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 66fd49 was 66fd49, checked in by Frederik Heber <heber@…>, 14 years ago |
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Rewrite of FillVoidWithMoleculeAction.
FillVoidWithMoleculeAction:
- new parameter MinDistance and default value of 0.
- BUGFIX: filler is already created when parsing file, removed useless creation
of it initially (also caused lots of confusion due to an "extra" molecule).
- Undo implemented, regression test inserted.
- Redo is somewhat hard to implement, as one would use performCall() if it only
it would not retrieve its values from ValueStorage ...
FillVoidWithMolecule():
- filler is now the zeroth not the last molecule, marked by firstInsertion and
firstInserter. Filler is removed if no molecules are filled.
- outsourced stuff into smaller functions
- removed FillIt to through every atom despite only
CurrentPosition, indepedent of atom position, is checked.
TESTFIXES:
- Analysis/3: test.xyz changed because boundary is now 1.5 instead of 2.1 as
2.1 is not enough of molecules get filled in (and the filler already is).
- Analysis/3: tensid.data was actually lacking water at (0,0,0) which is after
the rewrite present.
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-
Property mode
set to
100644
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File size:
1.5 KB
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| 1 | /*
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| 2 | * FillVoidWithMoleculeAction.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 | #include "LinearAlgebra/Vector.hpp"
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| 10 | class MoleculeListClass;
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| 11 |
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| 12 | // i.e. there is an integer with variable name Z that can be found in
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| 13 | // ValueStorage by the token "Z" -> first column: int, Z, "Z"
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| 14 | // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
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| 15 | #define paramtypes (boost::filesystem::path)(Vector)(Vector)(double)(bool)
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| 16 | #define paramtokens ("fill-void")("distances")("lengths")("MinDistance")("DoRotate")
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| 17 | #define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("list of three of lengths in space, one for each axis direction")("minimum distance to boundary")("whether to rotate or not")
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| 18 | #define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("0.")("0")
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| 19 | #define paramreferences (fillername)(distances)(lengths)(MinDistance)(DoRotate)
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| 20 |
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| 21 | #define statetypes (std::vector<molecule *>)
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| 22 | #define statereferences (fillermolecules)
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| 23 |
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| 24 | // some defines for all the names, you may use ACTION, STATE and PARAMS
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| 25 | #define CATEGORY Molecule
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| 26 | #define MENUNAME "molecule"
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| 27 | #define MENUPOSITION 5
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| 28 | #define ACTIONNAME FillVoidWithMolecule
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| 29 | #define TOKEN "fill-void"
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| 30 |
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| 31 |
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| 32 | // finally the information stored in the ActionTrait specialization
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| 33 | #define DESCRIPTION "fill void space of box with a filler molecule"
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| 34 | #undef SHORTFORM
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