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 9f9b5a was 274d45, checked in by Frederik Heber <heber@…>, 15 years ago |
FIX: Atoms were stored not in the sequence they were loaded.
- The main problem is molecule::atomSet which is a set<atom *>, i.e. atoms are sorted by their appearance in memory. As memory need not be allocated sequentially, this gives rise to extreme arbitririty which is not desired. Instead the atoms should be stored in the sequence they were loaded/created. The solution is as follows:
- config::SaveAll()
- molecule::atomSet is now a list<atom *>
- molecule::atomIds is a new set<atomId_t> (atomIdSet) which controls that (global) ids remain unique in the no more Atomset's set (but list)
- molecule::erase() erases also in atomIds
- molecule::insert() checks whether id is present by atomIds
- molecule::find() as std::list does not have a find, we just go through the list until the object is found (or not), this may be speeded up by another internal list.
- molecule::InternalPointer made lots of confusion as virtual function GoToFirst() is const, hence begin() (needed therein) returns const_iterator, which then cannot be simply re-cast into an iterator: We make it a pointer, reinterpret_cast the pointer and reference it back. Although InternalPointer is mutable, the compiler cannot use the non-const function begin() (it cannot be made const, as overloading is not allowed). (this is noted in the code also extensively.)
- molecule::containsAtom() does not use count but the new find, as it returns only boolean anyway.
- rewrote MoleculeListClass::SimpleMerge() to get rid of the extra iterator, as we remove all atoms in the end anyway.
- FIX: MoleculeListClass::SimpleMultiMerge() - the created mol was not inserted into the moleculelist in the end, although it is the only one to remain.
- All other databases had missing headers with respect to those stored in elements_db.cpp. Hence, valence of hydrogen was not parsed and this caused several failures in CalculateOrbitals() (Psi numbers and MaxMinSetp in pcp conf file).
- Subsequenytly, various test cases (12, 21, 30, 31, 36-38, 39) were broken. This had two reasons:
- Seemingly, CalculateOrbitals() was broken before hence MaxMinStep (pcp config) and MaxPsiDouble/PsiMaxNn[Up|Down] were always 0. (10-21,30-31,39)
- As the order is now correct, fixes from commits c9217161ec2a5d5db508557fe98a32068461f45b and 22a6da8380911571debebd69444d2615450bbbd8 were obselete and have been reverted (order of the Ion?_Type...): Molecules/6 (30), Molecules/7 (31), Filling/1 (39)
- Due to different ordering, Tesselation/3 (38) had completely different .dat file (though same tesselation)
- r3d had small differences, mostly order or epsilon (0 not being 0 but ..-e16), hence diffing was deactivated, as r3d is deprecated anyway (since vmd can render triangles as well and better).
Signed-off-by: Frederik Heber <heber@…>
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File size:
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1 | #atomic number bond distances for single, double and triple bond (-1 no bond)
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2 | 1 0.74 -1 -1
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3 | 2 0.77429209 -1 -1
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4 | 5 1.23 1.19 1.18
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5 | 6 1.09 1.076 1.06
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6 | 7 1.04 1.02 1.01
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7 | 8 0.96 0.957 -1
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8 | 14 1.48 1.48 1.48
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9 | 15 1.42 -1 -1
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10 | 16 1.35 -1 -1
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11 | 17 1.29 -1 -1
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12 | 20 1.09 1.09 -1
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13 | 34 1.47 -1 -1
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14 | 35 1.44 -1 -1
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