Changeset 9e1bfb for doc/userguide/userguide.xml

Timestamp:

Oct 19, 2014, 5:09:30 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:

b119a0

Parents:

2ed3bf (diff), 0ea063 (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 'Refactoring_PotentialActions' into Candidate_v1.4.9

File:

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

doc/userguide/userguide.xml

@@ -2123 +2123 @@
             a fragment of order 1, e.g. a single hydrogen atom.</para>
           </note>
+        </section>
+
+        <section xml:id='potentials.fit-compound-potential'>
+          <title xml:id='potentials.fit-compound-potential.title'>Fitting
+          many empirical potentials simultaneously</title>
+
 
           <para>Another way is using a file containing a specific set of
@@ -2128 +2134 @@
 
           <programlisting>
-                ... --fit-potential \
+                ... --fit-compound-potential \
                     --fragment-charges 8 1 1 \
                     --potential-file water.potentials \
@@ -2150 +2156 @@
           type of analysis.</para>
 
-          <para>Note that you can combine the two ways, i.e. start with the
-          first but give an empty potential file. The resulting parameters are
-          stored in this way. Fit other potentials and give different file
-          names for each. Eventually, you have to combine the file in a text
-          editor at the moment.</para>
+          <para>Note that you can combine the two ways, i.e. start with a
+          fit-potential call but give an empty potential file. The resulting
+          parameters are stored in it. Fit other potentials and give different
+          file names for each in turn. Eventually, you have to combine the file
+          in a text editor at the moment. And perform a fit-compound-potential
+          with this file.</para>
+        </section>
+
+        
+        <section xml:id='potentials.parse-potential'>
+          <title xml:id='potentials.parse-potential.title'>Parsing an
+          empirical potentials file</title>
+
+          <para>Responsible for the compound potential is every potential
+          function whose signature matches with the designated fragment-charges
+          and who is currently known to an internal instance called the
+          PotentialRegistry.</para>
+
+          <para>More potentials can be registered (fit-potential will also
+          register the potential it fits) by parsing them from a file.</para>
+
+          <programlisting>
+                ... --parse-potentials water.potentials
+          </programlisting>
+
+          <note>Currently, only <productname>TREMOLO</productname> potential
+          files are understood and can be parsed.</note>
+        </section>
+
+        <section xml:id='potentials.save-potential'>
+          <title xml:id='potentials.save-potential.title'>Saving an
+          empirical potentials file</title>
+
+          <para>The opposite to parse-potentials is save-potentials that writes
+          every potential currently known to the PotentialRegistry to the given
+          file along with the currently fitted parameters</para>
+
+          <programlisting>
+                ... --save-potentials water.potentials
+          </programlisting>
+
+          <note>Again, only the <productname>TREMOLO</productname> potential
+          format is understood currently and is written.</note>
         </section>