Changeset 57d8b0 for src

Timestamp:

Oct 15, 2008, 5:16:43 PM (16 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:

19f3d6

Parents:

2b4a40

Message:

molecule::VerletForceIntegration() different code, same algorithm (still bug-hunting)

File:

• src/molecules.cpp (modified) (6 diffs)

src/molecules.cpp

@@ -1026 +1026 @@
   string token;
   stringstream item;
-  double a, IonMass, Vector[NDIM];
+  double a, IonMass;
   ForceMatrix Force;
+  Vector tmpvector;
 
   CountElements();  // make sure ElementsInMolecule is up to date
@@ -1045 +1046 @@
     }
     // correct Forces
-    for(int d=0;d<NDIM;d++)
-      Vector[d] = 0.;
-    for(int i=0;i<AtomCount;i++)
-      for(int d=0;d<NDIM;d++) {
-        Vector[d] += Force.Matrix[0][i][d+5];
-      }
-    for(int i=0;i<AtomCount;i++)
-      for(int d=0;d<NDIM;d++) {
-        Force.Matrix[0][i][d+5] -= Vector[d]/(double)AtomCount;
-      }
+//    for(int d=0;d<NDIM;d++)
+//      tmpvector.x[d] = 0.;
+//    for(int i=0;i<AtomCount;i++)
+//      for(int d=0;d<NDIM;d++) {
+//        tmpvector.x[d] += Force.Matrix[0][i][d+5];
+//      }
+//    for(int i=0;i<AtomCount;i++)
+//      for(int d=0;d<NDIM;d++) {
+//        Force.Matrix[0][i][d+5] -= tmpvector.x[d]/(double)AtomCount;
+//      }
     // and perform Verlet integration for each atom with position, velocity and force vector
     runner = elemente->start;
@@ -1074 +1075 @@
               Trajectories[walker].F.resize(MDSteps+10);
             }
-            
-            // Update R (and F)
+            // 1. calculate x(t+\delta t)
             for (int d=0; d<NDIM; d++) {
-              Trajectories[walker].F.at(MDSteps).x[d] = -Force.Matrix[0][AtomNo][d+5]*(IsAngstroem ? AtomicLengthToAngstroem : 1.);
+              Trajectories[walker].F.at(MDSteps).x[d] = -Force.Matrix[0][AtomNo][d+5];
               Trajectories[walker].R.at(MDSteps).x[d] = Trajectories[walker].R.at(MDSteps-1).x[d];
               Trajectories[walker].R.at(MDSteps).x[d] += delta_t*(Trajectories[walker].U.at(MDSteps-1).x[d]);
-              Trajectories[walker].R.at(MDSteps).x[d] += delta_t*a*(Trajectories[walker].F.at(MDSteps).x[d]);     // F = m * a and s = 0.5 * F/m * t^2 = F * a * t
+              Trajectories[walker].R.at(MDSteps).x[d] += 0.5*delta_t*delta_t*(Trajectories[walker].F.at(MDSteps-1).x[d])/IonMass;     // F = m * a and s = 0.5 * F/m * t^2 = F * a * t
             }
-            // Update U
+            // 2. Calculate v(t+\delta t)
             for (int d=0; d<NDIM; d++) {
-              Trajectories[walker].U.at(MDSteps).x[d] = Trajectories[walker].U.at(MDSteps-1).x[d]; 
-              Trajectories[walker].U.at(MDSteps).x[d] += a * (Trajectories[walker].F.at(MDSteps).x[d]+Trajectories[walker].F.at(MDSteps-1).x[d]);
+              Trajectories[walker].U.at(MDSteps).x[d] = Trajectories[walker].U.at(MDSteps-1).x[d];
+              Trajectories[walker].U.at(MDSteps).x[d] += 0.5*delta_t*(Trajectories[walker].F.at(MDSteps-1).x[d]+Trajectories[walker].F.at(MDSteps).x[d])/IonMass;
             }
 //            cout << "Integrated position&velocity of step " << (MDSteps) << ": ("; 
@@ -1102 +1102 @@
   }
 //  // correct velocities (rather momenta) so that center of mass remains motionless
-//  for(int d=0;d<NDIM;d++)
-//    Vector[d] = 0.;
+//  tmpvector.zero()
 //  IonMass = 0.;
 //  walker = start;
@@ -1110 +1109 @@
 //    IonMass += walker->type->mass;  // sum up total mass
 //    for(int d=0;d<NDIM;d++) {
-//      Vector[d] += Trajectories[walker].U.at(MDSteps).x[d]*walker->type->mass;
+//      tmpvector.x[d] += Trajectories[walker].U.at(MDSteps).x[d]*walker->type->mass;
 //    }
 //  }
@@ -1117 +1116 @@
 //    walker = walker->next;
 //    for(int d=0;d<NDIM;d++) {
-//      Trajectories[walker].U.at(MDSteps).x[d] -= Vector[d]*walker->type->mass/IonMass;
+//      Trajectories[walker].U.at(MDSteps).x[d] -= tmpvector.x[d]*walker->type->mass/IonMass;
 //    }
 //  }