Changeset 321470 for src

Timestamp:

Aug 12, 2013, 11:30:31 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:

57ba6f

Parents:

3e93bd4

git-author:

Frederik Heber <heber@…> (07/12/13 14:59:19)

git-committer:

Frederik Heber <heber@…> (08/12/13 11:30:31)

Message:

FIX: Fragmentation's OrderAtSite was written per molecule and with local ids.

• introduced global_local_bimap in Fragmentation::FragmentMolecule().
• ParseOrderAtSite and StoreOrderAtSite need to use global ids.
• StoreOrderAtSite now appends.
• FragmentationAction removes OrderAtSite file for the moment. Probably, we should get rid of it.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Fragmentation/Fragmentation.cpp (modified) (9 diffs)
• Fragmentation/Fragmentation.hpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -176 +176 @@
   }
   LOG(0, "STATUS: There are " << TotalGraph.size() << " fragments.");
+
+  {
+    // remove OrderAtSite file
+    std::string line;
+    std::ofstream file;
+    line = params.prefix.get() + ORDERATSITEFILE;
+    file.open(line.c_str(), std::ofstream::out | std::ofstream::trunc);
+    file << "";
+    file.close();
+  }
 
   // now add interfragments

src/Fragmentation/Fragmentation.cpp

@@ -33 +33 @@
 #endif
 
+#include <boost/bimap.hpp>
+
 #include "CodePatterns/MemDebug.hpp"
 
@@ -39 +41 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Info.hpp"
+#include "CodePatterns/IteratorAdaptors.hpp"
 #include "CodePatterns/Log.hpp"
 
@@ -127 +130 @@
   // ===== 1. Check whether bond structure is same as stored in files ====
 
+  // create a lookup global <-> local id for atomic ids valid in World and in molecule
+  Global_local_bimap_t Global_local_bimap;
+  for (std::vector<local_t>::const_iterator iter = atomids.begin();
+      iter != atomids.end();
+      ++iter) {
+    const atom * _atom = mol->FindAtom(*iter);
+    ASSERT( _atom != NULL,
+        "Fragmentation::FragmentMolecule() - could not find atom "+toString(*iter)+".");
+    Global_local_bimap.insert(
+        idpair_t(
+            (global_t)(_atom->getId()), (local_t)(*iter)
+            )
+        );
+  }
+
   // === compare it with adjacency file ===
   {
-    const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
+    const std::vector<atomId_t> globalids(
+        MapKeyConstIterator<Global_local_bimap_t::left_const_iterator>(Global_local_bimap.left.begin()),
+        MapKeyConstIterator<Global_local_bimap_t::left_const_iterator>(Global_local_bimap.left.end())
+        );
     AdjacencyList WorldAdjacency(globalids);
     FragmentationToDo = FragmentationToDo && (FileChecker > WorldAdjacency);
@@ -143 +164 @@
 
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
-  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(atomids, prefix);
+  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(atomids, prefix, Global_local_bimap);
 
   // =================================== Begin of FRAGMENTATION ===============================
@@ -398 +419 @@
  * \return true - file writable, false - not writable
  */
-bool Fragmentation::StoreOrderAtSiteFile(const std::string &path)
+bool Fragmentation::StoreOrderAtSiteFile(
+    const std::string &path)
 {
   string line;
@@ -404 +426 @@
 
   line = path + ORDERATSITEFILE;
-  file.open(line.c_str());
+  file.open(line.c_str(), std::ofstream::out | std::ofstream::app);
   std::stringstream output;
   output << "INFO: Writing OrderAtSite " << ORDERATSITEFILE << " ... ";
   if (file.good()) {
-    for_each(mol->begin(),mol->end(),bind2nd(mem_fun(&atom::OutputOrder), &file));
+    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      file << (*iter)->getId()
+          << "\t" << (int)(*iter)->AdaptiveOrder
+          << "\t" << (int)(*iter)->MaxOrder << std::endl;
+    }
     file.close();
     output << "done.";
@@ -423 +449 @@
  * Atoms not present in the file get "0".
  * \param atomids atoms to fragment, used in AtomMask
- * \param &path path to file ORDERATSITEFILEe
+ * \param &path path to file ORDERATSITEFILE
+ * \param global_local_bimap translate global to local id
  * \return true - file found and scanned, false - file not found
  * \sa ParseKeySetFile() and CheckAdjacencyFileAgainstMolecule() as this is meant to be used in conjunction with the two
  */
-bool Fragmentation::ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path)
+bool Fragmentation::ParseOrderAtSiteFromFile(
+    const std::vector<atomId_t> &atomids,
+    const std::string &path,
+    const Global_local_bimap_t &global_local_bimap)
 {
 //  Info FunctionInfo(__func__);
@@ -435 +465 @@
   AtomMask_t MaxArray(atomids);
   bool status;
-  int AtomNr, value;
+  int AtomNr, ordervalue, maxvalue;
   string line;
   ifstream file;
@@ -445 +475 @@
       AtomNr = -1;
       file >> AtomNr;
+      file >> ordervalue;
+      file >> maxvalue;
       if (AtomNr != -1) {   // test whether we really parsed something (this is necessary, otherwise last atom is set twice and to 0 on second time)
-        file >> value;
-        OrderArray[AtomNr] = value;
-        file >> value;
-        MaxArray.setValue(AtomNr, (bool)value);
-        //LOG(2, "AtomNr " << AtomNr << " with order " << (int)OrderArray[AtomNr] << " and max order set to " << (int)MaxArray[AtomNr] << ".");
+        // parsed id is global, must be translated to local id
+        Global_local_bimap_t::left_const_iterator iter = global_local_bimap.left.find(AtomNr);
+        // skip global ids we don't know about, must be in other molecule
+        if (iter != global_local_bimap.left.end()) {
+          const int LocalId = iter->second;
+          OrderArray[LocalId] = ordervalue;
+          MaxArray.setValue(LocalId, (bool)maxvalue);
+          //LOG(2, "AtomNr " << LocalId << " with order " << (int)OrderArray[LocalId] << " and max order set to " << (int)MaxArray[LocalId] << ".");
+        }
       }
     }

src/Fragmentation/Fragmentation.hpp

@@ -25 +25 @@
 #include <vector>
 
+#include <boost/bimap.hpp>
+
 class atom;
 class AtomMask_t;
@@ -33 +35 @@
 class Fragmentation
 {
+  // some typedefs for intermediat global id <-> local id bimap
+  typedef atomId_t global_t;
+  typedef atomId_t local_t;
+  typedef boost::bimap< global_t, local_t > Global_local_bimap_t;
+  typedef Global_local_bimap_t::value_type idpair_t;
 public:
   Fragmentation(
@@ -54 +61 @@
   bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, const std::string &path, bool LoopDoneAlready);
   bool StoreOrderAtSiteFile(const std::string &path);
-  bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path);
+  bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, const std::string &path, const Global_local_bimap_t &global_local_bimap);
 
   // storing fragments