Changeset da2d5c for src/Potentials


Ignore:
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:
035c0d
Parents:
3d2559
git-author:
Frederik Heber <heber@…> (12/19/12 12:38:49)
git-committer:
Frederik Heber <heber@…> (02/27/13 12:43:29)
Message:

Removed parameter charges from getFragmentSpecificExtractor().

Location:
src/Potentials/Specifics
Files:
10 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

    r3d2559 rda2d5c  
    683683
    684684FunctionModel::extractor_t
    685 ManyBodyPotential_Tersoff::getFragmentSpecificExtractor(
    686     const charges_t &charges) const
    687 {
    688   ASSERT(charges.size() <= (size_t)2,
    689       "ManyBodyPotential_Tersoff::getFragmentSpecificExtractor() - requires 1 charge.");
     685ManyBodyPotential_Tersoff::getFragmentSpecificExtractor() const
     686{
    690687  FunctionModel::extractor_t returnfunction =
    691688      boost::bind(&Extractors::gatherAllDistances,

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

    r3d2559 rda2d5c  
    179179   * from a Fragment.
    180180   *
    181    * \param charges vector of charges to be extracted
    182181   * \return bound function extracting distances from a fragment
    183182   */
    184   FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     183  FunctionModel::extractor_t getFragmentSpecificExtractor() const;
    185184
    186185  /** Sets the magic triple function that we use for getting angle distances.

  • src/Potentials/Specifics/PairPotential_Angle.cpp

    r3d2559 rda2d5c  
    4141#include <boost/assign/list_of.hpp> // for 'map_list_of()'
    4242#include <boost/bind.hpp>
     43#include <boost/lambda/lambda.hpp>
    4344#include <string>
    4445
    … …  
    206207
    207208FunctionModel::extractor_t
    208 PairPotential_Angle::getFragmentSpecificExtractor(
    209     const charges_t &charges) const
    210 {
    211   ASSERT(charges.size() == (size_t)3,
    212       "PairPotential_Angle::getFragmentSpecificExtractor() - requires 3 charges.");
     209PairPotential_Angle::getFragmentSpecificExtractor() const
     210{
     211  Fragment::charges_t charges;
     212  charges.resize(getParticleTypes().size());
     213  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
     214      charges.begin(), boost::lambda::_1);
    213215  FunctionModel::extractor_t returnfunction =
    214216      boost::bind(&Extractors::gatherDistancesFromFragment,
    215217          boost::bind(&Fragment::getPositions, _1),
    216218          boost::bind(&Fragment::getCharges, _1),
    217           boost::cref(charges),
     219          charges,
    218220          _2);
    219221  return returnfunction;

  • src/Potentials/Specifics/PairPotential_Angle.hpp

    r3d2559 rda2d5c  
    156156   * from a Fragment.
    157157   *
    158    * \param charges vector of charges to be extracted
    159158   * \return bound function extracting distances from a fragment
    160159   */
    161   FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     160  FunctionModel::extractor_t getFragmentSpecificExtractor() const;
    162161
    163162  enum parameter_enum_t {

  • src/Potentials/Specifics/PairPotential_Harmonic.cpp

    r3d2559 rda2d5c  
    4141#include <boost/assign/list_of.hpp> // for 'map_list_of()'
    4242#include <boost/bind.hpp>
     43#include <boost/lambda/lambda.hpp>
    4344#include <string>
    4445
    … …  
    182183
    183184FunctionModel::extractor_t
    184 PairPotential_Harmonic::getFragmentSpecificExtractor(
    185     const charges_t &charges) const
    186 {
    187   ASSERT(charges.size() == (size_t)2,
    188       "PairPotential_Harmonic::getFragmentSpecificExtractor() - requires 2 charges.");
     185PairPotential_Harmonic::getFragmentSpecificExtractor() const
     186{
     187  Fragment::charges_t charges;
     188  charges.resize(getParticleTypes().size());
     189  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
     190      charges.begin(), boost::lambda::_1);
    189191  FunctionModel::extractor_t returnfunction =
    190192      boost::bind(&Extractors::gatherDistancesFromFragment,
    191193          boost::bind(&Fragment::getPositions, _1),
    192194          boost::bind(&Fragment::getCharges, _1),
    193           boost::cref(charges),
     195          charges,
    194196          _2);
    195197  return returnfunction;

