Changeset bae7bc for src/Fragmentation

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/Fragmentation/Automation

Files:

• FragmentJobQueue.cpp (modified) (2 diffs)
• FragmentJobQueue.hpp (modified) (2 diffs)
• FragmentationChargeDensity.cpp (modified) (3 diffs)
• FragmentationChargeDensity.hpp (modified) (4 diffs)
• FragmentationResults.cpp (modified) (2 diffs)
• FragmentationResults.hpp (modified) (2 diffs)

src/Fragmentation/Automation/FragmentJobQueue.cpp ¶

@@ -45 +45 @@
 
 #include "Box.hpp"
+#include "Fragmentation/Automation/parseKeySetFile.hpp"
 #include "Helpers/defs.hpp"
 #include "Jobs/MPQCJob.hpp"
@@ -89 +90 @@
 }
 
+bool FragmentJobQueue::addKeySetsFromFiles(
+    const boost::filesystem::path &path,
+    const size_t FragmentCounter,
+    const enum KeySetFileType keysettype
+    )
+{
+  const size_t NoJobs = KeySets.KeySets.size();
+  parseKeySetFile(KeySets, path.string(), FragmentCounter, NonHydrogenKeySets);
+  ASSERT( (KeySets.KeySets.size()-NoJobs) == FragmentCounter,
+      "FragmentJobQueue::addKeySetsFromFiles() - mismatching number of new fragments "
+      +toString(KeySets.KeySets.size()-NoJobs)+" and number of Keyset "
+      +toString(FragmentCounter)+".");
+  return (KeySets.KeySets.size() > NoJobs);
+}
+
+bool FragmentJobQueue::addFullKeySetsFromFiles(
+    const boost::filesystem::path &path,
+    const size_t FragmentCounter,
+    const enum KeySetFileType keysettype
+    )
+{
+  const size_t NoJobs = FullKeySets.KeySets.size();
+  parseKeySetFile(FullKeySets, path.string(), FragmentCounter, NonHydrogenKeySets);
+  ASSERT( (FullKeySets.KeySets.size()-NoJobs) == FragmentCounter,
+      "FragmentJobQueue::addKeySetsFromFiles() - mismatching number of fragments "
+      +toString(FullKeySets.KeySets.size()-NoJobs)+" and number of FullKeyset "
+      +toString(FragmentCounter)+".");
+  return (FullKeySets.KeySets.size() > NoJobs);
+}
+
 void FragmentJobQueue::clear()
 {

src/Fragmentation/Automation/FragmentJobQueue.hpp ¶

@@ -21 +21 @@
 
 #include "Fragmentation/KeySetsContainer.hpp"
+#include "Fragmentation/Automation/parseKeySetFile.hpp"
 #include "Jobs/MPQCJob.hpp"
 
@@ -77 +78 @@
       const unsigned int level);
 
+  /** Adds keysets after fragments have been added by file.
+   *
+   */
+  bool addKeySetsFromFiles(
+      const boost::filesystem::path &path,
+      const size_t FragmentCounter,
+      const enum KeySetFileType keysettype
+      );
+
+  /** Adds keysets after fragments have been added by file.
+   *
+   */
+  bool addFullKeySetsFromFiles(
+      const boost::filesystem::path &path,
+      const size_t FragmentCounter,
+      const enum KeySetFileType keysettype
+      );
+
   /** Getter for the container of all KeySets to the jobs.
    *

src/Fragmentation/Automation/FragmentationChargeDensity.cpp ¶

@@ -57 +57 @@
 FragmentationChargeDensity::FragmentationChargeDensity(
     const std::map<JobId_t,MPQCData> &fragmentData,
-    const std::string &KeySetFilename)
+    const KeySetsContainer &KeySet)
 {
   // create a vector of all job ids
@@ -70 +70 @@
   const std::map< JobId_t, size_t > MatrixNrLookup =
       createMatrixNrLookup(jobids, FragmentCounter);
-
-  // initialise keysets
-  KeySetsContainer KeySet;
-  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
 
