Changeset 184943

Timestamp:

Nov 21, 2012, 10:03:24 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:

f3bc5f

Parents:

c74fdb

git-author:

Frederik Heber <heber@…> (08/08/12 13:36:24)

git-committer:

Frederik Heber <heber@…> (11/21/12 10:03:24)

Message:

Added Fragment to MPQCData fusion maps and is used in FragmentationAutomationAction.

• new helpers Fragment::getPositions() and ::getCharges().
• SumUpChargeDensity() now also sums up a full Fragment.
• the Fragment is used by createLongRangeJobs to extract required posittions and charges from.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (9 diffs)
• Fragmentation/SetValues/Fragment.cpp (modified) (3 diffs)
• Fragmentation/SetValues/Fragment.hpp (modified) (4 diffs)
• Jobs/MPQCDataFused.hpp (modified) (1 diff)
• Jobs/MPQCDataMap.hpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -52 +52 @@
 #include "Fragmentation/ForceMatrix.hpp"
 #include "Fragmentation/Fragmentation.hpp"
+#include "Fragmentation/SetValues/Fragment.hpp"
 #include "Fragmentation/SetValues/Histogram.hpp"
 #include "Fragmentation/SetValues/IndexedVectors.hpp"
@@ -378 +379 @@
 
 template <>
+void convertMPQCDataTo<MPQCDataFragmentMap_t>(
+    const std::vector<MPQCData> &fragmentData,
+    std::vector<MPQCDataFragmentMap_t> &MPQCData_Fragment_fused)
+{
+  // fragment
+  MPQCData_Fragment_fused.clear();
+  MPQCData_Fragment_fused.reserve(fragmentData.size());
+  for(std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
+      dataiter != fragmentData.end(); ++dataiter) {
+    const MPQCData &extractedData = *dataiter;
+    LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
+    MPQCDataFragmentMap_t instance;
+    boost::fusion::at_key<MPQCDataFused::fragment>(instance) =
+        Fragment(extractedData.positions, extractedData.charges);
+    MPQCData_Fragment_fused.push_back(instance);
+  }
+}
+
+template <>
 void convertMPQCDataTo<MPQCDataTimeMap_t>(
     const std::vector<MPQCData> &fragmentData,
@@ -429 +449 @@
  * @param KeySetFilename filename with keysets to associate forces correctly
  * @param NoAtoms total number of atoms
- * @param full_sample summed up charge from fragments on return
+ * @param full_sample summed up charge density of electrons from fragments on return
+ * @param full_fragment summed up positions and charges of nuclei from fragments on return
  */
 bool sumUpChargeDensity(
@@ -435 +456 @@
     const std::vector<MPQCData> &fragmentData,
     const std::string &KeySetFilename,
-    SamplingGrid &full_sample)
+    SamplingGrid &full_sample,
+    Fragment &full_fragment)
 {
   // create lookup from job nr to fragment number
@@ -468 +490 @@
     SumUpPerLevel<MPQCDataGridMap_t, MPQCDataGridVector_t>(
         fragmentData, jobids, MatrixNrLookup, container, subsetmap));
+  std::vector<MPQCDataFragmentMap_t> Result_Fragment_fused(
+    SumUpPerLevel<MPQCDataFragmentMap_t, MPQCDataFragmentVector_t>(
+        fragmentData, jobids, MatrixNrLookup, container, subsetmap));
   // obtain full grid
   full_sample = boost::fusion::at_key<MPQCDataFused::sampled_grid>(Result_Grid_fused.back());
+  full_fragment = boost::fusion::at_key<MPQCDataFused::fragment>(Result_Fragment_fused.back());
 
   return true;
@@ -673 +699 @@
     const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters &params,
     const std::vector<MPQCData> &fragmentData,
-    const SamplingGrid &full_sampled_grid)
+    const SamplingGrid &full_sampled_grid,
+    const Fragment &full_fragment)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -696 +723 @@
 //    ASSERT( M.determinant() == size*size*size,
 //        "createLongRangeJobs() - current domain matrix "+toString(M)+" is not cubic.");
-    const std::vector< std::vector<double> > positions;
-    const std::vector<double> charges;
+    const std::vector< std::vector<double> > positions(full_fragment.getPositions());
+    const std::vector<double> charges(full_fragment.getCharges());
     const JobId_t next_id = controller.getAvailableId();
     LOG(1, "INFO: Creating full VMGJob with " << full_sampled_grid.sampled_grid.size()
@@ -766 +793 @@
   LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
   SamplingGrid full_sample;
+  Fragment full_fragment;
   sumUpChargeDensity(
       MPQCresults,
       fragmentData,
       params.path.get(),
-      full_sample);
+      full_sample,
+      full_fragment);
 
