Context Navigation

-              r4f44ae
+              rbae7bc
 #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"
 …
+ *
  * @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
 …
   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
 …
   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);
+}
 …
 bool appendToHomologyFile(
     const boost::filesystem::path &homology_file,
+    const FragmentationResults &results,
+    const std::string &KeySetFilename)
+    const FragmentationResults &results)
+{
   /// read homology container (if present)
 …
   // 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;
 …
   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.");
 …
       fragmentData,
       longrangeData,
+      params.path.get());
+      FragmentJobQueue::getInstance().getKeySets(),
+      FragmentJobQueue::getInstance().getFullKeySets());
   results(
       fragmentData,
 …
       fullsolutionData,
       full_sample);
+  {
+    LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
+    printReceivedFullResults(results);
+  }
+  printReceivedFullResults(results);
   // append all keysets to homology file
 …
     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;
+    }
 …
     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;

Note: See TracChangeset for help on using the changeset viewer.

Context Navigation

Changeset bae7bc for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Legend:

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Download in other formats: