Changeset 2082637 for doc/userguide/userguide.xml

Timestamp:

May 7, 2016, 7:03:56 AM (9 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_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:

708ec1

Parents:

fde8e7

git-author:

Frederik Heber <heber@…> (02/29/16 17:14:58)

git-committer:

Frederik Heber <heber@…> (05/07/16 07:03:56)

Message:

Added Parse- and SaveParticleParametersAction to parse/save ParticleRegistry.

• added regression test for parsing and saving particles file.

File:

• doc/userguide/userguide.xml (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1843 +1843 @@
           to give the range of the excluded zone.</para>
         </section>
+        <section xml:id="potentials.parse-particle-parameters">
+          <title xml:id="potentials.parse-particle-parameters.title">Parsing a particles file</title>
+          <para>Empirical Potential contain parameters for function that model
+          interactions between two or more specific particles. However,
+          interactions can also be more general, such as a Coulomb 
+          potential, that interacts with any other particle with non-zero
+          charge, or Lennard-Jones potential that interacts with any other
+          particle close enough.
+          Parameters for these particles are encoded in the internal Particle
+          class and are parsed from and stored to a special particles file.
+          This parse particle parameters function loads the parameters from
+          a file, instantiates them in a new particle, and registers them
+          such that they are known within molecuilder.</para>
+          <para>More particles can be registered (<emphasis role="bold">fit-partial-charges</emphasis> will also
+          register the particles it fits) by parsing them from a file.</para>
+          <programlisting>
+  ... --parse-particle-parameters water.particles
+   </programlisting>
+          <note>Currently, only <productname>TREMOLO</productname>particles files are understood and can be parsed.</note>
+        </section>
+        <section xml:id="potentials.save-particle-parameters">
+          <title xml:id="potentials.save-particle-parameters.title">Saving a particles file</title>
+          <para>The opposite to <emphasis role="bold">parse-particle-parameters</emphasis> 
+          is to save all currently registered particle and their parameters to
+          the given file.</para>
+          <programlisting>
+  ... --save-particle-parameters water.particles
+   </programlisting>
+          <note>Again, only the <productname>TREMOLO</productname>particles format is understood currently and is written.</note>
+        </section>
       </section>
       <section xml:id="dynamics">