Changeset 6625c3 for src/Thermostats/Langevin.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/Thermostats/Langevin.cpp (modified) (6 diffs)

src/Thermostats/Langevin.cpp

@@ -20 +20 @@
 #include "ThermoStatContainer.hpp"
 
+#include <boost/random/mersenne_twister.hpp>
+#include <boost/random/normal_distribution.hpp>
+#include <boost/random/variate_generator.hpp>
+
 #include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
 #include "RandomNumbers/RandomNumberGenerator.hpp"
@@ -25 +29 @@
 Langevin::Langevin(double _TempFrequency,double _alpha) :
   TempFrequency(_TempFrequency),
-  alpha(_alpha)
-{
-  gsl_rng_env_setup();
-  T = gsl_rng_default;
-  r = gsl_rng_alloc (T);
-}
+  alpha(_alpha),
+  rng_engine(new boost::mt19937),
+  rng_distribution(NULL)
+{}
 
 Langevin::Langevin() :
   TempFrequency(2.5),
-  alpha(0.)
+  alpha(0.),
+  rng_engine(new boost::mt19937),
+  rng_distribution(NULL)
 {}
 
 Langevin::~Langevin()
 {
-  gsl_rng_free (r);
+  delete rng_engine;
+  delete rng_distribution;
 }
 
@@ -76 +81 @@
 double Langevin::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
   DoLog(2) && (Log() << Verbose(2) <<  "Applying Langevin thermostat..." << endl);
-  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator("mt19937", "normal_distribution");
   const double rng_min = random.min();
   const double rng_max = random.max();
@@ -82 +87 @@
   for(ForwardIterator iter=begin;iter!=end;++iter){
     double sigma  = sqrt(getContainer().TargetTemp/(*iter)->getType()->getMass()); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
-    Vector &U = (*iter)->Trajectory.U.at(step);
-    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
+    rng_distribution = new boost::normal_distribution<>(0,sigma);
+    boost::variate_generator<boost::mt19937&, boost::normal_distribution<> > rng(*rng_engine, *rng_distribution);
+    Vector &U = (*iter)->getAtomicVelocity(step);
+    if ((*iter)->getFixedIon() == 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 (((((random()/(rng_max-rng_min)))*TempFrequency) < 1.)) {
@@ -89 +96 @@
         // 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);
+          U[d] = rng();
         }
         DoLog(2) && (Log() << Verbose(2) << U.Norm() << endl);
@@ -95 +102 @@
       ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
     }
+    delete rng_distribution;
+    rng_distribution = NULL;
   }
   return ekin;