Changeset 73a5f7 for doc


Ignore:
Timestamp:
Sep 9, 2016, 5:10:10 PM (8 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_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, 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, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable
Children:
d20335
Parents:
ce0f63
git-author:
Frederik Heber <heber@…> (09/04/16 14:26:38)
git-committer:
Frederik Heber <heber@…> (09/09/16 17:10:10)
Message:

Added parsing and saving of fragment results container state.

  • TEST: Added regression test on saving and parsing results, including undo and redo tests.
  • DOCU: Both actions are fully documented.
File:
1 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    rce0f63 r73a5f7  
    16121612  ... --fragment-automation \
    16131613      --fragment-executable mpqc \
    1614       --fragment-resultfile BondFragment_results.dat \
    16151614      --DoLongrange 1 \
    16161615      --DoValenceOnly 1 \
    … …  
    16251624          <para>The executable is required if you do not have a patched
    16261625          version of <productname>MPQC</productname> that may directly act as
    1627           a client to JobMarket&apos;s server. All calculated results are placed in
    1628           the result file. If none is given, they are instead again placed in
    1629           an internal storage for later access.</para>
     1626          a client to JobMarket&apos;s server.</para>
    16301627          <note>
    16311628            <para>Long-calculations are only possible with a client that knows
    … …  
    16361633          of long-range interactions. We only sample valence charges on the
    16371634          grid, i.e. not core electrons and the nuclei charges are reduced
    1638 suitably. This avoids problems with sampling highly localized
     1635          suitably. This avoids problems with sampling highly localized
    16391636          charges on the grid and is in general recommended. Next, there
    16401637          follow parameters for the multi grid solver, namely the resolution
    … …  
    16441641          their recommend values.</para>
    16451642          <para>In the last line, parameters are given on how to access the
    1646           JobMarket server, namely it address and its port. If the JobMarket package is not available, then these option values cannot be given. Instead the solver is called internally on the same machine and one fragment energy is calculated after the other.</para>
     1643          JobMarket server, namely it address and its port. If the JobMarket
     1644          package is not available, then these option values cannot be given.
     1645          Instead the solver is called internally on the same machine and one
     1646          fragment energy is calculated after the other.</para>
     1647          <note>The structure storing the fragment results internally is
     1648          cleared prior to this action and calculated fragment results
     1649          is inserted afterwards, i.e. it contains only the
     1650          calculations from the current run.</note>
     1651          <note>All calculated results may be placed in a result file for
     1652          later parsing, see
     1653          <link linkend="molecule.save-fragment-results">save fragment results</link>
     1654          .</note>
    16471655        </section>
    16481656        <section xml:id="fragmentation.analyse-fragment-results">
    … …  
    16551663  ... --analyse-fragment-results \
    16561664      --fragment-prefix &quot;BondFragment&quot; \
    1657       --fragment-resultfile BondFragment_results.dat \
    16581665      --store-grids 1
    16591666   </programlisting>
    1660           <para>The purpose of the prefix should already be known to you, same
    1661           with the result file that is the file parsed by MoleCuilder. The
     1667          <para>The purpose of the prefix should already be known to you. The
    16621668          last option states that the sampled charge densities and the
    16631669          calculated potential from the long-range calculations should be
    … …  
    16711677          <link linkend="molecule.verlet-integration">verlet integration</link>
    16721678          is possible afterwards.</para>
     1679          <note>If not obtained by
     1680          <link linkend="molecule.fragment-automation">fragment automation</link>
     1681          then fragment results need to be parsed from file, see
     1682          <link linkend="molecule.parse-fragment-results">parse fragment results</link>
     1683          .</note>
    16731684        </section>
    16741685        <section xml:id="fragmentation.store-saturated-fragment">
    … …  
    16841695      --output-types xyz
    16851696       </programlisting>
     1697        </section>
     1698        <section xml:id="fragmentation.parse-fragment-jobs">
     1699          <title xml:id="fragmentation.parse-fragment-jobs.title">Parse fragment jobs from files</title>
     1700          <para>The fragment jobs that are created by
     1701          <link linkend="molecule.fragment-molecule">fragment molecule</link>
     1702          may also be placed in a file for later retrieval. See the details of
     1703          this action on how to create one file per job.</para>
     1704          <para>Later, for parsing these job files, we need to use the parse
     1705          fragment jobs action as follows:</para>
     1706          <programlisting>
     1707  ... --parse-fragment-jobs \
     1708      --fragment-jobs &quot;BondFragment00.in&quot; &quot;BondFragment01.in&quot; \
     1709      --fragment-path &quot;./&quot;
     1710   </programlisting>
     1711        <para>Here, we give a list of files by the first option and the second
     1712        option gives an optional path where all these files are stored.</para>
     1713        </section>
     1714        <section xml:id="fragmentation.parse-fragment-results">
     1715          <title xml:id="fragmentation.parse-fragment-results.title">Parse calculated fragment results from file</title>
     1716          <para>Fragment results can either be obtained directly from
     1717          solving the associated electronic structure problem for each
     1718          of the fragment jobs. Or if that has been done at some earlier
     1719          stage and results have been written to a file, see
     1720          <link linkend="molecule.save-fragment-results">save fragment results</link>
     1721          , then we may also parse these results.</para>
     1722          <programlisting>
     1723  ... --parse-fragment-results &quot;results.dat&quot;
     1724   </programlisting>
     1725        </section>
     1726        <section xml:id="fragmentation.save-fragment-results">
     1727          <title xml:id="fragmentation.save-fragment-results.title">Save calculated fragment results to file</title>
     1728          <para>Calculated fragment results may be stored to a single file
     1729          for later analysis as follows:</para>
     1730          <programlisting>
     1731  ... --save-fragment-results &quot;results.dat&quot;
     1732   </programlisting>
     1733        <note>Beware though that files from long-range calculations may be
     1734        very large and are stored quite inefficiently at the moment.</note>
    16861735        </section>
    16871736      </section>
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