Changeset b760bc3


Ignore:
Timestamp:
Feb 27, 2013, 12:36:17 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:
dbf8c8
Parents:
93e908
git-author:
Frederik Heber <heber@…> (11/28/12 11:47:59)
git-committer:
Frederik Heber <heber@…> (02/27/13 12:36:17)
Message:

Added ParticleTypeChecker functions in own namespace and added checks to every specific potential.

  • these check whether typesin argument_t matches with potential's ParticleTypes.
  • replaced row of Asserts with ParticleTypeChecker call in all specific potentials.
Location:
src/Potentials
Files:
2 added
6 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Makefile.am

    r93e908 rb760bc3  
    44POTENTIALSSOURCE = \
    55  Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
     6  Potentials/ParticleTypeCheckers.cpp \
    67  Potentials/PotentialRegistry.cpp \
    78  Potentials/SerializablePotential.cpp \
    … …  
    1516  Potentials/Exceptions.hpp \
    1617  Potentials/helpers.hpp \
     18  Potentials/ParticleTypeCheckers.hpp \
    1719  Potentials/PotentialRegistry.hpp \
    1820  Potentials/SerializablePotential.hpp \

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

    r93e908 rb760bc3  
    4949
    5050#include "Potentials/helpers.hpp"
     51#include "Potentials/ParticleTypeCheckers.hpp"
    5152
    5253// static definitions
    … …  
    165166      ++argiter) {
    166167    const argument_t &r_ij = *argiter;
    167     ASSERT( arguments[0].types.first == getParticleTypes()[0],
    168         "ManyBodyPotential_Tersoff::operator() - first charge "
    169         +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    170     ASSERT( arguments[0].types.second == getParticleTypes()[1],
    171         "ManyBodyPotential_Tersoff::operator() - second charge "
    172         +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
    173 
     168    ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
     169        arguments_t(1, r_ij), getParticleTypes()),
     170        "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments.");
     171 
    174172    const double cutoff = function_cutoff(r_ij.distance);
    175173    const double temp = (cutoff == 0.) ?
    … …  
    224222      ++argiter) {
    225223    const argument_t &r_ij = *argiter;
    226     ASSERT( arguments[0].types.first == getParticleTypes()[0],
    227         "ManyBodyPotential_Tersoff::operator() - first charge "
    228         +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    229     ASSERT( arguments[0].types.second == getParticleTypes()[1],
    230         "ManyBodyPotential_Tersoff::operator() - second charge "
    231         +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     224    ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
     225        arguments_t(1, r_ij), getParticleTypes()),
     226        "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments.");
    232227
    233228  switch (index) {

