Changeset bae7bc for src/Actions

Timestamp:

Apr 15, 2013, 10:28:25 AM (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:

503acc1

Parents:

4f44ae

git-author:

Frederik Heber <heber@…> (03/04/13 14:14:10)

git-committer:

Frederik Heber <heber@…> (04/15/13 10:28:25)

Message:

Outsourced parsing of fragment files into ParseFragmentJobsAction from FragmentationAutomationAction.

• We now solely rely on the job queue to contain all the information we need.
• FragmentationAutomationAction now clears queue after calculation.

Location:

src/Actions

Files:

• FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• FragmentationAction/FragmentationAutomationAction.cpp (modified) (11 diffs)
• FragmentationAction/FragmentationAutomationAction.def (modified) (1 diff)
• FragmentationAction/ParseFragmentJobsAction.cpp (added)
• FragmentationAction/ParseFragmentJobsAction.def (added)
• FragmentationAction/ParseFragmentJobsAction.hpp (added)
• GlobalListOfActions.hpp (modified) (1 diff)
• Makefile.am (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -75 +75 @@
   LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
       << params.distance.get() << " up to "
-      << params.order.get() << " order. Fragment files begin with "
-      << params.prefix.get() << " and are stored as: "
-      << params.types.get() << "." << std::endl);
+      << params.order.get() << " order. ");
+  if (params.types.get().size() != 0)
+    LOG(0, "STATUS: Fragment files begin with "
+        << params.prefix.get() << " and are stored as: "
+        << params.types.get() << "." << std::endl);
 
   // check for selected atoms

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -60 +60 @@
 #include "Fragmentation/Automation/FragmentationResults.hpp"
 #include "Fragmentation/Automation/MPQCFragmentController.hpp"
-#include "Fragmentation/Automation/parseKeySetFile.hpp"
 #include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
 #include "Fragmentation/Automation/VMGFragmentController.hpp"
@@ -224 +223 @@
  *
  * @param fragmentData MPQCData resulting from the jobs, associated to job id
- * @param KeySetFilename filename with keysets to associate forces correctly
+ * @param MatrixNrLookup map with enumerated jobids
+ * @param KeySet KeySets of all (non-hydrogen) atoms
+ * @param ForceKeySet KeySets of all atoms except those added by saturation
  * @param NoAtoms total number of atoms
- * @param full_sample summed up charge from fragments on return
  */
 bool printReceivedMPQCResults(
     const std::map<JobId_t, MPQCData> &fragmentData,
-    const std::string &KeySetFilename,
+    const std::map< JobId_t, size_t > MatrixNrLookup,
+    KeySetsContainer KeySet,
+    const KeySetsContainer &ForceKeySet,
     size_t NoAtoms)
 {
-  // create a vector of all job ids
-  std::vector<JobId_t> jobids;
-  std::transform(fragmentData.begin(),fragmentData.end(),
-      std::back_inserter(jobids),
-      boost::bind( &std::map<JobId_t,MPQCData>::value_type::first, boost::lambda::_1 )
-  );
-
-  // create lookup from job nr to fragment number
-  size_t FragmentCounter = 0;
-  const std::map< JobId_t, size_t > MatrixNrLookup=
-      createMatrixNrLookup(jobids, FragmentCounter);
+  size_t FragmentCounter = MatrixNrLookup.size();
 
   // place results into maps
@@ -253 +245 @@
   if (!Energy.InitialiseIndices()) return false;
 
-  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
-
-  // initialise keysets
-  KeySetsContainer KeySet;
-  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
-  KeySetsContainer ForceKeySet;
-  parseKeySetFile(ForceKeySet, KeySetFilename, FragmentCounter, HydrogenKeySets);
+  if (!Force.ParseIndices(ForceKeySet)) return false;
 
