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
|
Last change
on this file since bcb593 was bcb593, checked in by Frederik Heber <heber@…>, 12 years ago |
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FIX: VerletIntegrationAction now assumes forces have just been calculated.
- according to Wikipedia's Velocity_Verlet info, we first integrate position,
then calculate forces, then integrate velocity. This assumes that forces
based on next time step's position are already known. This is possible when
parsed from file but not if they are calculated dynamically via
fragmentation.
Hence, we now integrate velocity from last time step to current, then
integrate position from current time step to next. Then we are in the
position to calculate forces and do this cycle again.
- for this, VelocityVerletUpdate was split into ..X() and ..U() for independent
integration of position and velocity.
- VelocityVerletIntegration::operator() now first corrects forces, then
integrates velocites, corrects them too and finally integrates positions
according to the above new scheme.
- removed option MDSteps from VerletIntegrationAction.
- TESTFIX: Had to change regression rest on VerletIntegration since the
cycle sequence has changed. It was nonsense before to have the forces
already in some file respective to future position that actually first need
to come out of the time integration.
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-
Property mode
set to
100644
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File size:
1.6 KB
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| 1 | /*
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| 2 | * VerletIntegrationAction.def
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| 3 | *
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| 4 | * Created on: Aug 26, 2010
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | // all includes and forward declarations necessary for non-integral types below
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| 9 | class MoleculeListClass;
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| 10 |
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| 11 | #include "Parameters/Validators/DummyValidator.hpp"
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| 12 | #include "Parameters/Validators/GenericValidators.hpp"
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| 13 | #include "Parameters/Validators/Ops_Validator.hpp"
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| 14 | #include "Parameters/Validators/Specific/FilePresentValidator.hpp"
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| 15 |
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| 16 | // i.e. there is an integer with variable name Z that can be found in
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| 17 | // ValueStorage by the token "Z" -> first column: int, Z, "Z"
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| 18 | // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
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| 19 | #define paramtypes (boost::filesystem::path)(double)(bool)
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| 20 | #define paramtokens ("forces-file")("deltat")("keep-fixed-CenterOfMass")
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| 21 | #define paramdescriptions ("file containing")("time step width")("whether forces and velocities shall be corrected such that center of mass remains at rest")
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| 22 | #define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)
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| 23 | #define paramreferences (forcesfile)(Deltat)(FixedCenterOfMass)
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| 24 | #define paramvalids \
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| 25 | (DummyValidator< boost::filesystem::path >()) \
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| 26 | (PositiveValidator< double >()) \
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| 27 | (DummyValidator< bool >())
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| 28 |
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| 29 | #undef statetypes
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| 30 | #undef statereferences
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| 31 |
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| 32 | // some defines for all the names, you may use ACTION, STATE and PARAMS
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| 33 | #define CATEGORY Molecule
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| 34 | #define MENUNAME "molecule"
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| 35 | #define MENUPOSITION 14
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| 36 | #define ACTIONNAME VerletIntegration
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| 37 | #define TOKEN "verlet-integration"
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| 38 |
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| 39 |
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| 40 | // finally the information stored in the ActionTrait specialization
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| 41 | #define DESCRIPTION "perform verlet integration of a given force file"
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| 42 | #define SHORTFORM "P"
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