- Timestamp:
- Feb 27, 2013, 11:44:01 AM (12 years ago)
- 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:
- 93e908
- Parents:
- b3eabc
- git-author:
- Frederik Heber <heber@…> (11/26/12 22:24:11)
- git-committer:
- Frederik Heber <heber@…> (02/27/13 11:44:01)
- Location:
- src/Potentials/Specifics
- Files:
-
- 8 edited
Legend:
- Unmodified
- Added
- Removed
-
src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp
rb3eabc r55fe788 165 165 ++argiter) { 166 166 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])); 173 167 174 const double cutoff = function_cutoff(r_ij.distance); 168 175 const double temp = (cutoff == 0.) ? … … 217 224 ++argiter) { 218 225 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])); 232 219 233 switch (index) { 220 234 // case R: -
src/Potentials/Specifics/PairPotential_Angle.cpp
rb3eabc r55fe788 119 119 ASSERT( arguments.size() == 3, 120 120 "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])); 121 139 const argument_t &r_ij = arguments[0]; 122 140 const argument_t &r_ik = arguments[1]; … … 136 154 ASSERT( arguments.size() == 3, 137 155 "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])); 138 174 derivative_components_t result; 139 175 const argument_t &r_ij = arguments[0]; … … 154 190 ASSERT( arguments.size() == 3, 155 191 "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])); 156 210 const argument_t &r_ij = arguments[0]; 157 211 const argument_t &r_ik = arguments[1]; -
src/Potentials/Specifics/PairPotential_Harmonic.cpp
rb3eabc r55fe788 100 100 ASSERT( arguments.size() == 1, 101 101 "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])); 102 108 const argument_t &r_ij = arguments[0]; 103 109 const result_t result = … … 115 121 ASSERT( arguments.size() == 1, 116 122 "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])); 117 129 derivative_components_t result; 118 130 const argument_t &r_ij = arguments[0]; … … 131 143 ASSERT( arguments.size() == 1, 132 144 "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])); 133 151 const argument_t &r_ij = arguments[0]; 134 152 switch (index) { -
src/Potentials/Specifics/PairPotential_Morse.cpp
rb3eabc r55fe788 105 105 ASSERT( arguments.size() == 1, 106 106 "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])); 107 113 const argument_t &r_ij = arguments[0]; 108 114 // Maple: f(r,D,k,R,c) := D * (1 - exp(-k*(r-R)))^(2)+c … … 121 127 ASSERT( arguments.size() == 1, 122 128 "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])); 123 135 derivative_components_t result; 124 136 const argument_t &r_ij = arguments[0]; … … 142 154 ASSERT( arguments.size() == 1, 143 155 "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])); 144 162 const argument_t &r_ij = arguments[0]; 145 163 switch (index) { -
src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp
rb3eabc r55fe788 294 294 argument_t arg; 295 295 arg.indices = std::make_pair(i,j); 296 arg.types = std::make_pair(0,1); 296 297 arg.distance = CurrentConfiguration[i].distance(CurrentConfiguration[j]); 297 298 arg.globalid = index; // this is needed for the triplefunction to the configuration -
src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp
rb3eabc r55fe788 71 71 angles += -0.5, -.4, -.3, -.2, -.1, 0., .1, .2, .3, .4, .5; 72 72 FunctionModel::arguments_t tempvector(3); 73 tempvector[0] = argument_t( std::make_pair(0,1), std::make_pair( 1,1), 1.);74 tempvector[1] = argument_t( std::make_pair(0,2), std::make_pair( 1,1), 1.);73 tempvector[0] = argument_t( std::make_pair(0,1), std::make_pair(0,1), 1.); 74 tempvector[1] = argument_t( std::make_pair(0,2), std::make_pair(0,1), 1.); 75 75 tempvector[2] = argument_t( std::make_pair(1,2), std::make_pair(1,1), 0.); 76 76 for (angles_t::const_iterator iter = angles.begin(); iter != angles.end(); ++iter) { -
