Changeset adb5cda for src/Dynamics

Timestamp:

Dec 28, 2011, 3:25:49 PM (13 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:

401f90

Parents:

afa9d8

git-author:

Frederik Heber <heber@…> (12/23/11 15:17:07)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:49)

Message:

Removed typedef molecule::atomSet and some commented-out, deprecated sections.

• required changes to LinearInterpolationBetweenSteps, MinimiseConstrainedPotential, MinimiseConstrainedPotential, and VerletForceIntegration.
• replaced molecule::atomset by World::AtomComposite.

Location:

src/Dynamics

Files:

• LinearInterpolationBetweenSteps.hpp (modified) (1 diff)
• MinimiseConstrainedPotential.cpp (modified) (14 diffs)
• MinimiseConstrainedPotential.hpp (modified) (3 diffs)
• VerletForceIntegration.hpp (modified) (1 diff)

src/Dynamics/LinearInterpolationBetweenSteps.hpp

@@ -55 +55 @@
     if (!MapByIdentity) {
       LOG(1, "STATUS: Constructing atom mapping from start to end position.");
-      molecule::atomSet atoms_list;
-      for (typename AtomSetMixin<Set>::const_iterator iter = atoms.begin();
-          iter != atoms.end(); ++iter)
-        atoms_list.insert(*iter);
-      MinimiseConstrainedPotential Minimiser(atoms_list, PermutationMap);
+      MinimiseConstrainedPotential Minimiser(atoms, PermutationMap);
       Minimiser(startstep, endstep, IsAngstroem);
     } else {

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -40 +40 @@
 
 MinimiseConstrainedPotential::MinimiseConstrainedPotential(
-    molecule::atomSet &_atoms,
+    World::AtomComposite &_atoms,
     std::map<atom*, atom *> &_PermutationMap) :
   atoms(_atoms),
@@ -59 +59 @@
   PermutationMap.clear();
   DoubleList.clear();
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     DistanceList[*iter].clear();
   }
@@ -90 +90 @@
     LOG(2, "Starting round " << ++round << ", at current potential " << OldPotential << " ... ");
     OlderPotential = OldPotential;
-    molecule::atomSet::const_iterator iter;
+    World::AtomComposite::const_iterator iter;
     do {
       iter = atoms.begin();
@@ -105 +105 @@
         //LOG(2, "Current Walker: " << *(*iter) << " with old/next candidate " << *Sprinter << "/" << *DistanceIterators[(*iter)]->second << ".");
         // find source of the new target
-        molecule::atomSet::const_iterator runner = atoms.begin();
+        World::AtomComposite::const_iterator runner = atoms.begin();
         for (; runner != atoms.end(); ++runner) { // find the source whose toes we might be stepping on (Walker's new target should be in use by another already)
           if (PermutationMap[(*runner)] == DistanceIterators[(*iter)]->second) {
@@ -165 +165 @@
 void MinimiseConstrainedPotential::FillDistanceList()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
-    for (molecule::atomSet::const_iterator runner = atoms.begin(); runner != atoms.end(); ++runner) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+    for (World::AtomComposite::const_iterator runner = atoms.begin(); runner != atoms.end(); ++runner) {
       DistanceList[(*iter)].insert( DistancePair((*iter)->getPositionAtStep(startstep).distance((*runner)->getPositionAtStep(endstep)), (*runner)) );
     }
@@ -174 +174 @@
 void MinimiseConstrainedPotential::CreateInitialLists()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     StepList[(*iter)] = DistanceList[(*iter)].begin();    // stores the step to the next iterator that could be a possible next target
     PermutationMap[(*iter)] = DistanceList[(*iter)].begin()->second;   // always pick target with the smallest distance
@@ -185 +185 @@
 void MinimiseConstrainedPotential::MakeInjectivePermutation()
 {
-  molecule::atomSet::const_iterator iter = atoms.begin();
+  World::AtomComposite::const_iterator iter = atoms.begin();
   DistanceMap::iterator NewBase;
   double Potential = fabs(ConstrainedPotential());
@@ -204 +204 @@
     Potential = TryNextNearestNeighbourForInjectivePermutation((*iter), Potential);
   }
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     // now each single entry in the DoubleList should be <=1
     if (DoubleList[*iter] > 1) {
@@ -216 +216 @@
 unsigned int MinimiseConstrainedPotential::CalculateDoubleList()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
     DoubleList[*iter] = 0;
   unsigned int doubles = 0;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
       DoubleList[ PermutationMap[*iter] ]++;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
     if (DoubleList[*iter] > 1)
       doubles++;
@@ -235 +235 @@
   zeile1 << "PermutationMap: ";
   zeile2 << "                ";
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     zeile1 << (*iter)->getName() << " ";
     zeile2 << (PermutationMap[*iter])->getName() << " ";
   }
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     std::map<atom *, unsigned int>::const_iterator value_iter = DoubleList.find(*iter);
     if (value_iter->second > (unsigned int)1)
@@ -255 +255 @@
   // go through every atom
   atom *Runner = NULL;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     // first term: distance to target
     Runner = PermutationMap[(*iter)];   // find target point
@@ -299 +299 @@
 {
   double result = 0.;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((PermutationMap[Walker] == PermutationMap[(*iter)]) && (Walker < (*iter))) {
 //    atom *Sprinter = PermutationMap[Walker->nr];
@@ -324 +324 @@
   double Norm1, Norm2, tmp, result = 0.;
 
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((*iter) == Walker) // hence, we only go up to the Walker, not beyond (similar to i=0; i<j; i++)
       break;
@@ -407 +407 @@
   /// evaluate forces (only the distance to target dependent part) with the final PermutationMap
   LOG(1, "Calculating forces and adding onto ForceMatrix ... ");
-  for(molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for(World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     atom *Sprinter = PermutationMap[(*iter)];
     // set forces

src/Dynamics/MinimiseConstrainedPotential.hpp

@@ -19 +19 @@
 #include <map>
 
-#include "molecule.hpp"
+#include "World.hpp"
 
 /** Structure to contain parameters needed for evaluation of constraint potential.
@@ -33 +33 @@
    * @return
    */
-  MinimiseConstrainedPotential(molecule::atomSet &_atoms, std::map<atom*, atom *> &_PermutationMap);
+  MinimiseConstrainedPotential(World::AtomComposite &_atoms, std::map<atom*, atom *> &_PermutationMap);
 
   /** Destructor.
@@ -79 +79 @@
   typedef std::pair < DistanceMap::iterator, bool> DistanceTestPair;
 
-  molecule::atomSet atoms;
+  World::AtomComposite atoms;
   int startstep; //!< start configuration (MDStep in atom::trajectory)
   int endstep; //!< end configuration (MDStep in atom::trajectory)

src/Dynamics/VerletForceIntegration.hpp

@@ -98 +98 @@
       // calculate forces and potential
       std::map<atom *, atom*> PermutationMap;
-      molecule::atomSet atoms_list;
-      for (typename AtomSetMixin<T>::const_iterator iter = atoms.begin();
-          iter != atoms.end(); ++iter)
-        atoms_list.insert(*iter);
-      MinimiseConstrainedPotential Minimiser(atoms_list, PermutationMap);
+      MinimiseConstrainedPotential Minimiser(atoms, PermutationMap);
       //double ConstrainedPotentialEnergy =
       Minimiser(DoConstrainedMD, 0, IsAngstroem);