORYPARTICLE_HPP_ */
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