  • src/Potentials/Specifics/PairPotential_Angle.cpp

    r93e908 rb760bc3  
    4545
    4646#include "Potentials/helpers.hpp"
     47#include "Potentials/ParticleTypeCheckers.hpp"
    4748
    4849// static definitions
    … …  
    119120  ASSERT( arguments.size() == 3,
    120121      "PairPotential_Angle::operator() - requires exactly three arguments.");
    121   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    122       "PairPotential_Angle::operator() - first charge of first distance "
    123       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    124   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    125       "PairPotential_Angle::operator() - second charge of first distance "
    126       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
    127   ASSERT( arguments[1].types.first == getParticleTypes()[0],
    128       "PairPotential_Angle::operator() - first charge of second distance "
    129       +toString(arguments[1].types.first)+" is not "+toString(getParticleTypes()[0]));
    130   ASSERT( arguments[1].types.second == getParticleTypes()[2],
    131       "PairPotential_Angle::operator() - second charge of second distance "
    132       +toString(arguments[1].types.second)+" is not "+toString(getParticleTypes()[2]));
    133   ASSERT( arguments[2].types.first == getParticleTypes()[1],
    134       "PairPotential_Angle::operator() - first charge of third distance "
    135       +toString(arguments[2].types.first)+" is not "+toString(getParticleTypes()[1]));
    136   ASSERT( arguments[2].types.second == getParticleTypes()[2],
    137       "PairPotential_Angle::operator() - second charge of third distance "
    138       +toString(arguments[2].types.second)+" is not "+toString(getParticleTypes()[2]));
     122  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     123      arguments, getParticleTypes()),
     124      "PairPotential_Angle::operator() - types don't match with ones in arguments.");
    139125  const argument_t &r_ij = arguments[0];
    140126  const argument_t &r_ik = arguments[1];
    … …  
    154140  ASSERT( arguments.size() == 3,
    155141      "PairPotential_Angle::operator() - requires exactly three arguments.");
    156   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    157       "PairPotential_Angle::derivative() - first charge of first distance "
    158       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    159   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    160       "PairPotential_Angle::derivative() - second charge of first distance "
    161       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
    162   ASSERT( arguments[1].types.first == getParticleTypes()[0],
    163       "PairPotential_Angle::derivative() - first charge of second distance "
    164       +toString(arguments[1].types.first)+" is not "+toString(getParticleTypes()[0]));
    165   ASSERT( arguments[1].types.second == getParticleTypes()[2],
    166       "PairPotential_Angle::derivative() - second charge of second distance "
    167       +toString(arguments[1].types.second)+" is not "+toString(getParticleTypes()[2]));
    168   ASSERT( arguments[2].types.first == getParticleTypes()[1],
    169       "PairPotential_Angle::derivative() - first charge of third distance "
    170       +toString(arguments[2].types.first)+" is not "+toString(getParticleTypes()[1]));
    171   ASSERT( arguments[2].types.second == getParticleTypes()[2],
    172       "PairPotential_Angle::derivative() - second charge of third distance "
    173       +toString(arguments[2].types.second)+" is not "+toString(getParticleTypes()[2]));
     142  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     143      arguments, getParticleTypes()),
     144      "PairPotential_Angle::operator() - types don't match with ones in arguments.");
    174145  derivative_components_t result;
    175146  const argument_t &r_ij = arguments[0];
    … …  
    190161  ASSERT( arguments.size() == 3,
    191162      "PairPotential_Angle::parameter_derivative() - requires exactly three arguments.");
    192   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    193       "PairPotential_Angle::parameter_derivative() - first charge of first distance "
    194       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    195   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    196       "PairPotential_Angle::parameter_derivative() - second charge of first distance "
    197       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
    198   ASSERT( arguments[1].types.first == getParticleTypes()[0],
    199       "PairPotential_Angle::parameter_derivative() - first charge of second distance "
    200       +toString(arguments[1].types.first)+" is not "+toString(getParticleTypes()[0]));
    201   ASSERT( arguments[1].types.second == getParticleTypes()[2],
    202       "PairPotential_Angle::parameter_derivative() - second charge of second distance "
    203       +toString(arguments[1].types.second)+" is not "+toString(getParticleTypes()[2]));
    204   ASSERT( arguments[2].types.first == getParticleTypes()[1],
    205       "PairPotential_Angle::parameter_derivative() - first charge of third distance "
    206       +toString(arguments[2].types.first)+" is not "+toString(getParticleTypes()[1]));
    207   ASSERT( arguments[2].types.second == getParticleTypes()[2],
    208       "PairPotential_Angle::parameter_derivative() - second charge of third distance "
    209       +toString(arguments[2].types.second)+" is not "+toString(getParticleTypes()[2]));
     163  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     164      arguments, getParticleTypes()),
     165      "PairPotential_Angle::operator() - types don't match with ones in arguments.");
    210166  const argument_t &r_ij = arguments[0];
    211167  const argument_t &r_ik = arguments[1];

  • src/Potentials/Specifics/PairPotential_Harmonic.cpp

    r93e908 rb760bc3  
    4545
    4646#include "Potentials/helpers.hpp"
     47#include "Potentials/ParticleTypeCheckers.hpp"
    4748
    4849// static definitions
    … …  
    100101  ASSERT( arguments.size() == 1,
    101102      "PairPotential_Harmonic::operator() - requires exactly one argument.");
    102   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    103       "PairPotential_Harmonic::operator() - first charge "
    104       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    105   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    106       "PairPotential_Harmonic::operator() - second charge "
    107       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     103  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     104      arguments, getParticleTypes()),
     105      "PairPotential_Harmonic::operator() - types don't match with ones in arguments.");
    108106  const argument_t &r_ij = arguments[0];
    109107  const result_t result =
    … …  
    121119  ASSERT( arguments.size() == 1,
    122120      "PairPotential_Harmonic::operator() - requires exactly one argument.");
    123   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    124       "PairPotential_Harmonic::derivative() - first charge "
    125       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    126   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    127       "PairPotential_Harmonic::derivative() - second charge "
    128       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     121  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     122      arguments, getParticleTypes()),
     123      "PairPotential_Harmonic::operator() - types don't match with ones in arguments.");
    129124  derivative_components_t result;
    130125  const argument_t &r_ij = arguments[0];
    … …  
    143138  ASSERT( arguments.size() == 1,
    144139      "PairPotential_Harmonic::parameter_derivative() - requires exactly one argument.");
    145   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    146       "PairPotential_Harmonic::parameter_derivative() - first charge "
    147       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    148   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    149       "PairPotential_Harmonic::parameter_derivative() - second charge "
    150       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     140  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
     141      arguments, getParticleTypes()),
     142      "PairPotential_Harmonic::operator() - types don't match with ones in arguments.");
    151143  const argument_t &r_ij = arguments[0];
    152144  switch (index) {

