Changeset 6625c3 for src/molecule_dynamics.cpp

Timestamp:

Feb 24, 2011, 5:46:46 PM (14 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:

056e70

Parents:

54b42e

git-author:

Frederik Heber <heber@…> (02/24/11 11:18:59)

git-committer:

Frederik Heber <heber@…> (02/24/11 17:46:46)

Message:

Removed atom_trajectoryparticle*, replaced by AtomInfo class now having std::vector<> for trajectories.

AtomInfo:

• AtomInfo stores position, velocity, and force in vectors.
• getter and setter implemented for velocity and force.
• all functions from TrajectoryParticle put into AtomInfo.
• Direct access to velocity and force exchanged by getter/setter everywhere.
• FIX: molecule::LinearInterpolationBetweenConfiguration() extends trajectory to MaxSteps+1 (for endstep).

Other changes:

• gsl_rng_gaussian() exchanged by boost::random specific type.

File:

• src/molecule_dynamics.cpp (modified) (12 diffs)

src/molecule_dynamics.cpp

@@ -60 +60 @@
     // determine normalized trajectories direction vector (n1, n2)
     Sprinter = Params.PermutationMap[Walker->nr];   // find first target point
-    trajectory1 = Sprinter->Trajectory.R.at(Params.endstep) - Walker->Trajectory.R.at(Params.startstep);
+    trajectory1 = Sprinter->getPosition(Params.endstep) - Walker->getPosition(Params.startstep);
     trajectory1.Normalize();
     Norm1 = trajectory1.Norm();
     Sprinter = Params.PermutationMap[(*iter)->nr];   // find second target point
-    trajectory2 = Sprinter->Trajectory.R.at(Params.endstep) - (*iter)->Trajectory.R.at(Params.startstep);
+    trajectory2 = Sprinter->getPosition(Params.endstep) - (*iter)->getPosition(Params.startstep);
     trajectory2.Normalize();
     Norm2 = trajectory1.Norm();
     // check whether either is zero()
     if ((Norm1 < MYEPSILON) && (Norm2 < MYEPSILON)) {
-      tmp = Walker->Trajectory.R.at(Params.startstep).distance((*iter)->Trajectory.R.at(Params.startstep));
+      tmp = Walker->getPosition(Params.startstep).distance((*iter)->getPosition(Params.startstep));
     } else if (Norm1 < MYEPSILON) {
       Sprinter = Params.PermutationMap[Walker->nr];   // find first target point
-      trajectory1 = Sprinter->Trajectory.R.at(Params.endstep) - (*iter)->Trajectory.R.at(Params.startstep);
+      trajectory1 = Sprinter->getPosition(Params.endstep) - (*iter)->getPosition(Params.startstep);
       trajectory2 *= trajectory1.ScalarProduct(trajectory2); // trajectory2 is scaled to unity, hence we don't need to divide by anything
       trajectory1 -= trajectory2;   // project the part in norm direction away
@@ -78 +78 @@
     } else if (Norm2 < MYEPSILON) {
       Sprinter = Params.PermutationMap[(*iter)->nr];   // find second target point
-      trajectory2 = Sprinter->Trajectory.R.at(Params.endstep) - Walker->Trajectory.R.at(Params.startstep);  // copy second offset
+      trajectory2 = Sprinter->getPosition(Params.endstep) - Walker->getPosition(Params.startstep);  // copy second offset
       trajectory1 *= trajectory2.ScalarProduct(trajectory1); // trajectory1 is scaled to unity, hence we don't need to divide by anything
       trajectory2 -= trajectory1;   // project the part in norm direction away
@@ -87 +87 @@
   //        Log() << Verbose(0) << " and ";
   //        Log() << Verbose(0) << trajectory2;
-      tmp = Walker->Trajectory.R.at(Params.startstep).distance((*iter)->Trajectory.R.at(Params.startstep));
+      tmp = Walker->getPosition(Params.startstep).distance((*iter)->getPosition(Params.startstep));
   //        Log() << Verbose(0) << " with distance " << tmp << "." << endl;
     } else { // determine distance by finding minimum distance
@@ -106 +106 @@
         gsl_matrix_set(A, 1, i, trajectory2[i]);
         gsl_matrix_set(A, 2, i, normal[i]);
-        gsl_vector_set(x,i, (Walker->Trajectory.R.at(Params.startstep)[i] - (*iter)->Trajectory.R.at(Params.startstep)[i]));
+        gsl_vector_set(x,i, (Walker->getPosition(Params.startstep)[i] - (*iter)->getPosition(Params.startstep)[i]));
       }
       // solve the linear system by Householder transformations
@@ -117 +117 @@
       trajectory2.Scale(gsl_vector_get(x,1));
       normal.Scale(gsl_vector_get(x,2));
-      TestVector = (*iter)->Trajectory.R.at(Params.startstep) + trajectory2 + normal
-                   - (Walker->Trajectory.R.at(Params.startstep) + trajectory1);
+      TestVector = (*iter)->getPosition(Params.startstep) + trajectory2 + normal
+                   - (Walker->getPosition(Params.startstep) + trajectory1);
       if (TestVector.Norm() < MYEPSILON) {
   //          Log() << Verbose(2) << "Test: ok.\tDistance of " << tmp << " is correct." << endl;
@@ -150 +150 @@
   //    atom *Sprinter = PermutationMap[Walker->nr];
   //        Log() << Verbose(0) << *Walker << " and " << *(*iter) << " are heading to the same target at ";
-  //        Log() << Verbose(0) << Sprinter->Trajectory.R.at(endstep);
+  //        Log() << Verbose(0) << Sprinter->getPosition(endstep);
   //        Log() << Verbose(0) << ", penalting." << endl;
       result += Params.PenaltyConstants[2];
@@ -183 +183 @@
     // first term: distance to target
     Runner = Params.PermutationMap[(*iter)->nr];   // find target point
-    tmp = ((*iter)->Trajectory.R.at(Params.startstep).distance(Runner->Trajectory.R.at(Params.endstep)));
+    tmp = ((*iter)->getPosition(Params.startstep).distance(Runner->getPosition(Params.endstep)));
     tmp *= Params.IsAngstroem ? 1. : 1./AtomicLengthToAngstroem;
     result += Params.PenaltyConstants[0] * tmp;
@@ -239 +239 @@
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
     for (molecule::const_iterator runner = mol->begin(); runner != mol->end(); ++runner) {
-      Params.DistanceList[(*iter)->nr]->insert( DistancePair((*iter)->Trajectory.R.at(Params.startstep).distance((*runner)->Trajectory.R.at(Params.endstep)), (*runner)) );
+      Params.DistanceList[(*iter)->nr]->insert( DistancePair((*iter)->getPosition(Params.startstep).distance((*runner)->getPosition(Params.endstep)), (*runner)) );
     }
   }
@@ -489 +489 @@
     // set forces
     for (int i=NDIM;i++;)
-      Force->Matrix[0][_atom->nr][5+i] += 2.*constant*sqrt(_atom->Trajectory.R.at(startstep).distance(Sprinter->Trajectory.R.at(endstep)));
+      Force->Matrix[0][_atom->nr][5+i] += 2.*constant*sqrt(_atom->getPosition(startstep).distance(Sprinter->getPosition(endstep)));
   }
   DoLog(1) && (Log() << Verbose(1) << "done." << endl);
@@ -525 +525 @@
 
