Changeset 83f176 for src/atom_trajectoryparticle.cpp

Timestamp:

Aug 19, 2010, 3:23:37 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:

2a7457

Parents:

1ee380f

git-author:

Frederik Heber <heber@…> (08/17/10 17:21:25)

git-committer:

Frederik Heber <heber@…> (08/19/10 15:23:37)

Message:

Made all member variables of class element private, added accessor functions and periodentafel is friend.

File:

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

src/atom_trajectoryparticle.cpp

@@ -50 +50 @@
 {
   for (int i=NDIM;i--;)
-    *temperature += getType()->mass * Trajectory.U.at(step)[i]* Trajectory.U.at(step)[i];
+    *temperature += getType()->getMass() * Trajectory.U.at(step)[i]* Trajectory.U.at(step)[i];
 };
 
@@ -77 +77 @@
   for(int d=0;d<NDIM;d++) {
     Trajectory.U.at(Step)[d] -= CoGVelocity->at(d);
-    *ActualTemp += 0.5 * getType()->mass * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
+    *ActualTemp += 0.5 * getType()->getMass() * Trajectory.U.at(Step)[d] * Trajectory.U.at(Step)[d];
   }
 };
@@ -125 +125 @@
     Trajectory.R.at(NextStep)[d] = Trajectory.R.at(NextStep-1)[d];
     Trajectory.R.at(NextStep)[d] += configuration->Deltat*(Trajectory.U.at(NextStep-1)[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
-    Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/getType()->mass);     // F = m * a and s =
+    Trajectory.R.at(NextStep)[d] += 0.5*configuration->Deltat*configuration->Deltat*(Trajectory.F.at(NextStep)[d]/getType()->getMass());     // F = m * a and s =
   }
   // Update U
   for (int d=0; d<NDIM; d++) {
     Trajectory.U.at(NextStep)[d] = Trajectory.U.at(NextStep-1)[d];
-    Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/getType()->mass); // v = F/m * t
+    Trajectory.U.at(NextStep)[d] += configuration->Deltat * (Trajectory.F.at(NextStep)[d]+Trajectory.F.at(NextStep-1)[d]/getType()->getMass()); // v = F/m * t
   }
   // Update R (and F)
@@ -149 +149 @@
 void TrajectoryParticle::SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const
 {
-  *TotalMass += getType()->mass;  // sum up total mass
+  *TotalMass += getType()->getMass();  // sum up total mass
   for(int d=0;d<NDIM;d++) {
-    TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*getType()->mass;
+    TotalVelocity->at(d) += Trajectory.U.at(Step)[d]*getType()->getMass();
   }
 };
@@ -166 +166 @@
     for (int d=0; d<NDIM; d++) {
       U[d] *= ScaleTempFactor;
-      *ekin += 0.5*getType()->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
     }
 };
@@ -182 +182 @@
     for (int d=0; d<NDIM; d++) {
       *G += U[d] * F[d];
-      *E += U[d]*U[d]*getType()->mass;
+      *E += U[d]*U[d]*getType()->getMass();
     }
 };
@@ -197 +197 @@
   if (FixedIon == 0) // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-      U[d] += configuration->Deltat/getType()->mass * ( (G_over_E) * (U[d]*getType()->mass) );
-      *ekin += getType()->mass * U[d]*U[d];
+      U[d] += configuration->Deltat/getType()->getMass() * ( (G_over_E) * (U[d]*getType()->getMass()) );
+      *ekin += getType()->getMass() * U[d]*U[d];
     }
 };
@@ -210 +210 @@
 void TrajectoryParticle::Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration)
 {
-  double sigma  = sqrt(configuration->Thermostats->TargetTemp/getType()->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
+  double sigma  = sqrt(configuration->Thermostats->TargetTemp/getType()->getMass()); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
   Vector &U = Trajectory.U.at(Step);
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
@@ -223 +223 @@
     }
     for (int d=0; d<NDIM; d++)
-      *ekin += 0.5*getType()->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
   }
 };
@@ -239 +239 @@
     for (int d=0; d<NDIM; d++) {
       U[d] *= sqrt(1+(configuration->Deltat/configuration->Thermostats->TempFrequency)*(ScaleTempFactor-1));
-      *ekin += 0.5*getType()->mass * U[d]*U[d];
+      *ekin += 0.5*getType()->getMass() * U[d]*U[d];
     }
   }
@@ -253 +253 @@
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-      *delta_alpha += U[d]*U[d]*getType()->mass;
+      *delta_alpha += U[d]*U[d]*getType()->getMass();
     }
   }
@@ -268 +268 @@
   if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
     for (int d=0; d<NDIM; d++) {
-        U[d] += configuration->Deltat/getType()->mass * (configuration->Thermostats->alpha * (U[d] * getType()->mass));
-        *ekin += (0.5*getType()->mass) * U[d]*U[d];
+        U[d] += configuration->Deltat/getType()->getMass() * (configuration->Thermostats->alpha * (U[d] * getType()->getMass()));
+        *ekin += (0.5*getType()->getMass()) * U[d]*U[d];
       }
   }