src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp
rb3eabc r55fe788 97 97 PairPotential_Harmonic harmonic(types, .5,1.,.1); 98 98 for (size_t index = 0; index < input.size(); ++index) { 99 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), input[index]); 99 100 CPPUNIT_ASSERT( 100 101 Helpers::isEqual( 101 102 output[index], 102 harmonic( FunctionModel::arguments_t(1,arg ument_t(input[index])) )[0]103 harmonic( FunctionModel::arguments_t(1,arg) )[0] 103 104 ) 104 105 ); … … 115 116 ; 116 117 PairPotential_Harmonic harmonic(types, .5,1.,.1); 118 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), 1.); 117 119 CPPUNIT_ASSERT( 118 120 Helpers::isEqual( 119 121 0., 120 122 harmonic.derivative( 121 FunctionModel::arguments_t(1,arg ument_t(1.))123 FunctionModel::arguments_t(1,arg) 122 124 )[0] 123 125 ) … … 135 137 ; 136 138 PairPotential_Harmonic harmonic(types, .5,1.,.1); 139 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), 1.); 137 140 CPPUNIT_ASSERT( 138 141 Helpers::isEqual( 139 142 0., 140 143 harmonic.parameter_derivative( 141 FunctionModel::arguments_t(1,arg ument_t(1.)),144 FunctionModel::arguments_t(1,arg), 142 145 0 143 146 )[0] … … 148 151 0., 149 152 harmonic.parameter_derivative( 150 FunctionModel::arguments_t(1,arg ument_t(1.)),153 FunctionModel::arguments_t(1,arg), 151 154 1 152 155 )[0] … … 157 160 1., 158 161 harmonic.parameter_derivative( 159 FunctionModel::arguments_t(1,arg ument_t(1.)),162 FunctionModel::arguments_t(1,arg), 160 163 2 161 164 )[0] -
src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp
rb3eabc r55fe788 113 113 PairPotential_Morse Morse(types, a,c,D,d); 114 114 for (size_t index = 0; index < input.size(); ++index) { 115 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), input[index]); 115 116 CPPUNIT_ASSERT( 116 117 Helpers::isEqual( 117 118 output[index], 118 Morse( FunctionModel::arguments_t(1,arg ument_t(input[index])) )[0],119 Morse( FunctionModel::arguments_t(1,arg) )[0], 119 120 1.e-4/std::numeric_limits<double>::epsilon() // only compare four digits 120 121 ) … … 132 133 ; 133 134 PairPotential_Morse Morse(types, a,c,D,d); 135 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), c); 134 136 CPPUNIT_ASSERT( 135 137 Helpers::isEqual( 136 138 0., 137 139 Morse.derivative( 138 FunctionModel::arguments_t(1,arg ument_t(c))140 FunctionModel::arguments_t(1,arg) 139 141 )[0], 140 142 1.e+6 … … 153 155 ; 154 156 PairPotential_Morse Morse(types, a,c,D,d); 157 argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), c); 155 158 CPPUNIT_ASSERT( 156 159 Helpers::isEqual( 157 160 0., 158 161 Morse.parameter_derivative( 159 FunctionModel::arguments_t(1,arg ument_t(c)),162 FunctionModel::arguments_t(1,arg), 160 163 0 161 164 )[0], … … 167 170 0., 168 171 Morse.parameter_derivative( 169 FunctionModel::arguments_t(1,arg ument_t(c)),172 FunctionModel::arguments_t(1,arg), 170 173 1 171 174 )[0], … … 177 180 0., 178 181 Morse.parameter_derivative( 179 FunctionModel::arguments_t(1,arg ument_t(c)),182 FunctionModel::arguments_t(1,arg), 180 183 2 181 184 )[0], … … 187 190 1., 188 191 Morse.parameter_derivative( 189 FunctionModel::arguments_t(1,arg ument_t(c)),192 FunctionModel::arguments_t(1,arg), 190 193 3 191 194 )[0],
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