Changeset 46fcc0 for src

Timestamp:

Feb 27, 2013, 12:42:37 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:

77552d

Parents:

39a07a

git-author:

Frederik Heber <heber@…> (12/11/12 10:42:50)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:37)

Message:

LevMartester has new option fragment such that fragment to use as training data may be defined.

File:

• src/LevMartester.cpp (modified) (5 diffs)

src/LevMartester.cpp

@@ -81 +81 @@
 using namespace boost::assign;
 
-HomologyGraph getFirstGraphwithTimesSpecificElement(
+HomologyGraph getFirstGraphwithSpecifiedElements(
     const HomologyContainer &homologies,
-    const size_t _number,
-    const size_t _times)
+    const FunctionModel::charges_t &charges)
 {
-  for (HomologyContainer::container_t::const_iterator iter =
-      homologies.begin(); iter != homologies.end(); ++iter) {
-    if (iter->first.hasTimesAtomicNumber(_number,_times))
-      return iter->first;
+  ASSERT( !charges.empty(),
+      "getFirstGraphwithSpecifiedElements() - charges is empty?");
+  // convert into count map
+  Extractors::elementcounts_t counts_per_charge =
+      Extractors::_detail::getElementCounts(charges);
+  ASSERT( !counts_per_charge.empty(),
+      "getFirstGraphwithSpecifiedElements() - charge counts are empty?");
+  LOG(2, "DEBUG: counts_per_charge is " << counts_per_charge << ".");
+  // we want to check each (unique) key only once
+  HomologyContainer::const_key_iterator olditer = homologies.key_end();
+  for (HomologyContainer::const_key_iterator iter =
+      homologies.key_begin(); iter != homologies.key_end(); olditer = iter++) {
+    // if it's the same as the old one, skip it
+    if (*olditer == *iter)
+      continue;
+    // if it's a new key, check if every element has the right number of counts
+    Extractors::elementcounts_t::const_iterator countiter = counts_per_charge.begin();
+    for (; countiter != counts_per_charge.end(); ++countiter)
+      if (!(*iter).hasTimesAtomicNumber(countiter->first,countiter->second))
+        break;
+    if( countiter == counts_per_charge.end())
+      return *iter;
   }
   return HomologyGraph();
@@ -176 +193 @@
       ("homology-file", po::value< boost::filesystem::path >(), "homology file to parse")
       ("fit-potential", po::value< std::string >(), "potential type to fit")
-      ("charges", po::value< FunctionModel::charges_t >()->multitoken(), "charges specifying the fragment")
+      ("charges", po::value< FunctionModel::charges_t >()->multitoken(), "charges specifying the potential")
+      ("fragment", po::value< FunctionModel::charges_t >()->multitoken(), "all charges in the fragment")
   ;
 
@@ -211 +229 @@
   if (vm.count("charges")) {
     charges = vm["charges"].as< FunctionModel::charges_t >();
+  } else {
+    ELOG(0, "Vector of charges specifying the potential (charges) was not set.");
+    return 1;
+  }
+
+  // fragment
+  FunctionModel::charges_t fragment;
+  if (vm.count("fragment")) {
+    fragment = vm["fragment"].as< FunctionModel::charges_t >();
   } else {
     ELOG(0, "Vector of charges specifying the fragment (charges) was not set.");
@@ -237 +264 @@
   for (HomologyContainer::container_t::const_iterator iter =
       homologies.begin(); iter != homologies.end(); ++iter) {
-    LOG(1, "INFO: graph " << iter->first << " has Fragment "
-        << iter->second.first << " and associated energy " << iter->second.second << ".");
-  }
-
-  LOG(0, "STATUS: I'm training now a " << potentialtype << " potential on charges " << charges << ".");
+    LOG(1, "INFO: graph " << iter->first << " has Fragment " << iter->second.first
+        << " and associated energy " << iter->second.second << ".");
+  }
+
+  LOG(0, "STATUS: I'm training now a " << potentialtype << " potential on charges "
+      << charges << ".");
 
   /******************** TRAINING ********************/
@@ -254 +282 @@
   {
     // then we ought to pick the right HomologyGraph ...
-    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,8,1);
+    const HomologyGraph graph = getFirstGraphwithSpecifiedElements(homologies,fragment);
     if (graph != HomologyGraph()) {
-      LOG(1, "First representative graph containing charges is " << graph << ".");
+      LOG(1, "First representative graph containing fragment "
+          << fragment << " is " << graph << ".");
 
       // Afterwards we go through all of this type and gather the distance and the energy value