Changeset 1ba51c for doc


Ignore:
Timestamp:
Jun 19, 2017, 8:24:16 AM (8 years ago)
Author:
Frederik Heber <frederik.heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChangeBugEmailaddress, ChemicalSpaceEvaluator, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_Verbose_Codepatterns, ForceAnnealing_oldresults, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps
Children:
fd4e8c
Parents:
f79d65
git-author:
Frederik Heber <heber@…> (03/30/17 22:02:06)
git-committer:
Frederik Heber <frederik.heber@…> (06/19/17 08:24:16)
Message:

Updated userguide with lots of notes on using geometry object.

File:
1 edited

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  • doc/userguide/userguide.xml

    rf79d65 r1ba51c  
    750750        name. This allows for a very powerful and handy manipulation of the
    751751       molecular system afterwards. And to give a concrete example, let's have
    752        a look at translating a set of selected atoms. </para>
     752       a look at translating a set of selected atoms, see subsection on
     753       <link linkend='atoms.translate-atom'>Translating atoms</link>. </para>
    753754       <programlisting>
    754755... --translate-atoms &quot;unitVectorX&quot;
    … …  
    866867          <para>where the element is given via its chemical symbol and the
    867868          vector gives the position within the domain</para>
     869         <para>Note that instead of giving an explicit vector you may also use
     870        a vector stored as a geometry object, see section
     871        <link linkend='geometry'>Geometry</link>.</para>
    868872        </section>
    869873        <section xml:id="atoms.remove-atom">
    … …  
    881885  ... --saturate-atoms
    882886   </programlisting>
    883           <para>A number of hydrogen atoms is added around each selected atom corresponding to the valence of the chemical element. The hydrogen atoms are placed in the same
    884           distance to this atom and approximately with same distance to their
    885    nearest neighbors. Already present bonds (i.e. the position of neighboring atoms) is taken into account.</para>
     887          <para>A number of hydrogen atoms is added around each selected atom
     888          corresponding to the valence of the chemical element. The hydrogen
     889          atoms are placed in the same distance to this atom and approximately
     890          with same distance to their nearest neighbors. Already present bonds
     891          (i.e. the position of neighboring atoms) is taken into account.</para>
    886892        </section>
    887893        <section xml:id="atoms.translate-atom">
    … …  
    896902          mind the boundary conditions, i.e. it might shift atoms outside of the
    897903          domain.</para>
     904         <para>Again, note that instead of giving an explicit vector you may
     905         also use a vector stored as a geometry object, see section
     906        <link linkend='geometry'>Geometry</link>.</para>
    898907        </section>
    899908        <section xml:id="atoms.mirror-atoms">
    … …  
    907916                    --periodic 0
    908917   </programlisting>
     918         <para>And of course instead of giving an explicit vector you may also
     919         use a vector stored as a geometry object, see section
     920        <link linkend='geometry'>Geometry</link>.</para>
    909921        </section>
    910922        <section xml:id="atoms.translate-to-origin">
    … …  
    11171129          and adds new bonds in between these copied atoms such that their
    11181130          bond subgraphs are identical.</para>
     1131         <para>Here, instead of giving an explicit vector you may also use
     1132        a vector stored as a geometry object, see section
     1133        <link linkend='geometry'>Geometry</link>.</para>
    11191134        </section>
    11201135        <section xml:id="molecule.change-molname">
    … …  
    11471162   specific offset..</para>
    11481163          <programlisting>... -translate-molecules</programlisting>
    1149           <para>As before, this is actually just an operation on all of the molecule&apos;s atoms, namely translating them.</para>
     1164          <para>As before, this is actually just an operation on all of the
     1165          molecule&apos;s atoms, namely translating them.</para>
     1166         <para>Same as with <link linkend='atoms.translate-atom'>translate-atoms</link>
     1167         instead of giving an explicit vector you may also use a vector stored
     1168         as a geometry object, see section
     1169        <link linkend='geometry'>Geometry</link>.</para>
    11501170        </section>
    11511171        <section xml:id="molecule.rotate-around-self">
    … …  
    11681188   </programlisting>
    11691189          <para>This rotates the molecule around an axis from the origin to
    1170           the position (0,0,1), i.e. around the z axis, by 90 degrees.</para>
     1190          the position (0,0,1), i.e. around the z axis, by 90 degrees, where
     1191          for the position you may also use a stored vector, see section
     1192        <link linkend='geometry'>Geometry</link>.</para>
    11711193        </section>
    11721194        <section xml:id="molecule.rotate-to-principal-axis-system">
    … …  
    11811203          </programlisting>
    11821204          <para>This rotates the molecule in such a manner that the ellipsoids
    1183           largest axis is aligned with the z axis. <remark>Note that &quot;0,0,-1&quot; would align anti-parallel.</remark></para>
     1205          largest axis is aligned with the z axis. <remark>Note that
     1206          &quot;0,0,-1&quot; would align anti-parallel.</remark></para>
     1207         <para>Again instead of giving the coordinates explicitly you may also
     1208         use a vector stored as a geometry object, see section
     1209        <link linkend='geometry'>Geometry</link>.</para>
    11841210        </section>
    11851211        <section xml:id="molecule.verlet-integration">
    … …  
    14261452      --Alignment-Axis &quot;0,0,1&quot;
    14271453   </programlisting>
     1454         <para>Note that instead of giving an explicit axis you may also use
     1455        a vector stored as a geometry object, see section
     1456        <link linkend='geometry'>Geometry</link>.</para>
    14281457        </section>
    14291458        <section xml:id="filling.suspend-in-molecule">
    … …  
    15331562          <para>This would calculate the correlation of all hydrogen and
    15341563          oxygen atoms with respect to the origin.</para>
     1564         <para>Naturally, instead of giving explicit coordinates you may also
     1565         use a vector stored as a geometry object for position, see section
     1566        <link linkend='geometry'>Geometry</link>.</para>
    15351567        </section>
    15361568        <section xml:id="analysis.surface-correlation">
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