Changeset 88afc9 for doc/userguide/userguide.xml

Timestamp:

Feb 13, 2015, 9:18:04 AM (10 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, 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:

b9b49e

Parents:

2fcef3

git-author:

Frederik Heber <heber@…> (01/29/15 00:25:11)

git-committer:

Frederik Heber <heber@…> (02/13/15 09:18:04)

Message:

Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms.

• renamed add/remove-bond -> add/remove-bond(s) to emphasize this.
• added regression test on three selected atoms.
• modified userguide entry for both actions.

File:

• doc/userguide/userguide.xml (modified) (2 diffs)

doc/userguide/userguide.xml

@@ -1150 +1150 @@
         </section>
 
-        <section xml:id='bond.add-bond'>
-          <title xml:id='bond.add-bond.title'>Adding a bond manually</title>
+        <section xml:id='bond.adds-bond'>
+          <title xml:id='bond.adds-bond.title'>Adding a bond manually</title>
 
           <para>When the automatically created adjacency or bond graph
           contains faulty bonds or lacks some, you can add them manually.
-          First, you must have selected two atoms.</para>
-
-          <programlisting>... --add-bond</programlisting>
-        </section>
-
-        <section xml:id='bond.remove-bond'>
-          <title xml:id='bond.remove-bond.title'>Removing a bond manually
+          </para>
+
+          <programlisting>... --add-bonds</programlisting>
+
+          <para>If two atoms are selected, the single bond in between, if not
+          present, is added. If more than two atoms are selected, than the
+          bond between any pair of these is added.</para>
+         <note><para>This is especially useful in conjunction with the
+          fragmentation scheme. If you want to know the contribution from
+          certain fragments whose subgraph is not connected you can simply
+          make the associated subset of atoms connected by selecting all
+          bonds and adding the bonds.</para>
+         </note>
+        </section>
+
+        <section xml:id='bond.remove-bonds'>
+          <title xml:id='bond.remove-bonds.title'>Removing a bond manually
           </title>
 
@@ -1167 +1177 @@
           bond.</para>
 
-          <programlisting>... --remove-bond</programlisting>
+          <programlisting>... --remove-bonds</programlisting>
+
+          <para>Similarly, if more than two atoms are selected, then all bonds
+          found between any pair of these is removed.</para>
         </section>