Changeset eb33c4

Timestamp:

Mar 2, 2011, 9:40:51 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:

435065

Parents:

e355762

Message:

LinearInterpolationofTrajectoriesAction only interpolates, does not save.

• This should make the action more versatile.
• Saving generated paths can easily be done (and is done so for regression test) by a specific SaveSelected..Action.

Files:

• src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) (1 diff)
• src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) (2 diffs)
• src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) (5 diffs)
• tests/regression/Molecules/LinearInterpolationofTrajectories/post/teststep.conf (added)
• tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) (1 diff)

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

@@ -46 +46 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Linear interpolation between configuration " << params.start << " and " << params.end << "." << endl);
-  if (params.IdMapping)
-    DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
+  LOG(0, "STATUS: Linear interpolation between configuration " << params.start << " and " << params.end << "." << endl);
   ASSERT(params.end > params.start, "MoleculeLinearInterpolationofTrajectoriesAction() - start step greater than end step.");
   AtomSetMixin<std::vector<atom*> > set(World::getInstance().getSelectedAtoms());
-  LinearInterpolationBetweenSteps<std::vector<atom*> > LinearInterpolate(set,(unsigned int)(params.end-params.start));
-  if (!LinearInterpolate(params.start, params.end, params.filename.branch_path().string(), params.IdMapping))
-    DoLog(2) && (Log() << Verbose(2) << "Could not store " << params.filename << " files." << endl);
-  else
-    DoLog(2) && (Log() << Verbose(2) << "Steps created and " << params.filename << " files stored." << endl);
+  LinearInterpolationBetweenSteps<std::vector<atom*> > LinearInterpolate(set,(unsigned int)(params.interpolation_steps));
+  LinearInterpolate(params.start, params.end, params.IdMapping);
+  LOG(0, "STATUS: done." << endl);
 
   return Action::success;

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

@@ -12 +12 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(int)(int)(bool)
-#define paramtokens ("linear-interpolation-of-trajectories")("start-step")("end-step")("id-mapping")
-#define paramdescriptions ("path where to store the intermediate configurations")("first or start step")("last or end step")("whether the identity shall be used in mapping atoms onto atoms or not")
+#define paramtypes (int)(int)(int)(bool)
+#define paramtokens ("start-step")("interpolation-steps")("end-step")("id-mapping")
+#define paramdescriptions ("first or start step")("number of steps to interpolate in between start and end step")("last or end step")("whether the identity shall be used in mapping atoms onto atoms or not")
 #undef paramdefaults
-#define paramreferences (filename)(start)(end)(IdMapping)
+#define paramreferences (start)(interpolation_steps)(end)(IdMapping)
 
 #undef statetypes
@@ -31 +31 @@
 // finally the information stored in the ActionTrait specialization
 #define DESCRIPTION "linear interpolation in discrete steps between start and end position of a molecule"
-#define SHORTFORM "L"
+#undef SHORTFORM

src/Dynamics/LinearInterpolationBetweenSteps.hpp

@@ -18 +18 @@
 #include "atom.hpp"
 #include "AtomSet.hpp"
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "Dynamics/MinimiseConstrainedPotential.hpp"
@@ -31 +33 @@
 public:
   LinearInterpolationBetweenSteps(AtomSetMixin<Set> &_atoms, unsigned int _MaxOuterStep) :
-    MDSteps(0),
     MaxOuterStep(_MaxOuterStep),
     IsAngstroem(true),
@@ -44 +45 @@
    * \param startstep stating initial configuration in molecule::Trajectories
    * \param endstep stating final configuration in molecule::Trajectories
-   * \param &prefix path and prefix
    * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
-   * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
    */
-  bool operator()(int startstep, int endstep, std::string prefix, bool MapByIdentity)
+  void operator()(int startstep, int endstep, bool MapByIdentity)
   {
     // TODO: rewrite permutationMaps using enumeration objects
-    molecule *mol = NULL;
-    bool status = true;
     int MaxSteps = MaxOuterStep;
-    MoleculeListClass *MoleculePerStep = new MoleculeListClass(World::getPointer());
+
     // Get the Permutation Map by MinimiseConstrainedPotential
-    atom **PermutationMap = NULL;
-    atom *Sprinter = NULL;
+    std::map<atom*, atom *> PermutationMap;
     if (!MapByIdentity) {
-      std::map<atom *, atom*> PermutationMap;
+      LOG(1, "STATUS: Constructing atom mapping from start to end position.");
       molecule::atomSet atoms_list;
       copy(atoms.begin(), atoms.end(), atoms_list.begin());
@@ -65 +61 @@
       Minimiser(startstep, endstep, IsAngstroem);
     } else {
+      LOG(1, "STATUS: Using identity mapping.");
       // TODO: construction of enumeration goes here
-      PermutationMap = new atom *[atoms.size()];
       for(typename AtomSetMixin<Set>::const_iterator iter = atoms.begin(); iter != atoms.end();++iter){
-        PermutationMap[(*iter)->getNr()] = (*iter);
+        PermutationMap[(*iter)] = (*iter);
       }
     }
 
