Changeset 70f2a1 for doc


Ignore:
Timestamp:
Jul 12, 2017, 7:10:07 PM (8 years ago)
Author:
Frederik Heber <frederik.heber@…>
Branches:
Action_Thermostats, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_Verbose_Codepatterns, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps
Children:
f56e14
Parents:
33af20
git-author:
Frederik Heber <frederik.heber@…> (06/17/17 23:17:40)
git-committer:
Frederik Heber <frederik.heber@…> (07/12/17 19:10:07)
Message:

DOCU: Added restrictions of file formats to userguide.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r33af20 r70f2a1  
    268268      one into another (with possible loss of data outside of the intersection of
    269269      stored properties of the two involved file formats).</para>
     270      <para>Note that the various formats differ in how much information they
     271      can store. This restriction may come from two sources: either the file format
     272      specification does not support more or the implementation is still lacking
     273      specific features.</para>
     274      <para>What all formats can store at least is the element per atom and a
     275      position in three spatial coordinates for a single time step.</para>
     276      <para>In the following we list some restrictions:</para>
     277      <itemizedlist>
     278        <listitem>
     279          <para>Multiple time steps supported by</para>
     280          <itemizedlist>
     281            <listitem>
     282              <para>Pdb</para>
     283            </listitem>
     284            <listitem>
     285              <para>Tremolo (note entries allows to change over steps are: x, u, F)</para>
     286            </listitem>
     287            <listitem>
     288              <para>Xyz</para>
     289            </listitem>
     290          </itemizedlist>
     291        </listitem>
     292        <listitem>
     293          <para>Bond information supported by</para>
     294          <itemizedlist>
     295            <listitem>
     296              <para>Pdb</para>
     297            </listitem>
     298            <listitem>
     299              <para>Tremolo</para>
     300            </listitem>
     301          </itemizedlist>
     302        </listitem>
     303        <listitem>
     304          <para>Full atom state storable (i.e. position, velocity, and force)</para>
     305          <itemizedlist>
     306            <listitem>
     307              <para>Tremolo</para>
     308            </listitem>
     309          </itemizedlist>
     310        </listitem>
     311        <listitem>
     312          <para>Domain information (however, this is not parsed only stored)</para>
     313          <itemizedlist>
     314            <listitem>
     315              <para>Tremolo</para>
     316            </listitem>
     317          </itemizedlist>
     318        </listitem>
     319      </itemizedlist>
     320      <para>You easily notice that the <productname>Tremolo</productname> format is currently
     321      the most versatile. However, by advised that you need to give a specific
     322    <emphasis>ATOMINFO</emphasis> line that specifies what needs to be stored,
     323    see <link linkend="various-specific.set-tremolo-atomdata">set-tremolo-atomdata</link>.</para>
    270324    </section>
    271325  </chapter>
    … …  
    26412695          velocities and forces as well as the atoms positions and
    26422696          element.</para>
    2643           <programlisting>... --set-tremolo-atomdata &quot;ATOM id element u=3 v=3 F=3&quot; \
     2697          <programlisting>... --set-tremolo-atomdata &quot;id element u=3 v=3 F=3&quot; \
    26442698    --reset 1
    26452699   </programlisting>
    26462700          <para>This will not append but reset the old line and fill it with
    2647           the given string.</para>
     2701          the given string. </para>
     2702          <para>Find a list of all keys that are also used internally in MoleCuilder below:</para>
     2703          <itemizedlist>
     2704            <listitem><para>id number - Id</para></listitem>
     2705            <listitem><para>chemical element - type</para></listitem>
     2706            <listitem><para>position - x=3</para></listitem>
     2707            <listitem><para>velocity - u=3</para></listitem>
     2708            <listitem><para>force - F=3</para></listitem>
     2709            <listitem><para>enumerating bonded atom ids - neighbors=4</para></listitem>
     2710            <listitem><para>name of atom - name</para></listitem>
     2711            <listitem><para>charge - Charge</para></listitem>
     2712          </itemizedlist> 
     2713          <para>Furthermore, find the rest of all available keys:</para>
     2714          <itemizedlist>
     2715            <listitem><para>stress tensor - stress</para></listitem>
     2716            <listitem><para>enumerating bonded atom ids for improper potential - imprData</para></listitem>
     2717            <listitem><para>unknown - GroupMeasureTypeNo</para></listitem>
     2718            <listitem><para>group association for external forces - exttype</para></listitem>
     2719            <listitem><para>residual name of atom (see PDB) - resName</para></listitem>
     2720            <listitem><para>chain Id (see PDB) - chainId</para></listitem>
     2721            <listitem><para>residual sequence (see PDB) - resSeq</para></listitem>
     2722            <listitem><para>occupancy of electron orbitals - occupancy</para></listitem>
     2723            <listitem><para>temperature factor - tempFactor</para></listitem>
     2724            <listitem><para>segment id (see PDB) - segID</para></listitem>
     2725            <listitem><para>different charge - charge</para></listitem>
     2726            <listitem><para>unknown - GrpTypeNo</para></listitem>
     2727            <listitem><para>enumerating bonded atom ids for torsion potential - torsion</para></listitem>
     2728          </itemizedlist> 
    26482729          <para>One further specific action is required when loading certain
    26492730          <productname>TREMOLO</productname> configuration files. These
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