Changeset 750cff for src/documentation/constructs/tesselation.dox

Timestamp:

Oct 31, 2011, 5:13:52 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

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, Candidate_v1.7.1, 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

Children:

5982c5

Parents:

19bc74

Message:

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.

File:

• src/documentation/constructs/tesselation.dox (modified) (1 diff)

src/documentation/constructs/tesselation.dox

@@ -12 +12 @@
  *    Author: heber
  */
+
+/** \page tesselation Tesselation
+ *
+ * Tesselation is a first step towards recognizing molecular surfaces.
+ *
+ * Within the code it is used for calculating correlation functions with regard
+ * to such a surface.
+ *
+ * \section tesselation-procedure
+ *
+ * In the tesselation all atoms act as possible hindrance to a rolling sphere
+ * that moves in from infinity. whenever it rests uniquely on three distinct
+ * points (atoms) a triangle is created. The algorithm continues by flipping the
+ * sphere over one of the triangle's edges to eventually obtain a closed,
+ * tesselated surface of the molecule.
+ *
+ * \note This mesh is different to the usual sense of a molecular surface as
+ * atoms are directly located on it. Normally, one considers a so-called
+ * Van-der-Waals sphere around the atoms and tesselates over these. However,
+ * the mesh can easily be modified and even expanded to match the other
+ * (although the code for that is not yet fully implemented).
+ *
+ * \section tesselation-extension
+ *
+ * The main problem for extending the mesh to match with the normal sense is
+ * that triangles may suddenly intersect others when we have the case of a non-
+ * convex mesh (which is rather the normal case). And this has to be
+ * specifically treated. Also, it is not sure whether the procedure of
+ * expanding our current surface is optimal and one should not start on a
+ * different set of nodes created from virtual points resting on the
+ * van-der-Waals spheres.
+ *
+ * \date 2011-10-31
+ *
+ */