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
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Last change
on this file since 8c001a was 936a02, checked in by Frederik Heber <heber@…>, 14 years ago |
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Creating data dir for bondtables, databases, and molecules.
- Moved .db files from src/Element to data/databases.
- Added bondtable.dat from VSpeShape (kudos Christian Neuen) to data/bondtables
as an initial bond table from geometry optimization of bielemental systems.
- Added some abitrary molecules to data/molecules.
- Added src/documentation/data.dox to explain purpose of the folder.
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Property mode
set to
100644
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File size:
1.7 KB
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| 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
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| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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| 8 | /**
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| 9 | * \file data.dox
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| 10 | *
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| 11 | * Herein, we explain what the point of the data subfolder is.
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| 12 | *
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| 13 | * Created on: Nov 10, 2011
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| 14 | * Author: heber
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| 15 | */
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| 16 |
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| 17 | /**
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| 18 | * \page data Purpose of the data subfolder
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| 19 | *
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| 20 | * \section data-bondtables Bond tables
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| 21 | *
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| 22 | * In ./data/bondtables matrix-like files are contained that give bond
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| 23 | * information per element pair. "-1" specifies unknown bond length. This
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| 24 | * is used by the class \ref bondgraph to more accurately
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| 25 | * create the bonding structure of a molecular system. The formula is that
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| 26 | * the distance between two atoms must match the one in the table plus or
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| 27 | * minus a certain threshold (BondGraph::BondThreshold).
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| 28 | *
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| 29 | * \section data-databases Element databases
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| 30 | *
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| 31 | * In \b ./data/databases element databases are stored with standard information
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| 32 | * from the period table but also certain specific information such as color or
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| 33 | * valency. These can be parsed by the class function periodentafel::LoadPeriodentafel().
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| 34 | *
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| 35 | * \section data-molecules Molecules
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| 36 | *
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| 37 | * In \b ./data/molecules some molecules are stored in \a PDB format. The intent
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| 38 | * is that these are the building stone of a library to come from which molecules
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| 39 | * necessary for the building of systems can be chosen.
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| 40 | *
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| 41 | * If new molecules are added, please specify the source of the file, either in
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| 42 | * the commit message or (even better) in the comment section of the file. Please
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| 43 | * also use a format which stores both coordination and bonds (such as .pdb).
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| 44 | *
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| 45 | *
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| 46 | * \date 2011-11-10
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| 47 | *
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| 48 | */
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