Changeset 14c57a for src/atom_trajectoryparticle.cpp

Timestamp:

Aug 25, 2010, 12:04:11 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

51c3e4

Parents:

8d1dd4

Message:

Made all parts of the programm use the new thermostat structure

File:

• src/atom_trajectoryparticle.cpp (modified) (1 diff)

src/atom_trajectoryparticle.cpp

@@ -144 +144 @@
 };
 
-/** Scales velocity of atom according to Woodcock thermostat.
- * \param ScaleTempFactor factor to scale the velocities with (i.e. sqrt of energy scale factor)
- * \param Step MD step to scale
- * \param *ekin sum of kinetic energy
- */
-void TrajectoryParticle::Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin)
-{
-  Vector &U = Trajectory.U.at(Step);
-  if (FixedIon == 0) // even FixedIon moves, only not by other's forces
-    for (int d=0; d<NDIM; d++) {
-      U[d] *= ScaleTempFactor;
-      *ekin += 0.5*getType()->mass * U[d]*U[d];
-    }
-};
-
-/** Scales velocity of atom according to Gaussian thermostat.
- * \param Step MD step to scale
- * \param *G
- * \param *E
- */
-void TrajectoryParticle::Thermostat_Gaussian_init(int Step, double *G, double *E)
-{
-  Vector &U = Trajectory.U.at(Step);
-  Vector &F = Trajectory.F.at(Step);
-  if (FixedIon == 0) // even FixedIon moves, only not by other's forces
-    for (int d=0; d<NDIM; d++) {
-      *G += U[d] * F[d];
-      *E += U[d]*U[d]*getType()->mass;
-    }
-};
-
-/** Determines scale factors according to Gaussian thermostat.
- * \param Step MD step to scale
- * \param GE G over E ratio
- * \param *ekin sum of kinetic energy
- * \param *configuration configuration class with TempFrequency and TargetTemp
- */
-void TrajectoryParticle::Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration)
-{
-  Vector &U = Trajectory.U.at(Step);
-  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];
-    }
-};
-
-/** Scales velocity of atom according to Langevin thermostat.
- * \param Step MD step to scale
- * \param *r random number generator
- * \param *ekin sum of kinetic energy
- * \param *configuration configuration class with TempFrequency and TargetTemp
- */
-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)
-  Vector &U = Trajectory.U.at(Step);
-  if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
-    // throw a dice to determine whether it gets hit by a heat bath particle
-    if (((((rand()/(double)RAND_MAX))*configuration->Thermostats->TempFrequency) < 1.)) {
-      DoLog(3) && (Log() << Verbose(3) << "Particle " << *this << " was hit (sigma " << sigma << "): " << sqrt(U[0]*U[0]+U[1]*U[1]+U[2]*U[2]) << " -> ");
-      // pick three random numbers from a Boltzmann distribution around the desired temperature T for each momenta axis
-      for (int d=0; d<NDIM; d++) {
-        U[d] = gsl_ran_gaussian (r, sigma);
-      }
-      DoLog(2) && (Log() << Verbose(2) << sqrt(U[0]*U[0]+U[1]*U[1]+U[2]*U[2]) << endl);
-    }
-    for (int d=0; d<NDIM; d++)
-      *ekin += 0.5*getType()->mass * U[d]*U[d];
-  }
-};
-
-/** Scales velocity of atom according to Berendsen thermostat.
- * \param Step MD step to scale
- * \param ScaleTempFactor factor to scale energy (not velocity!) with
- * \param *ekin sum of kinetic energy
- * \param *configuration configuration class with TempFrequency and Deltat
- */
-void TrajectoryParticle::Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration)
-{
-  Vector &U = Trajectory.U.at(Step);
-  if (FixedIon == 0) { // even FixedIon moves, only not by other's forces
-    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];
-    }
-  }
-};
-
-/** Initializes current run of NoseHoover thermostat.
- * \param Step MD step to scale
- * \param *delta_alpha additional sum of kinetic energy on return
- */
-void TrajectoryParticle::Thermostat_NoseHoover_init(int Step, double *delta_alpha)
-{
-  Vector &U = Trajectory.U.at(Step);
-  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;
-    }
-  }
-};
-
-/** Initializes current run of NoseHoover thermostat.
- * \param Step MD step to scale
- * \param *ekin sum of kinetic energy
- * \param *configuration configuration class with TempFrequency and Deltat
- */
-void TrajectoryParticle::Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)
-{
-  Vector &U = Trajectory.U.at(Step);
-  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];
-      }
-  }
-};
-
-
 std::ostream & TrajectoryParticle::operator << (std::ostream &ost) const
 {