Changeset d8ed62 for doc

Timestamp:

May 18, 2016, 10:02:53 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, 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_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, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

01120c

Parents:

d9dbef

git-author:

Frederik Heber <heber@…> (03/07/16 13:51:28)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:53)

Message:

Rewrote FitPartialChargesAction to fit charges to currently selected atoms.

• required AtomFragmentsMap in order to associate fragments to atoms.
• updated documentation to match change in action.

File:

• doc/userguide/userguide.xml (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1845 +1845 @@
           behavior in the molecular fragment, namely the (covalently) bonded interaction.
           In order to model the Coulomb long-range interaction as well without solving
-          for the electronic ground state in each time step, particle charges
+          for the electronic ground state in each time step, partial charges
           are used that capture to some degree the created dipoles due to
-          charge transfer from one atom to another when bonded.</para>
-          <para>Note that so far the placement of partial charges is restricted to the position of nuclei in the molecular system. There are more complex ways of placing partial charges, e.g. as employed in higher TIP water molecules, that also use anti-bonding potentials. This is so far not implemented.</para>
+          charge transfer from one atom to another when bonded. These are called
+          partial charges because they combine both nuclei and electronic
+          charges to yield an in general fractional charge.</para>
+          <para>Note that so far the placement of partial charges is restricted 
+          to the position of nuclei in the molecular system. There are more
+          complex ways of placing partial charges, e.g. as employed in higher
+          TIP water molecules, that also use anti-bonding potentials. This is
+          so far not implemented.</para>
           <para>To allow least-squares regression of these partial charges, we
           need the results of long-range calculations and the <emphasis role="bold">store-grids</emphasis>
-          option (see above under <link linkend="fragmentation">Fragmentation </link>) must have been given. With these sampled charge density and 
-          Coulomb potential stored in the homology containers, we call this 
-          action as follows.</para>
+          option (see above under <link linkend="fragmentation">Fragmentation </link>) 
+          must have been given.</para>
+          <para>Furthermore, we require associations between selected atoms and
+          the fragments, residing in the <link linkend="homology">Homology container</link>.
+          These are contained in the <link linkend="atomfragments">AtomFragments association</link>
+          container, that can also be parsed and stored.</para>
+          <para>With these sampled charge density and Coulomb potential stored 
+          in the homology containers, we call this action as follows.</para>
           <programlisting>
   ... --fit-partial-charges \
-      --fragment-charges 8 1 1 \
-      --potential-file water.potentials \
-      --radius 0.2
-   </programlisting>
-          <para>This will again use a water molecule as homologous fragment
-          &quot;key&quot; to request all configurations of this type from the homologies container. Results are
-          stored in <filename>water.potentials</filename>. The radius is used
-          to mark the region directly around the nuclei from the fit
-          procedure. As here the charges of the core electrons and the nuclei
-          itself dominate, we however are only interested in a good
+      --potential-file water.particles \
+      --radius 1.5
+   </programlisting>
+          <para>Assume that a water molecule has been selected previously. Then
+          all homologous fragments that contain any of the water molecules are
+          used as &quot;key&quot; to request all configurations of this type
+          from the homologies container. For each of the atoms then an average
+          partial charge is computed by fitting their respective Coulomb 
+          potential to the obtained from the fragment calculations. Resulting
+          values are stored in <filename>water.particles</filename>. The
+          radius is used to mask a certain region directly around the nuclei
+          from the fit procedure. As here the charges of the core electrons and
+          the nuclei itself dominate, we however are only interested in a good
           approximation to the long-range potential, this mask radius allows
           to give the range of the excluded zone.</para>