Changeset 30c753 for src/molecule_geometry.cpp

Timestamp:

Dec 28, 2011, 3:25:48 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:

59fff1

Parents:

f99714

git-author:

Frederik Heber <heber@…> (12/22/11 13:14:16)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:48)

Message:

Removed atomSet atoms in class molecule and replaced by a boost::transform_iterator.

• atoms causes us a O(N^{2) complexity due to having to remove atoms from this linearized vector (in O(N) not O(log N) as for the atomIds.}
• marked Molecules/BondFile and Tesselation/BigNonConvex as XFAIL due to interchanged ids.
• thanks to Jan Hamaekers for pointing this out.

• NOTE: so far we have not specialized molecule::const_iterator, it simply points to molecule::iterator.

File:

• src/molecule_geometry.cpp (modified) (17 diffs)

src/molecule_geometry.cpp

@@ -55 +55 @@
 
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    std::cout << "atom before is at " << *iter << std::endl;
-    *iter -= *Center;
-    *iter += *CenterBox;
-    std::cout << "atom after is at " << *iter << std::endl;
-  }
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    if (DoLog(4) && (*Center != *CenterBox))
+      LOG(4, "INFO: atom before is at " << **iter);
+    **iter -= *Center;
+    **iter += *CenterBox;
+    if (DoLog(4) && (*Center != *CenterBox))
+      LOG(4, "INFO: atom after is at " << **iter);
+  }
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
   delete(Center);
@@ -78 +80 @@
 
   // go through all atoms
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
   return status;
@@ -92 +94 @@
   Vector *min = new Vector;
 
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   if (iter != end()) { //list not empty?
     for (int i=NDIM;i--;) {
@@ -120 +122 @@
 {
   int Num = 0;
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector Center;
 
@@ -139 +141 @@
 Vector * molecule::DetermineCenterOfAll() const
 {
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector *a = new Vector();
   double Num = 0;
@@ -172 +174 @@
 Vector * molecule::DetermineCenterOfGravity() const
 {
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector *a = new Vector();
   Vector tmp;
@@ -200 +202 @@
   DeterminePeriodicCenter(NewCenter);
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= NewCenter;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter -= NewCenter;
   }
 };
@@ -213 +215 @@
 {
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= *newcenter;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter -= *newcenter;
   }
 };
@@ -231 +233 @@
 
   // sum up inertia tensor
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     Vector x = (*iter)->getPosition();
     x -= *CenterOfGravity;
@@ -284 +286 @@
 
   // and rotate
-  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     *(*iter) -= *CenterOfGravity;
     (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
@@ -304 +306 @@
 void molecule::Scale(const double ** const factor)
 {
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     for (size_t j=0;j<(*iter)->getTrajectorySize();j++) {
       Vector temp = (*iter)->getPositionAtStep(j);
@@ -318 +320 @@
 void molecule::Translate(const Vector *trans)
 {
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     for (size_t j=0;j<(*iter)->getTrajectorySize();j++) {
       (*iter)->setPositionAtStep(j, (*iter)->getPositionAtStep(j) + (*trans));
@@ -334 +336 @@
 
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter += *trans;
-  }
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter += *trans;
+  }
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
 };
@@ -349 +351 @@
   OBSERVE;
   Plane p(*n,0);
-  atoms.transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
+  getAtomSet().transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
 };
 
@@ -369 +371 @@
     Center.Zero();
     flag = true;
-    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    for (const_iterator iter = begin(); iter != end(); ++iter) {
       if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) {
         Testvector = inversematrix * (*iter)->getPosition();
@@ -433 +435 @@
   alpha = atan(-n->at(0)/n->at(2));
   LOG(1, "INFO: Z-X-angle: " << alpha << " ... ");
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(0);
     (*iter)->set(0,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
@@ -453 +455 @@
   alpha = atan(-n->at(1)/n->at(2));
   LOG(1, "INFO: Z-Y-angle: " << alpha << " ... ");
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(1);
     (*iter)->set(1,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));