Changeset 035c0d

Timestamp:

Feb 27, 2013, 12:43:29 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:

64bdfd

Parents:

da2d5c

git-author:

Frederik Heber <heber@…> (12/19/12 12:41:52)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:43:29)

Message:

Removed typedef charges_t from FunctionModel, using SerializationPotential's instead.

Location:

src

Files:

• FunctionApproximation/FunctionModel.hpp (modified) (1 diff)
• LevMartester.cpp (modified) (6 diffs)
• Potentials/PotentialFactory.cpp (modified) (1 diff)
• Potentials/PotentialFactory.hpp (modified) (2 diffs)
• Potentials/Specifics/SaturationPotential.cpp (modified) (1 diff)

src/FunctionApproximation/FunctionModel.hpp

@@ -45 +45 @@
   //!> typedef for a function containing how to extract required information from a Fragment.
   typedef boost::function< arguments_t (const Fragment &, const size_t)> extractor_t;
-  //!> typedef for a vector of particle tyoes
-  typedef std::vector< double > charges_t;
   //!> typedef for the magic triple function that gets the other two distances for a given argument
   typedef boost::function< std::vector<arguments_t>(const argument_t &, const double)> triplefunction_t;

src/LevMartester.cpp

@@ -45 +45 @@
 #include <boost/foreach.hpp>
 #include <boost/function.hpp>
+#include <boost/lambda/lambda.hpp>
 #include <boost/program_options.hpp>
 
@@ -83 +84 @@
 HomologyGraph getFirstGraphwithSpecifiedElements(
     const HomologyContainer &homologies,
-    const FunctionModel::charges_t &charges)
+    const SerializablePotential::ParticleTypes_t &types)
 {
-  ASSERT( !charges.empty(),
+  ASSERT( !types.empty(),
       "getFirstGraphwithSpecifiedElements() - charges is empty?");
+  // create charges
+  Fragment::charges_t charges;
+  charges.resize(types.size());
+  std::transform(types.begin(), types.end(),
+      charges.begin(), boost::lambda::_1);
   // convert into count map
   Extractors::elementcounts_t counts_per_charge =
@@ -187 +193 @@
   std::cout << "Hello to the World from LevMar!" << std::endl;
 
+//  setVerbosity(4);
+
   // load homology file
   po::options_description desc("Allowed options");
@@ -193 +201 @@
       ("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 potential")
-      ("fragment", po::value< FunctionModel::charges_t >()->multitoken(), "all charges in the fragment")
+      ("charges", po::value< SerializablePotential::ParticleTypes_t >()->multitoken(), "charges specifying the potential")
+      ("fragment", po::value< SerializablePotential::ParticleTypes_t >()->multitoken(), "all charges in the fragment")
   ;
 
@@ -226 +234 @@
 
   // charges
-  FunctionModel::charges_t charges;
+  SerializablePotential::ParticleTypes_t charges;
   if (vm.count("charges")) {
-    charges = vm["charges"].as< FunctionModel::charges_t >();
+    charges = vm["charges"].as< SerializablePotential::ParticleTypes_t >();
   } else {
     ELOG(0, "Vector of charges specifying the potential (charges) was not set.");
@@ -235 +243 @@
 
   // fragment
-  FunctionModel::charges_t fragment;
+  SerializablePotential::ParticleTypes_t fragment;
   if (vm.count("fragment")) {
-    fragment = vm["fragment"].as< FunctionModel::charges_t >();
+    fragment = vm["fragment"].as< SerializablePotential::ParticleTypes_t >();
   } else {
     ELOG(0, "Vector of charges specifying the fragment (charges) was not set.");

src/Potentials/PotentialFactory.cpp

@@ -71 +71 @@
 FunctionModel *PotentialFactory::createInstance(
     const std::string &potentialtype,
-    const FunctionModel::charges_t &charges) const
+    const SerializablePotential::ParticleTypes_t &types) const
 {
   ASSERT (NameToType.count(potentialtype),
       "PotentialFactory::createInstance() - cannot find potential of name "+potentialtype);
-  SerializablePotential::ParticleTypes_t types;
-  types.resize(charges.size());
-  std::transform(charges.begin(), charges.end(), types.begin(), boost::lambda::_1);
   switch (NameToType[potentialtype]) {
   case tersoff:

src/Potentials/PotentialFactory.hpp

@@ -19 +19 @@
 
 #include "FunctionApproximation/FunctionModel.hpp"
+#include "Potentials/SerializablePotential.hpp"
 
 /** Class that creates instances of potentials.
@@ -38 +39 @@
   FunctionModel *createInstance(
       const std::string &potentialtype,
-      const FunctionModel::charges_t &charges) const;
+      const SerializablePotential::ParticleTypes_t &charges) const;
 
   //!> enumeration of all known and createable potentials

src/Potentials/Specifics/SaturationPotential.cpp

@@ -422 +422 @@
     // only that saturation potential never has its middle element twice!
     // hence, we skip the firstpair but keep the code for later generalization
-    charges_t secondpair(2, boost::cref(charges[1]));
-    const charges_t &thirdpair = charges;
+    Fragment::charges_t secondpair(2, boost::cref(charges[1]));
+    const Fragment::charges_t &thirdpair = charges;
     returnfunction =
 //        boost::bind(&Extractors::reorderArgumentsByParticleTypes,