Changeset 240c3e for src/Actions/FragmentationAction

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".

Location:

src/Actions/FragmentationAction

Files:

• FragmentationAutomationAction.cpp (modified) (4 diffs)
• FragmentationAutomationAction.def (modified) (2 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;
   }
 

src/Actions/FragmentationAction/FragmentationAutomationAction.def

@@ -21 +21 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)
-#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")
-#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))
-#define paramreferences (jobfiles)(path)(host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)
+#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)
+#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("homology-file")
+#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("path to file containing homology containerto append to")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))
+#define paramreferences (jobfiles)(path)(host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(homology_file)
 #define paramvalids \
 (STLVectorValidator< std::vector< boost::filesystem::path > >(ParserFileValidator() && FilePresentValidator())) \
@@ -35 +35 @@
 (RangeValidator< unsigned int >(1, 20)) \
 (RangeValidator< unsigned int >(1, 10)) \
-(DummyValidator< bool >())
+(DummyValidator< bool >()) \
+(DummyValidator< boost::filesystem::path >())
 
 #undef statetypes