Changeset e1fe7e for src/Potentials/Specifics/PairPotential_Morse.cpp

Timestamp:

Jun 27, 2014, 9:32:55 PM (11 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:

550f2a

Parents:

16227a

git-author:

Frederik Heber <heber@…> (02/27/14 20:15:41)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:55)

Message:

FunctionModel now uses list_of_arguments to split sequence of subsets of distances.

• this fixes ambiguities with the set of distances: Imagine the distances within a water molecule as OH (A) and HH (B). We then may have a sequence of argument_t as AABAAB. And with the current implementation of CompoundPotential::splitUpArgumentsByModels() we would always choose the latter (and more complex) model. Hence, we make two calls to TriplePotential_Angle, instead of calls twice to PairPotential_Harmonic for A, one to PairPotential_Harmonic for B, and once to TriplePotential_Angle for AAB.
• now, we new list looks like A,A,B,AAB where each tuple of distances can be uniquely associated with a specific potential.
• changed signatures of EmpiricalPotential::operator(), ::derivative(), ::parameter_derivative(). This involved changing all of the current specific potentials and CompoundPotential.
• TrainingData must discern between the InputVector_t (just all distances) and the FilteredInputVector_t (tuples of subsets of distances).
• FunctionApproximation now has list_of_arguments_t as parameter to evaluate() and evaluate_derivative().
• DOCU: docu change in TrainingData.

File:

• src/Potentials/Specifics/PairPotential_Morse.cpp (modified) (2 diffs)

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -124 +124 @@
 PairPotential_Morse::results_t
 PairPotential_Morse::operator()(
-    const arguments_t &arguments
+    const list_of_arguments_t &listarguments
     ) const
 {
-  ASSERT( arguments.size() == 1,
-      "PairPotential_Morse::operator() - requires exactly one argument.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
-      arguments, getParticleTypes()),
-      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
-  const argument_t &r_ij = arguments[0];
-  // Maple: f(r,D,k,R,c) := D * (1 - exp(-k*(r-R)))^(2)+c
-  const result_t result =
-      params[dissociation_energy] * Helpers::pow( 1.
-          - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2);
+  result_t result = 0.;
+  for(list_of_arguments_t::const_iterator iter = listarguments.begin();
+      iter != listarguments.end(); ++iter) {
+    const arguments_t &arguments = *iter;
+    ASSERT( arguments.size() == 1,
+        "PairPotential_Morse::operator() - requires exactly one argument.");
+    ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
+        arguments, getParticleTypes()),
+        "PairPotential_Morse::operator() - types don't match with ones in arguments.");
+    const argument_t &r_ij = arguments[0];
+    // Maple: f(r,D,k,R,c) := D * (1 - exp(-k*(r-R)))^(2)+c
+    result +=
+        params[dissociation_energy] * Helpers::pow( 1.
+            - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2);
+  }
   return std::vector<result_t>(1, result);
 }
@@ -142 +147 @@
 PairPotential_Morse::derivative_components_t
 PairPotential_Morse::derivative(
-    const arguments_t &arguments
+    const list_of_arguments_t &listarguments
     ) const
 {
-  ASSERT( arguments.size() == 1,
-      "PairPotential_Morse::operator() - requires exactly one argument.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
-      arguments, getParticleTypes()),
-      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
-  derivative_components_t result;
-  const argument_t &r_ij = arguments[0];
-  // Maple result: 2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
-  result.push_back(
-      2. * params[dissociation_energy]
-      * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-      * (- params[spring_constant]) * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-  );
-  ASSERT( result.size() == 1,
-      "PairPotential_Morse::operator() - we did not create exactly one component.");
-  return result;
+  result_t result = 0.;
+  for(list_of_arguments_t::const_iterator iter = listarguments.begin();
+      iter != listarguments.end(); ++iter) {
+    const arguments_t &arguments = *iter;
+    ASSERT( arguments.size() == 1,
+        "PairPotential_Morse::operator() - requires exactly one argument.");
+    ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
+        arguments, getParticleTypes()),
+        "PairPotential_Morse::operator() - types don't match with ones in arguments.");
+    const argument_t &r_ij = arguments[0];
+    // Maple result: 2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
+    result +=
+        2. * params[dissociation_energy]
+        * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
+        * (- params[spring_constant]) * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]));
+  }
+  return derivative_components_t(1, result);
 }
 
 PairPotential_Morse::results_t
 PairPotential_Morse::parameter_derivative(
-    const arguments_t &arguments,
+    const list_of_arguments_t &listarguments,
     const size_t index
     ) const
 {
-  ASSERT( arguments.size() == 1,
-      "PairPotential_Morse::parameter_derivative() - requires exactly one argument.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
-      arguments, getParticleTypes()),
-      "PairPotential_Morse::operator() - types don't match with ones in arguments.");
-  const argument_t &r_ij = arguments[0];
-  switch (index) {
-    case spring_constant:
-    {
-      // Maple result: -2*D*(1-exp(-k*(r-R)))*(-r+R)*exp(-k*(r-R))
-      const result_t result =
-          - 2. * params[dissociation_energy]
-          * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-          * (- r_ij.distance + params[equilibrium_distance])
-          * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-          ;
-      return std::vector<result_t>(1, result);
-      break;
+  result_t result = 0.;
+  for(list_of_arguments_t::const_iterator iter = listarguments.begin();
+      iter != listarguments.end(); ++iter) {
+    const arguments_t &arguments = *iter;
+    ASSERT( arguments.size() == 1,
+        "PairPotential_Morse::parameter_derivative() - requires exactly one argument.");
+    ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
+        arguments, getParticleTypes()),
+        "PairPotential_Morse::operator() - types don't match with ones in arguments.");
+    const argument_t &r_ij = arguments[0];
+    switch (index) {
+      case spring_constant:
+      {
+        // Maple result: -2*D*(1-exp(-k*(r-R)))*(-r+R)*exp(-k*(r-R))
+        result +=
+            - 2. * params[dissociation_energy]
+            * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
+            * (- r_ij.distance + params[equilibrium_distance])
+            * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
+            ;
+        break;
+      }
+      case equilibrium_distance:
+      {
+        // Maple result: -2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
+        result +=
+            - 2. * params[dissociation_energy]
+            * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
+            * params[spring_constant] * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
+            ;
+        break;
+      }
+      case dissociation_energy:
+      {
+        // Maple result: (1-exp(-k*(r-R)))^2
+        result +=
+            Helpers::pow(1.
+                - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2);
+        break;
+      }
+      default:
+        ASSERT(0, "PairPotential_Morse::parameter_derivative() - derivative to unknown parameter desired.");
+        break;
     }
-    case equilibrium_distance:
-    {
-      // Maple result: -2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
-      const result_t result =
-          - 2. * params[dissociation_energy]
-          * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-          * params[spring_constant] * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-          ;
-      return std::vector<result_t>(1, result);
-      break;
-    }
-    case dissociation_energy:
-    {
-      // Maple result: (1-exp(-k*(r-R)))^2
-      const result_t result =
-          Helpers::pow(1.
-              - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2);
-      return std::vector<result_t>(1, result);
-      break;
-    }
-    default:
-      ASSERT(0, "PairPotential_Morse::parameter_derivative() - derivative to unknown parameter desired.");
-      break;
   }
-  return std::vector<result_t>(1, 0.);
+  return results_t(1, result);
 }