   // combine all found data
@@ -295 +281 @@
 
   return true;
+}
+
+/** Print MPQCData from received results.
+ *
+ * @param fragmentData MPQCData resulting from the jobs, associated to job id
+ * @param KeySetFilename filename with keysets to associate forces correctly
+ * @param NoAtoms total number of atoms
+ */
+bool printReceivedMPQCResults(
+    const std::map<JobId_t, MPQCData> &fragmentData,
+    const std::string &KeySetFilename,
+    size_t NoAtoms)
+{
+  // create a vector of all job ids
+  std::vector<JobId_t> jobids;
+  std::transform(fragmentData.begin(),fragmentData.end(),
+      std::back_inserter(jobids),
+      boost::bind( &std::map<JobId_t,MPQCData>::value_type::first, boost::lambda::_1 )
+  );
+
+  // create lookup from job nr to fragment number
+  size_t FragmentCounter = 0;
+  const std::map< JobId_t, size_t > MatrixNrLookup =
+      createMatrixNrLookup(jobids, FragmentCounter);
+
+  // initialise keysets
+  KeySetsContainer KeySet;
+  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
+  KeySetsContainer ForceKeySet;
+  parseKeySetFile(ForceKeySet, KeySetFilename, FragmentCounter, HydrogenKeySets);
+
+  return printReceivedMPQCResults(
+      fragmentData,
+      MatrixNrLookup,
+      KeySet,
+      ForceKeySet,
+      NoAtoms);
+}
+
+/** Print MPQCData from received results.
+ *
+ * @param fragmentData MPQCData resulting from the jobs, associated to job id
+ * @param KeySet KeySets of all (non-hydrogen) atoms
+ * @param ForceKeySet KeySets of all atoms except those added by saturation
+ * @param NoAtoms total number of atoms
+ */
+bool printReceivedMPQCResults(
+    const std::map<JobId_t, MPQCData> &fragmentData,
+    const KeySetsContainer &KeySet,
+    const KeySetsContainer &ForceKeySet,
+    size_t NoAtoms)
+{
+  // create a vector of all job ids
+  std::vector<JobId_t> jobids;
+  std::transform(fragmentData.begin(),fragmentData.end(),
+      std::back_inserter(jobids),
+      boost::bind( &std::map<JobId_t,MPQCData>::value_type::first, boost::lambda::_1 )
+  );
+
+  // create lookup from job nr to fragment number
+  size_t FragmentCounter = 0;
+  const std::map< JobId_t, size_t > MatrixNrLookup =
+      createMatrixNrLookup(jobids, FragmentCounter);
+
+  return printReceivedMPQCResults(
+      fragmentData,
+      MatrixNrLookup,
+      KeySet,
+      ForceKeySet,
+      NoAtoms);
 }
 
@@ -382 +438 @@
 bool appendToHomologyFile(
     const boost::filesystem::path &homology_file,
-    const FragmentationResults &results,
-    const std::string &KeySetFilename)
+    const FragmentationResults &results)
 {
   /// read homology container (if present)
@@ -479 +534 @@
   // TODO: Have io_service run in second thread and merge with current again eventually
 
-  // check some things prior to work
-  enum OutputType_t {
-    ToFiles,
-    ToJobs,
-    ToNone
-  };
-  enum OutputType_t outputtype = ToNone;
-  if (params.jobfiles.get().size() != 0) {
-    // we got no job files, hence we use FragmentJobQueue
-    if (params.path.get().size() == 0) {
-      ELOG(1, "Missing path to fragment files.");
-      return Action::failure;
-    }
-    outputtype = ToFiles;
-
-    // parse in fragment-jobs if given
-    if(!FragmentJobQueue::getInstance().addJobsFromFiles(
-        params.jobfiles.get(),
-        params.level.get()))
-      return Action::failure;
-  } else {
-    if (params.path.get().size() != 0) {
-      ELOG(2, "Path to fragment given although we use FragmentJobQueue.");
-    }
-    outputtype = ToJobs;
-  }
-
   size_t Exitflag = 0;
   std::map<JobId_t, MPQCData> fragmentData;
@@ -537 +565 @@
   FragmentationChargeDensity summedChargeDensity(
       fragmentData,
-      params.path.get());
+      FragmentJobQueue::getInstance().getKeySets());
   const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
-
   LOG(1, "INFO: There are " << fragmentData.size() << " short-range and "
       << full_sample.size() << " level-wise long-range jobs.");
@@ -587 +614 @@
       fragmentData,
       longrangeData,
-      params.path.get());
+      FragmentJobQueue::getInstance().getKeySets(),
+      FragmentJobQueue::getInstance().getFullKeySets());
   results(
       fragmentData,
@@ -593 +621 @@
       fullsolutionData,
       full_sample);
-  {
-    LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
-    printReceivedFullResults(results);
-  }
+  printReceivedFullResults(results);
 