   // Phase Four: obtain more ids
@@ -777 +806 @@
 
   // Phase Five: create VMGJobs
-  if (!createLongRangeJobs(controller, params, fragmentData, full_sample))
+  if (!createLongRangeJobs(controller, params, fragmentData, full_sample, full_fragment))
     return Action::failure;
   RunService(io_service, "Adding VMGJobs");

src/Fragmentation/SetValues/Fragment.cpp

@@ -38 +38 @@
 #include "Fragment.hpp"
 
+#include <iostream>
+
 #include "CodePatterns/Assert.hpp"
 
@@ -43 +45 @@
 {}
 
-Fragment::Fragment(positions_t &_positions, charges_t &_charges)
+Fragment::Fragment(const positions_t &_positions, const charges_t &_charges)
 {
   ASSERT( _positions.size() == _charges.size(),
@@ -101 +103 @@
 }
 
+Fragment::positions_t Fragment::getPositions() const
+{
+  positions_t positions;
+  for (nuclei_t::const_iterator iter = nuclei.begin();
+      iter != nuclei.end(); ++iter)
+    positions.push_back(iter->first);
+  return positions;
+}
+
+Fragment::charges_t Fragment::getCharges() const
+{
+  charges_t charges;
+  for (nuclei_t::const_iterator iter = nuclei.begin();
+      iter != nuclei.end(); ++iter)
+    charges.push_back(iter->second);
+  return charges;
+}
+
+std::ostream & operator<<(std::ostream &ost, const Fragment &f)
+{
+  size_t NucleiCounter = 1;
+  for (Fragment::nuclei_t::const_iterator iter = f.nuclei.begin();
+      iter != f.nuclei.end(); ++iter)
+    ost << NucleiCounter++ << "\t" << iter->first << " with charge " << iter->second << std::endl;
+  return ost;
+}
+
 template<> Fragment ZeroInstance<Fragment>()
 {

src/Fragmentation/SetValues/Fragment.hpp

@@ -15 +15 @@
 #endif
 
+#include <iosfwd>
 #include <vector>
 
 class Fragment {
+  //!> grant ostream operator access
+  friend std::ostream & operator<<(std::ostream &ost, const Fragment &f);
 public:
   typedef std::vector< std::vector<double> > positions_t;
@@ -41 +44 @@
    * @param _charges given charges
    */
-  Fragment(std::vector< std::vector<double> > &_positions, std::vector< double > &_charges);
+  Fragment(const std::vector< std::vector<double> > &_positions, const std::vector< double > &_charges);
 
   /** Adding another fragment onto this one.
@@ -67 +70 @@
   Fragment& operator-=(const Fragment &other);
 
+  /** Getter for all stored positions.
+   *
+   * @return vector of positions
+   */
+  positions_t getPositions() const;
+
+  /** Getter for all stored charges.
+   *
+   * @return vector of charges
+   */
+  charges_t getCharges() const;
+
 private:
   /** Helper function that checks whether this nuclei is present.
@@ -87 +102 @@
 };
 
+std::ostream & operator<<(std::ostream &ost, const Fragment &f);
+
 template<typename T> T ZeroInstance();
 template<> Fragment ZeroInstance<Fragment>();

src/Jobs/MPQCDataFused.hpp

@@ -40 +40 @@
   struct sampled_grid {};
 
+  // keys for fragment
+  struct fragment {};
+
   // keys for times_t
   struct times_walltime {};

src/Jobs/MPQCDataMap.hpp

@@ -19 +19 @@
 #include "Jobs/MPQCDataFused.hpp"
 
+class Fragment;
 class Histogram;
 class IndexedVectors;
@@ -88 +89 @@
 
 /** This boost::fusion map defines key-value or rather key-type pairs with
+ * which we associate all sampled_grid data members in MPQCData and their type.
+ *
+ * This lets us resolves any ambiguitites of types in MPQCData, e.g.
+ * to know vector<double> is forces or energy_eigenvalues.
+ *
+ */
+typedef boost::fusion::map<
+    boost::fusion::pair<MPQCDataFused::fragment, Fragment >
+> MPQCDataFragmentMap_t;
+
+typedef boost::mpl::list<
+    MPQCDataFused::fragment
+> MPQCDataFragmentVector_t;
+
+/** This boost::fusion map defines key-value or rather key-type pairs with
  * which we associate all times_t data members in MPQCData and their type.
  *