Changeset 0f5956 for src/Actions/FragmentationAction/FragmentationAction.cpp

Timestamp:

Sep 6, 2016, 2:36:46 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, 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, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

c6f2c5

Parents:

d21933

git-author:

Frederik Heber <heber@…> (08/31/16 10:45:35)

git-committer:

Frederik Heber <heber@…> (09/06/16 14:36:46)

Message:

Added "parse-state-files" option to fragment-molecule which is off by default.

• this prevents accidental parsing of stale keysets, adjacency, or orderatsite files. These hard to find errors ever and again cause failing fragmentation because e.g. some hydrogen is suddenly in the keysets although hydrogens are excluded.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -41 +41 @@
 #include "Descriptors/AtomSelectionDescriptor.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Fragmentation/AdaptivityMap.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
@@ -117 +118 @@
   boost::shared_ptr<AdjacencyList> FileChecker;
   boost::filesystem::path filename(params.prefix.get() + std::string(ADJACENCYFILE));
-  if (boost::filesystem::exists(filename) && boost::filesystem::is_regular_file(filename)) {
+  if ((params.ParseStateFiles.get())
+    && boost::filesystem::exists(filename)
+    && boost::filesystem::is_regular_file(filename)) {
     std::ifstream File;
     File.open(filename.string().c_str(), ios::out);
@@ -140 +143 @@
   // we parse in the keysets from last time if present
   Graph StoredGraph;
-  StoredGraph.ParseKeySetFile(params.prefix.get());
+  if (params.ParseStateFiles.get()) {
+    StoredGraph.ParseKeySetFile(params.prefix.get());
+    // check parsed graph against the set of atoms
+    {
+      AdaptivityMap *amap = StoredGraph.GraphToAdaptivityMap();
+      bool status = true;
+      for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
+          iter != world.endAtomSelection(); ++iter) {
+        const atomId_t atomid = iter->second->getId();
+        // skip hydrogens in check if saturation is turned on
+        if ((iter->second->getType()->getAtomicNumber() != 1)
+            || (!params.DoSaturation.get())) {
+          if (amap->count(atomid) == 0) {
+            ELOG(1, "Atom #" << atomid << " not contained in KeySet file. ");
+            status = false;
+            break;
+          }
+        } else if (amap->count(atomid) != 0) {
+          ELOG(1, "Atom #" << atomid << " in KeySet file is a hydrogen, but is now excluded. ");
+          status = false;
+          break;
+        }
+      }
+      delete amap;
+
+      if (!status) {
+        ELOG(1, "KeySetsFile seems to contain leftover from an old fragmentation, hence not using file.");
+        StoredGraph.clear();
+      }
+    }
+  }
 
   start = clock();
@@ -170 +203 @@
     {
       Graph StoredLocalGraph(StoredGraph.getLocalGraph(mol));
-      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph);
+      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph, params.ParseStateFiles.get());
       if ((ExitFlag == 2) && (tempFlag != 2))
         ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others