  • src/Potentials/Specifics/PairPotential_Morse.cpp

    r93e908 rb760bc3  
    4646
    4747#include "Potentials/helpers.hpp"
     48#include "Potentials/ParticleTypeCheckers.hpp"
    4849
    4950// static definitions
    … …  
    105106  ASSERT( arguments.size() == 1,
    106107      "PairPotential_Morse::operator() - requires exactly one argument.");
    107   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    108       "PairPotential_Morse::operator() - first charge "
    109       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    110   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    111       "PairPotential_Morse::operator() - second charge "
    112       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     108  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
     109      arguments, getParticleTypes()),
     110      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
    113111  const argument_t &r_ij = arguments[0];
    114112  // Maple: f(r,D,k,R,c) := D * (1 - exp(-k*(r-R)))^(2)+c
    … …  
    127125  ASSERT( arguments.size() == 1,
    128126      "PairPotential_Morse::operator() - requires exactly one argument.");
    129   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    130       "PairPotential_Morse::derivative() - first charge "
    131       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    132   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    133       "PairPotential_Morse::derivative() - second charge "
    134       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     127  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
     128      arguments, getParticleTypes()),
     129      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
    135130  derivative_components_t result;
    136131  const argument_t &r_ij = arguments[0];
    … …  
    154149  ASSERT( arguments.size() == 1,
    155150      "PairPotential_Morse::parameter_derivative() - requires exactly one argument.");
    156   ASSERT( arguments[0].types.first == getParticleTypes()[0],
    157       "PairPotential_Morse::parameter_derivative() - first charge "
    158       +toString(arguments[0].types.first)+" is not "+toString(getParticleTypes()[0]));
    159   ASSERT( arguments[0].types.second == getParticleTypes()[1],
    160       "PairPotential_Morse::parameter_derivative() - second charge "
    161       +toString(arguments[0].types.second)+" is not "+toString(getParticleTypes()[1]));
     151  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
     152      arguments, getParticleTypes()),
     153      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
    162154  const argument_t &r_ij = arguments[0];
    163155  switch (index) {

  • src/Potentials/Specifics/SaturationPotential.cpp

    r93e908 rb760bc3  
    4848
    4949#include "Potentials/helpers.hpp"
     50#include "Potentials/ParticleTypeCheckers.hpp"
    5051
    5152using namespace boost::assign;
    … …  
    174175{
    175176  double result = 0.;
     177  const ParticleTypes_t &morse_types = morse.getParticleTypes();
    176178  for(arguments_t::const_iterator argiter = arguments.begin();
    177179      argiter != arguments.end();
    178180      ++argiter) {
    179181    const argument_t &r_ij = *argiter;
    180     if ((r_ij.indices.first == 0)) { // first item must be the non-hydrogen
     182    if (((r_ij.types.first == morse_types[0]) && (r_ij.types.second == morse_types[1]))
     183        || ((r_ij.types.first == morse_types[1]) && (r_ij.types.second == morse_types[0]))) {
    181184      arguments_t args(1, r_ij);
    182185
    183186      // Morse contribution
    184       result += morse(args)[0];
     187      const double tmp = morse(args)[0];
     188//      LOG(2, "DEBUG: Morse yields " << tmp << " for << " << r_ij << ".");
     189      result += tmp;
    185190      if (result != result)
    186191        ELOG(1, "result is NAN.");
    187192    }
    188193  }
    189   // Angle contribution
    190   result += angle(arguments)[0];  // as we have all distances we get both jk and kj
    191   if (result != result)
    192     ELOG(1, "result is NAN.");
    193 //
    194 //      // Angle contribution
    195 //      std::vector<arguments_t> triples = triplefunction(r_ij, saturation_cutoff);
    196 //      args.resize(3, r_ij);
    197 //      for (std::vector<arguments_t>::const_iterator iter = triples.begin();
    198 //          iter != triples.end(); ++iter) {
    199 //        ASSERT( iter->size() == 2,
    200 //            "SaturationPotential::function_derivative_c() - the triples result must contain exactly two distances.");
    201 //        const argument_t &r_ik = (*iter)[0];
    202 //        const argument_t &r_jk = (*iter)[1];
    203 //        args[1] = r_ik;
    204 //        args[2] = r_jk;
    205 //        result += .5*angle(args)[0];  // as we have all distances we get both jk and kj
    206 //        if (result != result)
    207 //          ELOG(1, "result is NAN.");
    208 //      }
    209 //    }
    210 //  }
     194  {
     195    // Angle contribution
     196    const double tmp = angle(arguments)[0];  // as we have all distances we get both jk and kj
     197//    LOG(2, "DEBUG: angle yields " << tmp << " for << " << arguments << ".");
     198    result += tmp;
     199    if (result != result)
     200      ELOG(1, "result is NAN.");
     201  }
    211202  return std::vector<result_t>(1, energy_offset + result);
    212203}
Note: See TracChangeset for help on using the changeset viewer.