Changeset f89b45 for src

Timestamp:

Nov 7, 2011, 4:13:18 PM (13 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:

f894fe

Parents:

55f299

git-author:

Frederik Heber <heber@…> (11/02/11 01:13:59)

git-committer:

Frederik Heber <heber@…> (11/07/11 16:13:18)

Message:

Added Reaction CalculateBoundingBoxAction.

• calculate bounding box via Box::getBoundingPlanes() of the current domain.
• also added regression test Analysis/CalculateBoundingBox.

exporting std::vector<double> as return value.

• had to add trick with exporting std::vector<double> to python with help from stackoverflow("does boost python support a function returning a vector, by ref or value?") answer. We construct a vec_item template class which exports getter/setter, append, ... functionality to python.
• This ends in typedef doubleVec in namespace MoleCuilder::PythonTypes, while within the Reaction its just a typedef defined in the .def file.
• this type had to be prefix with PythonType_ to make it distinguishable from the functions in dir(mol) for Python/AllActions regression test.
• TESTFIX: Also we modified Python/AllActions regression test to go in a loop over each command, thus stdout and stderr can be uniquely associated to the very command that caused them. This makes debugging a lot easier ... for this purpose the dir(mol) and filtering was placed into new listcmds.py.

Location:

src/Actions

Files:

• AnalysisAction/CalculateBoundingBoxAction.cpp (added)
• AnalysisAction/CalculateBoundingBoxAction.def (added)
• AnalysisAction/CalculateBoundingBoxAction.hpp (added)
• GlobalListOfActions.hpp (modified) (1 diff)
• Makefile.am (modified) (3 diffs)
• pyMoleCuilder.cpp (modified) (2 diffs)

src/Actions/GlobalListOfActions.hpp

@@ -48 +48 @@
         (ParserSetParserParameters) \
         (ParserSetOutputFormats) \
+        (AnalysisCalculateBoundingBox) \
         (AnalysisCalculateCellVolume) \
         (AnalysisCalculateMolarMass) \

src/Actions/Makefile.am

@@ -87 +87 @@
 
 ANALYSISACTIONSOURCE = \
+  Actions/AnalysisAction/CalculateBoundingBoxAction.cpp \
   Actions/AnalysisAction/CalculateCellVolumeAction.cpp \
   Actions/AnalysisAction/CalculateMolarMassAction.cpp \
@@ -97 +98 @@
   Actions/AnalysisAction/SurfaceCorrelationAction.cpp
 ANALYSISACTIONHEADER = \
+  Actions/AnalysisAction/CalculateBoundingBoxAction.hpp \
   Actions/AnalysisAction/CalculateCellVolumeAction.hpp \
   Actions/AnalysisAction/CalculateMolarMassAction.hpp \
@@ -107 +109 @@
   Actions/AnalysisAction/SurfaceCorrelationAction.hpp
 ANALYSISACTIONDEFS = \
+  Actions/AnalysisAction/CalculateBoundingBoxAction.def \
   Actions/AnalysisAction/CalculateCellVolumeAction.def \
   Actions/AnalysisAction/CalculateMolarMassAction.def \

src/Actions/pyMoleCuilder.cpp

@@ -61 +61 @@
 }
 
+} /* namespace detail */
+
+namespace PythonTypes {
+
+inline void IndexError(){
+    PyErr_SetString(PyExc_IndexError, "Index out of range");
+    boost::python::throw_error_already_set();
+}
+
+template<class T>
+struct vec_item{
+    typedef typename T::value_type V;
+    static V& get(T& x, int i){
+        static V nothing;
+        if(i < 0) i += x.size();
+        if(i >= 0 && i < int(x.size())) return x[i];
+        IndexError();
+        return nothing;
+    }
+    static void set(T& x, int i, V const& v){
+        if(i < 0) i += x.size();
+        if(i >= 0 && i < int(x.size())) x[i] = v;
+        else IndexError();
+    }
+    static void del(T& x, int i){
+        if(i < 0) i += x.size();
+        if(i >= 0 && i < int(x.size())) x.erase(x.begin() + i);
+        else IndexError();
+    }
+    static void add(T& x, V const& v){
+        x.push_back(v);
+    }
+};
+
+
+} /* namespace PythonTypes */
 } /* namespace MoleCuilder */
-} /* namespace detail */
 
 BOOST_PYTHON_MODULE(pyMoleCuilder)
@@ -77 +112 @@
 
   boost::python::def("reinit", MoleCuilder::detail::module_reinit, "Reinitializes the internal state of the python module as if it had been freshly imported, saves all input files beforehand.");
+
+  // STL Vectors:
+  // doubleVec
+  boost::python::class_< std::vector< double > >("PythonType_doubleVec")
+      .def("__len__", &std::vector< double >::size)
+      .def("clear", &std::vector< double >::clear)
+      .def("append", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::add,
+            boost::python::with_custodian_and_ward<1, 2>()) // let container keep value
+      .def("__getitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::get,
+           boost::python::return_value_policy<boost::python::copy_non_const_reference>())
+      .def("__setitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::set,
+           boost::python::with_custodian_and_ward<1,2>()) // to let container keep value
+      .def("__delitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::del)
+      .def("__iter__", boost::python::iterator< std::vector< double > >())
+  ;
+
+
 #define export_print(z,n,list) \
         BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();