  • src/Potentials/Specifics/PairPotential_Harmonic.hpp

    r3d2559 rda2d5c  
    138138   * from a Fragment.
    139139   *
    140    * \param charges vector of charges to be extracted
    141140   * \return bound function extracting distances from a fragment
    142141   */
    143   FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     142  FunctionModel::extractor_t getFragmentSpecificExtractor() const;
    144143
    145144  /** Return the token name of this specific potential.

  • src/Potentials/Specifics/PairPotential_Morse.cpp

    r3d2559 rda2d5c  
    4141#include <boost/assign/list_of.hpp> // for 'map_list_of()'
    4242#include <boost/bind.hpp>
     43#include <boost/lambda/lambda.hpp>
    4344#include <cmath>
    4445#include <string>
    … …  
    211212
    212213FunctionModel::extractor_t
    213 PairPotential_Morse::getFragmentSpecificExtractor(
    214     const charges_t &charges) const
    215 {
    216   ASSERT(charges.size() == (size_t)2,
    217       "PairPotential_Morse::getFragmentSpecificExtractor() - requires 2 charges.");
     214PairPotential_Morse::getFragmentSpecificExtractor() const
     215{
     216  Fragment::charges_t charges;
     217  charges.resize(getParticleTypes().size());
     218  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
     219      charges.begin(), boost::lambda::_1);
    218220  FunctionModel::extractor_t returnfunction =
    219221      boost::bind(&Extractors::gatherDistancesFromFragment,
    220222          boost::bind(&Fragment::getPositions, _1),
    221223          boost::bind(&Fragment::getCharges, _1),
    222           boost::cref(charges),
     224          charges,
    223225          _2);
    224226  return returnfunction;

  • src/Potentials/Specifics/PairPotential_Morse.hpp

    r3d2559 rda2d5c  
    155155   * from a Fragment.
    156156   *
    157    * \param charges vector of charges to be extracted
    158157   * \return bound function extracting distances from a fragment
    159158   */
    160   FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     159  FunctionModel::extractor_t getFragmentSpecificExtractor() const;
    161160
    162161  enum parameter_enum_t {

  • src/Potentials/Specifics/SaturationPotential.cpp

    r3d2559 rda2d5c  
    4141#include <boost/assign.hpp>
    4242#include <boost/assign/list_of.hpp> // for 'map_list_of()'
     43#include <boost/lambda/lambda.hpp>
    4344#include <iostream>
    4445#include <string>
    … …  
    396397
    397398FunctionModel::extractor_t
    398 SaturationPotential::getFragmentSpecificExtractor(
    399     const charges_t &charges) const
    400 {
    401   ASSERT(charges.size() == (size_t)2,
    402       "SaturationPotential::getFragmentSpecificExtractor() - requires 2 charges.");
     399SaturationPotential::getFragmentSpecificExtractor() const
     400{
     401  Fragment::charges_t charges;
     402  charges.resize(getParticleTypes().size());
     403  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
     404      charges.begin(), boost::lambda::_1);       
    403405  FunctionModel::extractor_t returnfunction;
    404406  if (charges[0] == charges[1]) {
    … …  
    409411            boost::bind(&Fragment::getPositions, _1),
    410412            boost::bind(&Fragment::getCharges, _1),
    411             boost::cref(charges),
     413            charges, // is only temporarily created, hence copy
    412414            _2);
    413415  } else {

  • src/Potentials/Specifics/SaturationPotential.hpp

    r3d2559 rda2d5c  
    181181   * from a Fragment.
    182182   *
    183    * \param charges vector of charges to be extracted
    184183   * \return bound function extracting distances from a fragment
    185184   */
    186   FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     185  FunctionModel::extractor_t getFragmentSpecificExtractor() const;
    187186
    188187  enum parameter_enum_t {
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