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
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Last change
on this file since 936a02 was 750cff, checked in by Frederik Heber <heber@…>, 13 years ago |
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HUGE: Update on documenation.
- a general skeleton of the documentation is now in place with all the major
components of MoleCuilder explained to some extent.
- some information has been transfered from TRAC (e.g. install procecure) into
this doxygen documentation where it is general and not specific to the
situation at our institute.
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Property mode
set to
100644
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File size:
1.8 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 tesselation.dox
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| 10 | *
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| 11 | * Created on: Oct 28, 2011
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | /** \page tesselation Tesselation
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| 16 | *
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| 17 | * Tesselation is a first step towards recognizing molecular surfaces.
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| 18 | *
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| 19 | * Within the code it is used for calculating correlation functions with regard
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| 20 | * to such a surface.
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| 21 | *
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| 22 | * \section tesselation-procedure
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| 23 | *
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| 24 | * In the tesselation all atoms act as possible hindrance to a rolling sphere
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| 25 | * that moves in from infinity. whenever it rests uniquely on three distinct
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| 26 | * points (atoms) a triangle is created. The algorithm continues by flipping the
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| 27 | * sphere over one of the triangle's edges to eventually obtain a closed,
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| 28 | * tesselated surface of the molecule.
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| 29 | *
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| 30 | * \note This mesh is different to the usual sense of a molecular surface as
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| 31 | * atoms are directly located on it. Normally, one considers a so-called
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| 32 | * Van-der-Waals sphere around the atoms and tesselates over these. However,
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| 33 | * the mesh can easily be modified and even expanded to match the other
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| 34 | * (although the code for that is not yet fully implemented).
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| 35 | *
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| 36 | * \section tesselation-extension
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| 37 | *
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| 38 | * The main problem for extending the mesh to match with the normal sense is
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| 39 | * that triangles may suddenly intersect others when we have the case of a non-
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| 40 | * convex mesh (which is rather the normal case). And this has to be
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| 41 | * specifically treated. Also, it is not sure whether the procedure of
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| 42 | * expanding our current surface is optimal and one should not start on a
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| 43 | * different set of nodes created from virtual points resting on the
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| 44 | * van-der-Waals spheres.
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| 45 | *
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| 46 | * \date 2011-10-31
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| 47 | *
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| 48 | */
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