   /// prepare for OrthogonalSummation
@@ -91 +87 @@
 }
 
+
 std::vector<SamplingGrid> FragmentationChargeDensity::getFullSampledGrid()
 {

src/Fragmentation/Automation/FragmentationChargeDensity.hpp ¶

@@ -16 +16 @@
 
 #include <map>
-#include <string>
 #include <vector>
 
@@ -27 +26 @@
 #include "Jobs/Grid/SamplingGrid.hpp"
 
+class KeySetsContainer;
+
 /** This structure is a container for the summed up charge density per level.
  *
@@ -35 +36 @@
    *
    * @param fragmentData MPQCData resulting from the jobs, each associated to a job
-   * @param KeySetFilename filename with keysets to associate forces correctly
+   * @param KeySet KeySets of all (non-hydrogen) atoms
    */
   FragmentationChargeDensity(
       const std::map<JobId_t,MPQCData> &fragmentData,
-      const std::string &KeySetFilename);
+      const KeySetsContainer& KeySet);
 
   std::vector<SamplingGrid> getFullSampledGrid();
@@ -54 +55 @@
   //!> results per IndexSet of summed up fragment positions and charges
   std::map<IndexSet::ptr, std::pair<MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> > Result_perIndexSet_Fragment;
+
+private:
+  /** Helper function to call OrthogonalSummation.
+   *
+   * \param fragmentData map of calculated jobs
+   * \param KeySet container of all keysets
+   * \param MatrixNrLookup map with enumerated job ids
+   */
+  void sumUp(
+      const std::map<JobId_t,MPQCData> &fragmentData,
+      const KeySetsContainer &KeySet,
+      const std::map< JobId_t, size_t > &MatrixNrLookup);
+
 };
 

src/Fragmentation/Automation/FragmentationResults.cpp ¶

@@ -58 +58 @@
 #include "Helpers/defs.hpp"
 
-
 FragmentationResults::FragmentationResults(
     const std::map<JobId_t,MPQCData> &fragmentData,
     std::map<JobId_t,VMGData> &longrangeData,
-    const std::string &KeySetFilename)
+    const KeySetsContainer& _KeySet,
+    const KeySetsContainer& _ForceKeySet) :
+    KeySet(_KeySet),
+    ForceKeySet(_ForceKeySet)
 {
   // create lookup from job nr to fragment number
@@ -74 +76 @@
   VMGMatrixNrLookup =
       createMatrixNrLookup(vmgjobids, VMGFragmentCounter);
-
-  // initialise keysets
-  parseKeySetFile(KeySet, KeySetFilename, MPQCFragmentCounter, NonHydrogenKeySets);
-  parseKeySetFile(ForceKeySet, KeySetFilename, MPQCFragmentCounter, HydrogenKeySets);
-
-  /// prepare for OrthogonalSummation
 
   // convert KeySetContainer to IndexSetContainer

src/Fragmentation/Automation/FragmentationResults.hpp ¶

@@ -16 +16 @@
 
 #include <map>
-#include <string>
 #include <vector>
 
@@ -42 +41 @@
 struct FragmentationResults
 {
-  /** Constructor for class FragmentationResults.
-   *
-   * Performs the summation and fills all result vectors.
+  /** Constructor for class FragmentationResults, based on KeySets.
    *
    * @param fragmentData results from short-range fragment calculations
    * @param longrangeData results from long-range fragment calculations
-   * @param fullsolutionData results from long-range full calculations
-   * @param KeySetFilename path to fragment files
-   * @param NoAtoms number of atoms of full system
-   * @param full_sample summed up grid charge
+   * @param _KeySet KeySets of all (non-hydrogen) atoms
+   * @param _ForceKeySet KeySets of all atoms except those added by saturation
    */
   FragmentationResults(
       const std::map<JobId_t,MPQCData> &fragmentData,
       std::map<JobId_t,VMGData> &longrangeData,
-      const std::string &KeySetFilename);
+      const KeySetsContainer& _KeySet,
+      const KeySetsContainer& _ForceKeySet);
 
+  /** Performs the summation and fills all result vectors.
+   *
+   * @param fragmentData results from short-range fragment calculations
+   * @param longrangeData results from long-range fragment calculations
+   * @param fullsolutionData long-range solution
+   * @param full_sample sampled density
+   */
   void operator()(
       const std::map<JobId_t,MPQCData> &fragmentData,