Changeset 240c3e for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Timestamp:

Dec 14, 2012, 5:39:40 PM (12 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:

07266b

Parents:

37ce5d

git-author:

Frederik Heber <heber@…> (09/27/12 14:42:38)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:40)

Message:

FragmentationAutomationAction now uses a file containing a serialized HomologyContainer.

• the idea is that we append the calculated keysets als HomologyGraphs to the instance that is afterwards again serialized to file.
• so far, we do not yet create the graphs, we only parse the file and write again the instance.
• new parameter "homology-file".

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -39 +39 @@
 #include "CodePatterns/MemDebug.hpp"
 
+// include headers that implement a archive in simple text format
+#include <boost/archive/text_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
+
+
 #include <boost/mpl/remove.hpp>
 #include <boost/lambda/lambda.hpp>
+
+#include <iostream>
 
 #include "CodePatterns/Assert.hpp"
@@ -57 +64 @@
 #include "Fragmentation/ForceMatrix.hpp"
 #include "Fragmentation/Fragmentation.hpp"
+#include "Fragmentation/Homology/HomologyContainer.hpp"
+#include "Fragmentation/Homology/HomologyGraph.hpp"
 #include "Fragmentation/SetValues/Fragment.hpp"
 #include "Fragmentation/SetValues/Histogram.hpp"
@@ -379 +388 @@
 }
 
+bool appendToHomologyFile(const boost::filesystem::path &homology_file)
+{
+  // read homology container (if present)
+  HomologyContainer homology_container;
+  if (boost::filesystem::exists(homology_file)) {
+    std::ifstream returnstream(homology_file.string().c_str());
+    if (returnstream.good()) {
+      boost::archive::text_iarchive ia(returnstream);
+      ia >> homology_container;
+    } else {
+      ELOG(2, "Failed to parse from " << homology_file.string() << ".");
+    }
+    returnstream.close();
+  } else {
+    LOG(2, "Could not open " << homology_file.string()
+        << ", creating empty container.");
+  }
+
+  // append all fragments to a HomologyContainer
+  HomologyContainer::container_t values;
+  // TODO: prepare HomologyGraphs ...
+  homology_container.insert(values);
+
+  // store homology container again
+  std::ofstream outputstream(homology_file.string().c_str());
+  if (outputstream.fail()) { // check if opened
+    boost::archive::text_oarchive oa(outputstream);
+    oa << homology_container;
+    if (outputstream.fail()) { // check if correctly written
+      LOG(1, "Failed to write to file " << homology_file.string() << ".");
+      return false;
+    } else
+      outputstream.close();
+  } else {
+    LOG(1, "Failed to open file " << homology_file.string()
+        << " for writing.");
+    return false;
+  }
+  return true;
+}
 
 Action::state_ptr FragmentationFragmentationAutomationAction::performCall() {
@@ -475 +524 @@
     LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
     printReceivedFullResults(results);
+  }
+
+  // append all keysets to homology file
+  if (Exitflag != 0) {
+    const boost::filesystem::path &homology_file = params.homology_file.get();
+    if (!appendToHomologyFile(homology_file))
+      Exitflag = 1;
   }