Changeset e5ebaf

Timestamp:

Jul 9, 2013, 6:21:05 AM (11 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:

f73351

Parents:

ec5d0c

git-author:

Frederik Heber <heber@…> (06/18/13 14:29:50)

git-committer:

Frederik Heber <heber@…> (07/09/13 06:21:05)

Message:

Forces obtained from fragmentation summation are now set.

• i.e. they are placed in AtomicForces for the corresponding atom.
• extended regression test on AnalyseFragmentationResults for this.
• IndexedVectors now has getter for the vectors.
• AnalyseFragmentationResultsAction writes forces only when full molecule is loaded.

Files:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (6 diffs)
• src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) (1 diff)
• tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (added)
• tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) (2 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -41 +41 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <boost/foreach.hpp>
 #include <boost/mpl/remove.hpp>
 
@@ -58 +59 @@
 #endif
 
+#include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
@@ -79 +81 @@
 #include "Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp"
 #endif
+#include "Helpers/defs.hpp"
 #include "World.hpp"
 
@@ -248 +251 @@
   IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
   IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
+
   /// go through all fragments
   for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
@@ -338 +342 @@
   const KeySetsContainer &forcekeysets = container.getForceKeySets();
   const bool DoLongrange = container.areFullRangeResultsPresent();
+  const bool IsAngstroem = true;
 
   if (keysets.KeySets.empty()) {
@@ -347 +352 @@
   shortrangeresults(shortrangedata);
   printReceivedShortResults(shortrangeresults);
+
+  // adding obtained forces
+  if ( World::getInstance().getAllAtoms().size() != 0) {
+    const IndexedVectors::indexedvectors_t forces =
+        boost::fusion::at_key<MPQCDataFused::forces>(
+            shortrangeresults.Result_Force_fused.back()
+            ).getVectors();
+        ;
+    for(IndexedVectors::indexedvectors_t::const_iterator iter = forces.begin();
+        iter != forces.end(); ++iter) {
+      const IndexedVectors::index_t &index = iter->first;
+      const IndexedVectors::vector_t &forcevector = iter->second;
+      ASSERT( forcevector.size() == NDIM,
+          "printReceivedShortResults() - obtained force vector has incorrect dimension.");
+      // note that mpqc calculates a gradient, hence force pointing into opposite direction
+      // we have to mind different units here: MPQC has a_o, while we may have angstroem
+      Vector ForceVector(-forcevector[0], -forcevector[1], -forcevector[2]);
+      if (IsAngstroem)
+        for (size_t i=0;i<NDIM;++i)
+          ForceVector[i] *= AtomicLengthToAngstroem;
+      atom *_atom = World::getInstance().getAtom(AtomById(index));
+      if(_atom != NULL)
+        _atom->setAtomicForce(_atom->getAtomicForce() + ForceVector);
+      else
+        ELOG(2, "Could not find atom to id " << index << ".");
+    }
+  } else {
+    LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
+  }
 
 #ifdef HAVE_VMG

src/Fragmentation/Summation/SetValues/IndexedVectors.hpp

@@ -95 +95 @@
   }
 
+  /** Const getter to index vectors.
+   *
+   * \return const reference to indexed vectors
+   */
+  const indexedvectors_t& getVectors() const
+  { return vectors; }
+
 private:
   /** Helper function that contains all the logic of how to superpose two

tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at

@@ -37 +37 @@
 AT_CLEANUP
 
+AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
+AT_KEYWORDS([fragmentation analyse-fragment-results forces])
+
+file=BondFragmentShortRangeResults.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --analyse-fragment-results --fragment-resultfile $file], 0, [ignore], [ignore])
+AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
 #
 # BondFragmentLongRangeResults.dat is created like this:
@@ -47 +58 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb --analyse-fragment-results --fragment-resultfile $file], 0, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --analyse-fragment-results --fragment-resultfile $file], 0, [ignore], [stderr])
+AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
 AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
 AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])