   // append all keysets to homology file
@@ -603 +628 @@
     if (homology_file.string() != "") {
       LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
-      if (!appendToHomologyFile(homology_file, results, params.path.get()))
+      if (!appendToHomologyFile(homology_file, results))
         Exitflag = 1;
     }
@@ -630 +655 @@
     printReceivedMPQCResults(
         fragmentData,
-        params.path.get(),
-        getNoAtomsFromAdjacencyFile(params.path.get()));
+        FragmentJobQueue::getInstance().getKeySets(),
+        FragmentJobQueue::getInstance().getFullKeySets(),
+        World::getInstance().getAllAtoms().size()));
   }
 #endif
+
+  // now clear all present jobs as we are done
+  FragmentJobQueue::getInstance().clear();
 
   return (Exitflag == 0) ? Action::success : Action::failure;

src/Actions/FragmentationAction/FragmentationAutomationAction.def

@@ -14 +14 @@
 #include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/RangeValidator.hpp"
-#include "Parameters/Validators/STLVectorValidator.hpp"
-#include "Parameters/Validators/Specific/ParserFileValidator.hpp"
-#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
 // 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)(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"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(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 paramtypes (std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)
+#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("homology-file")
+#define paramdescriptions ("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 (PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))
+#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(homology_file)
 #define paramvalids \
-(STLVectorValidator< std::vector< boost::filesystem::path > >(ParserFileValidator() && FilePresentValidator())) \
-(DummyValidator< std::string >()) \
 (DummyValidator< std::string >()) \
 (DummyValidator< std::string >()) \

src/Actions/GlobalListOfActions.hpp

@@ -137 +137 @@
 #define GLOBALLISTOFACTIONS \
     BOOST_PP_SEQ_PUSH_BACK( \
-        GLOBALLISTOFACTIONS_initial, \
-        FragmentationFragmentationAutomation \
-      )
+        BOOST_PP_SEQ_PUSH_BACK( \
+            GLOBALLISTOFACTIONS_initial, \
+            FragmentationFragmentationAutomation \
+        ), \
+        FragmentationParseFragmentJobs \
+    )
 #else
 #define GLOBALLISTOFACTIONS \

src/Actions/Makefile.am

@@ -222 +222 @@
 if CONDJOBMARKET
 FRAGMENTATIONACTIONSOURCE += \
-  Actions/FragmentationAction/FragmentationAutomationAction.cpp
+  Actions/FragmentationAction/FragmentationAutomationAction.cpp \
+  Actions/FragmentationAction/ParseFragmentJobsAction.cpp
 FRAGMENTATIONACTIONHEADER += \
-  Actions/FragmentationAction/FragmentationAutomationAction.hpp
+  Actions/FragmentationAction/FragmentationAutomationAction.hpp \
+  Actions/FragmentationAction/ParseFragmentJobsAction.hpp
 FRAGMENTATIONACTIONDEFS += \
-  Actions/FragmentationAction/FragmentationAutomationAction.def
+  Actions/FragmentationAction/FragmentationAutomationAction.def \
+  Actions/FragmentationAction/ParseFragmentJobsAction.def
 endif