     // check whether we have sufficient space in Trajectories for each atom
+    LOG(1, "STATUS: Extending trajectories.");
     for(typename AtomSetMixin<Set>::iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
       (*iter)->ResizeTrajectory(MaxSteps);
@@ -83 +80 @@
 
     // go through all steps and add the molecular configuration to the list and to the Trajectories of \a this molecule
-    DoLog(1) && (Log() << Verbose(1) << "Filling intermediate " << MaxSteps << " steps with MDSteps of " << MDSteps << "." << endl);
+    LOG(1, "STATUS: Filling intermediate " << MaxSteps << " steps." << endl);
     for (int step = 0; step <= MaxSteps; step++) {
-      mol = World::getInstance().createMolecule();
-      MoleculePerStep->insert(mol);
+      LOG(2, "INFO: Current step is " << step << "." << endl);
       for (typename AtomSetMixin<Set>::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
-        // add to molecule list
-        Sprinter = mol->AddCopyAtom((*iter));
         // add to Trajectories
-        Vector temp = (*iter)->getPositionAtStep(startstep) + (PermutationMap[(*iter)->getNr()]->getPositionAtStep(endstep) - (*iter)->getPositionAtStep(startstep))*((double)step/(double)MaxSteps);
-        Sprinter->setPosition(temp);
+        ASSERT(PermutationMap.count((*iter)),
+            "LinearInterpolationBetweenSteps::operator() - atom "+toString(**iter)+" not found in PermutationMap.");
+        Vector temp = (*iter)->getPositionAtStep(startstep) + (PermutationMap[(*iter)]->getPositionAtStep(endstep) - (*iter)->getPositionAtStep(startstep))*((double)step/(double)MaxSteps);
+        (*iter)->setPositionAtStep(step,temp);
         (*iter)->setAtomicVelocityAtStep(step, zeroVec);
         (*iter)->setAtomicForceAtStep(step, zeroVec);
-        //Log() << Verbose(3) << step << ">=" << MDSteps-1 << endl;
+        LOG(2, "INFO: Adding trajectory point for atom " << **iter << " at " << temp << ".");
       }
     }
-    MDSteps = MaxSteps+1;   // otherwise new Trajectories' points aren't stored on save&exit
 
-    // store the list to single step files
-    int *SortIndex = new int[atoms.size()];
-    for (int i=atoms.size(); i--; )
-      SortIndex[i] = i;
-
-    status = MoleculePerStep->OutputConfigForListOfFragments(prefix, SortIndex);
-    delete[](SortIndex);
-
-    // free and return
-    delete[](PermutationMap);
-    delete(MoleculePerStep);
-    return status;
+//    // store the list to single step files
+//    int *SortIndex = new int[atoms.size()];
+//    for (int i=atoms.size(); i--; )
+//      SortIndex[i] = i;
+//
+//    status = MoleculePerStep->OutputConfigForListOfFragments(prefix, SortIndex);
+//    delete[](SortIndex);
   };
 
 private:
-  unsigned int MDSteps;
   unsigned int MaxOuterStep;
   bool IsAngstroem;

tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at

@@ -2 +2 @@
 
 AT_SETUP([Molecules - Linear interpolation])
-# this is not working but the test as of now passes
-#AT_XFAIL_IF([/bin/true])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/LinearInterpolationofTrajectories/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 -L teststep --start-step 0 --end-step 1 --id-mapping 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf  --select-all-atoms --linear-interpolation-of-trajectories --start-step 0 --interpolation-steps 9 --end-step 1 --id-mapping 1 -S teststep.conf], 0, [stdout], [stderr])
+AT_CHECK([fgrep -c 'Ion_Type1_1' teststep.conf], 0, [10
+], [ignore])
+AT_CHECK([diff teststep.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/LinearInterpolationofTrajectories/post/teststep.conf], 0, [ignore], [ignore])
 AT_CLEANUP