Changeset 5c8807 for doc/userguide/userguide.xml

Timestamp:

Oct 19, 2014, 5:12:11 PM (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:

3b1798

Parents:

b119a0 (diff), c7fe90 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9

Conflicts:

doc/userguide/userguide.xml
tests/regression/Atoms/testsuite-atoms.at

• mirror-atoms and translate-to-origins occupied the same places.

File:

• doc/userguide/userguide.xml (modified) (3 diffs)

doc/userguide/userguide.xml

@@ -969 +969 @@
           </programlisting>
         </section>
+
+        <section xml:id='atoms.translate-to-origin'>
+          <title xml:id='atoms.translate-to-origin.title'>Translating atoms</title>
+
+          <para>The following Action is convenient to place a subset of atoms
+          at a known position, the origin, and then translate to some other
+          absolute coordinate. It calculates the average position of the set
+          of selected atoms and then translates all atoms by the negative of
+          this center, i.e. the center is afterwards at the origin.</para>
+
+          <programlisting>... --translate-to-origin</programlisting>
+        </section>
 
         <section xml:id='atoms.change-element'>
@@ -1758 +1770 @@
         </section>
 
-        <section xml:id='analysis.molecullar-volume'>
-          <title xml:id='analysis.molecullar-volume.title'>Molecular Volume
+        <section xml:id='analysis.molecular-volume'>
+          <title xml:id='analysis.molecular-volume.title'>Molecular Volume
           </title>
           
@@ -1767 +1779 @@
           that each node of the tesselation consists of an atom of the
           molecule.</para>
+
+          <programlisting>... --molecular-volume</programlisting>
+        </section>
+
+        <section xml:id='analysis.average-molecule-force'>
+          <title xml:id='analysis.average-molecule-forcetitle'>Average force
+          acting on a molecule</title>
+          
+          <para>This sums up all the forces of each atom of a currently 
+          selected molecule and returns the average force vector. This should
+          give you the general direction of acceleration of the molecule.
+          </para>
 
           <programlisting>... --molecular-volume</programlisting>