Changeset caece4 for src/documentation/userinterfaces/python.dox

Timestamp:

May 20, 2014, 9:14:56 AM (11 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:

6029a6

Parents:

74459a

git-author:

Frederik Heber <heber@…> (03/20/14 17:23:35)

git-committer:

Frederik Heber <heber@…> (05/20/14 09:14:56)

Message:

Enhanced documentation significantly.

• went through all of the constructs and updated each.
• enhanced documentation ofr Fragmentation::FragmentMolecule().

File:

• src/documentation/userinterfaces/python.dox (modified) (5 diffs)

src/documentation/userinterfaces/python.dox

@@ -2 +2 @@
  * Project: MoleCuilder
  * Description: creates and alters molecular systems
- * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Copyright (C)  2013 Frederik Heber. All rights reserved.
  * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
  */
@@ -22 +22 @@
  *  This is done in \b src/Python/PythonScripting.cpp.
  *
- *  There again some preprocessor magic is happening. One the one hand we
- *  need GlobalListOfActions.hpp to have a list of all actions available.
- *  Second, in AllActionPython.hpp we define export functions for every
- *  Action (in essence we use the COMMAND function, see Action_impl_pre.hpp,
- *  which makes an Action usable internally as a normal function).
+ *  There again some preprocessor magic is happening, very similar to constructs
+ *  we used for the Action's. One the one hand we need GlobalListOfActions.hpp to 
+ *  have a list of all actions available. Second, in AllActionPython.hpp we define
+ *  export functions for every Action (in essence we use the COMMAND function, see 
+ *  Action_impl_pre.hpp, which makes an Action usable internally as a normal 
+ *  function).
  *
  *  Then, at the beginning of the BOOST_PYTHON_MODULE declaration we initialize
@@ -48 +49 @@
  *  \endcode
  *  which loads a file \b test.xyz into the (internal) World, selects the first
- *  atom and removes it. Notice \b mol.wait() at the end. This might be necessary
- *  as actions are executed in a different thread than the python script itself.
+ *  atom and removes it.
+ *
+ *  \subsection userinterfaces-python-first-test-wait Wait may be important ...
+ *
+ *  \note Notice \b mol.wait() at the end. This might be necessary as actions are 
+ *  executed in a different thread than the python script itself. This is only
+ *  enabled when configure is called with \b enable-action-thread.
+ *
  *  Hence, if you require values from molecuilder you have to make sure that
  *  all your actions have been processed by this second thread. That's what
@@ -82 +89 @@
  *
  *  If in the current directory a file \b molecuilder.py is found, the contents
- *  is executed as a regular python script.
+ *  is executed as a regular python script prior to any other Action's.
  *
  *  \note Each commands needs to be taken from a molecule called \a pyMoleCuilder.
@@ -141 +148 @@
  *  gives you the docu string on WorldInputAction.
  *
- * \subsection userinterfaces-python-notes-wait Waiting for the action queue
- *
- * Note again that actions are executed in a different thread as the python
- * script. Hence, we require synchronization at certain intervals where you
- * require molecuilder to be up to speed. All commands you executed such
- * as
- * \code
- * import pyMoleCuilder as mol
- * mol.WorldInput("foo.xyz")
- * mol.wait()
- * \endcode
- * just queue this specific input action but not execute it right away. That's
- * left to the other thread. Hence, you need to wait() before:
- * -# you access mol.get...() functions as these are not actions themselves.
- * -# you need to have files written by molecuilder to be parsed in the python
- *    script.
  *
  *
- * \date 2013-09-28
+ * \date 2014-03-10
  *
  */