Changeset f904d5 for src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

Timestamp:

Dec 19, 2012, 3:25:54 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:

ca8d82

Parents:

752dc7

git-author:

Frederik Heber <heber@…> (10/05/12 20:28:13)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:54)

Message:

Added complete parameter derivatives to ManyBodyPotential_Tersoff.

• this is required as levmar_bc_dif is implemented via levmar_vc_der. Derivatives are taken from [Malshe, '08].
• extracted angle calculation from three lengths into function_theta.

File:

• src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) (7 diffs)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -44 +44 @@
 #include "CodePatterns/Assert.hpp"
 //#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
 
 #include "Potentials/helpers.hpp"
@@ -201 +202 @@
       const double result = (cutoff == 0.) ?
           0. :
-          -r_ij.distance * cutoff * params[mu] *(
+          -r_ij.distance * cutoff *(
           function_prefactor(
               params[beta],
@@ -259 +260 @@
               params[mu],
               r_ij.distance)
-          * (-.5) * params[beta] * (temp/params[beta])
+          * (-.5)
+          * function_prefactor(
+              params[beta],
+              function_zeta(r_ij))
+          * (temp/params[beta])
           / (1. + temp)
           ;
@@ -271 +276 @@
       const double cutoff = function_cutoff(r_ij.distance);
       const double result = (cutoff == 0.) ?
-          0. : cutoff *
+          0. : .5 * cutoff *
           function_smoother(
               -params[B],
               params[mu],
               r_ij.distance)
-          * params[B]
+          * function_prefactor(
+              params[beta],
+              function_zeta(r_ij))
           * ( log(1.+temp)/(params[n]*params[n]) - temp
               * (log(function_zeta(r_ij)) + log(params[beta]))
@@ -286 +293 @@
     case c:
     {
-      const double result = 0.;
-      return results_t(1, result);
+      const double zeta = function_zeta(r_ij);
+      const double temp =
+          pow(params[beta]*zeta, params[n]);
+      const double cutoff = function_cutoff(r_ij.distance);
+      const double result = (cutoff == 0.) ?
+          0. : - cutoff *
+          function_smoother(
+              -params[B],
+              params[mu],
+              r_ij.distance)
+          * function_prefactor(
+              params[beta],
+              zeta)
+          * (temp/zeta)/(1+(temp/zeta));
+      double factor = 0.;
+      std::vector<arguments_t> triples = triplefunction(r_ij, S);
+      for (std::vector<arguments_t>::const_iterator iter = triples.begin();
+          iter != triples.end(); ++iter) {
+        ASSERT( iter->size() == 2,
+            "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances.");
+        const argument_t &r_ik = (*iter)[0];
+        const argument_t &r_jk = (*iter)[1];
+        factor +=
+            function_cutoff(r_ik.distance)
+            * (params[c]/Helpers::pow(params[c],2))
+            * (1. - 1./(1.+(params[h]-function_theta(r_ij.distance, r_ik.distance, r_jk.distance))/Helpers::pow(params[c],2)));
+      }
+      return results_t(1, result*factor);
       break;
     }
     case d:
     {
-      const double result = 0.;
-      return results_t(1, result);
+      const double zeta = function_zeta(r_ij);
+      const double temp =
+          pow(params[beta]*zeta, params[n]);
+      const double cutoff = function_cutoff(r_ij.distance);
+      const double result = (cutoff == 0.) ?
+          0. : - cutoff *
+          function_smoother(
+              -params[B],
+              params[mu],
+              r_ij.distance)
+          * function_prefactor(
+              params[beta],
+              zeta)
+          * (temp/zeta)/(1+(temp/zeta));
+      double factor = 0.;
+      std::vector<arguments_t> triples = triplefunction(r_ij, S);
+      for (std::vector<arguments_t>::const_iterator iter = triples.begin();
+          iter != triples.end(); ++iter) {
+        ASSERT( iter->size() == 2,
+            "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances.");
+        const argument_t &r_ik = (*iter)[0];
+        const argument_t &r_jk = (*iter)[1];
+        factor +=
+            function_cutoff(r_ik.distance)
+            * (-Helpers::pow(params[c],2)/Helpers::pow(params[d],3)
+                - Helpers::pow(params[c],2) * params[d]
+                 / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance),2),2)
+            );
+      }
+      return results_t(1, result*factor);
       break;
     }
     case h:
     {
-      const double result = 0.;
-      return results_t(1, result);
+      const double zeta = function_zeta(r_ij);
+      const double temp =
+          pow(params[beta]*zeta, params[n]);
+      const double cutoff = function_cutoff(r_ij.distance);
+      const double result = (cutoff == 0.) ?
+          0. : - cutoff *
+          function_smoother(
+              -params[B],
+              params[mu],
+              r_ij.distance)
+          * function_prefactor(
+              params[beta],
+              zeta)
+          * (temp/zeta)/(1+(temp/zeta));
+      double factor = 0.;
+      std::vector<arguments_t> triples = triplefunction(r_ij, S);
+      for (std::vector<arguments_t>::const_iterator iter = triples.begin();
+          iter != triples.end(); ++iter) {
+        ASSERT( iter->size() == 2,
+            "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances.");
+        const argument_t &r_ik = (*iter)[0];
+        const argument_t &r_jk = (*iter)[1];
+        const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
+        factor +=
+            function_cutoff(r_ik.distance)
+            * (-1.*Helpers::pow(params[c],2)*tempangle)
+            / Helpers::pow(Helpers::pow(params[d],2)+Helpers::pow(tempangle,2),2)
+            ;
+      }
+      return results_t(1, result*factor);
       break;
     }
@@ -404 +493 @@
 
 ManyBodyPotential_Tersoff::result_t
+ManyBodyPotential_Tersoff::function_theta(
+    const double &r_ij,
+    const double &r_ik,
+    const double &r_jk
+  ) const
+{
+  const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2);
+  const double divisor = 2.* r_ij * r_ik;
+  if (divisor != 0.) {
+    LOG(2, "DEBUG: cos(theta)= " << angle/divisor);
+    return angle/divisor;
+  } else
+    return 0.;
+}
+
+ManyBodyPotential_Tersoff::result_t
 ManyBodyPotential_Tersoff::function_angle(
     const double &r_ij,
@@ -411 +516 @@
 {
 //  Info info(__func__);
-  const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2);
-  const double divisor = 2.* r_ij * r_ik;
+  const double angle = function_theta(r_ij, r_ik, r_jk);
 //  LOG(2, "DEBUG: cos(theta)= " << angle/divisor);
-  if (divisor != 0.) {
-    const double result =
-        1.
-        + (Helpers::pow(params[c]/params[d], 2))
-        - Helpers::pow(params[c], 2)/(Helpers::pow(params[d], 2) +
-            Helpers::pow(params[h] - angle/divisor,2));
+  const double result =
+      1.
+      + (Helpers::pow(params[c]/params[d], 2))
+      - Helpers::pow(params[c], 2)/(Helpers::pow(params[d], 2) +
+          Helpers::pow(params[h] - angle,2));
 
 //    LOG(2, "DEBUG: function_angle(" << r_ij << "," << r_ik << "," << r_jk << ") = " << result);
-    return result;
-  } else
-    return 0.;
-}
-
+  return result;
+}
+