   // check whether we have sufficient space in Trajectories for each atom
-  for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::ResizeTrajectory),MaxSteps));
+  LOG(1, "STATUS: Extending each trajectory size to " << MaxSteps+1 << ".");
+  for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::ResizeTrajectory),MaxSteps+1));
   // push endstep to last one
   for_each(atoms.begin(),atoms.end(),boost::bind(&atom::CopyStepOnStep,_1,MaxSteps,endstep));
@@ -538 +539 @@
       // add to molecule list
       Sprinter = mol->AddCopyAtom((*iter));
-      for (int n=NDIM;n--;) {
-        Sprinter->set(n, (*iter)->Trajectory.R.at(startstep)[n] + (PermutationMap[(*iter)->nr]->Trajectory.R.at(endstep)[n] - (*iter)->Trajectory.R.at(startstep)[n])*((double)step/(double)MaxSteps));
-        // add to Trajectories
-        //Log() << Verbose(3) << step << ">=" << MDSteps-1 << endl;
-        if (step < MaxSteps) {
-          (*iter)->Trajectory.R.at(step)[n] = (*iter)->Trajectory.R.at(startstep)[n] + (PermutationMap[(*iter)->nr]->Trajectory.R.at(endstep)[n] - (*iter)->Trajectory.R.at(startstep)[n])*((double)step/(double)MaxSteps);
-          (*iter)->Trajectory.U.at(step)[n] = 0.;
-          (*iter)->Trajectory.F.at(step)[n] = 0.;
-        }
-      }
+      // add to Trajectories
+      Vector temp = (*iter)->getPosition(startstep) + (PermutationMap[(*iter)->nr]->getPosition(endstep) - (*iter)->getPosition(startstep))*((double)step/(double)MaxSteps);
+      Sprinter->setPosition(temp);
+      (*iter)->setAtomicVelocity(step, zeroVec);
+      (*iter)->setAtomicForce(step, zeroVec);
+      //Log() << Verbose(3) << step << ">=" << MDSteps-1 << endl;
     }
   }
@@ -620 +617 @@
   // and perform Verlet integration for each atom with position, velocity and force vector
   // check size of vectors
-  for_each(atoms.begin(),
-           atoms.end(),
-           boost::bind(&atom::VelocityVerletUpdate,_1,MDSteps+1, &configuration, &Force, (const size_t) 0));
+  BOOST_FOREACH(atom *_atom, atoms) {
+    _atom->VelocityVerletUpdate(_atom->nr, MDSteps+1, &configuration, &Force, (const size_t) 0);
+  }
 
   // correct velocities (rather momenta) so that center of mass remains motionless