Changeset 05e2ed for src

Timestamp:

Dec 14, 2012, 1:02:50 PM (12 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:

fc41df

Parents:

67ab71

git-author:

Frederik Heber <heber@…> (10/25/12 08:29:25)

git-committer:

Frederik Heber <heber@…> (12/14/12 13:02:50)

Message:

FIX: TremoloParser did not load/save imprData or torsion correctly.

• this error was introduced when incorporating local-global-maps and conversions where this was not correctly done for the improper and torsion string:
  • conversion from local to global on load was present but went over all atoms, not just newly parsed ones. adapt.. now gets atom vector as param.
  • save did no global-local conversion. For this we generalized adaptIdDependentDataString() to get a function pointer converting ids.
• TEST: We added a new regression test on this matter where a .data file with impropers is loaded and stored.

Location:

src/Parser

Files:

• TremoloParser.cpp (modified) (7 diffs)
• TremoloParser.hpp (modified) (3 diffs)
• unittests/ParserTremoloUnitTest.cpp (modified) (6 diffs)

src/Parser/TremoloParser.cpp

@@ -56 +56 @@
 
 #include <algorithm>
+#include <boost/bind.hpp>
 #include <boost/lambda/lambda.hpp>
 #include <boost/lexical_cast.hpp>
@@ -103 +104 @@
  */
 FormatParser< tremolo >::FormatParser()  :
-  FormatParser_common(NULL)
+  FormatParser_common(NULL),
+  idglobalizer(boost::bind(&FormatParser< tremolo >::getGlobalId, this, _1)),
+  idlocalizer(boost::bind(&FormatParser< tremolo >::getLocalId, this, _1))
 {
   createKnownTypesByIdentity();
@@ -160 +163 @@
       boost::bind(&atom::getId, _1));
   processNeighborInformation(atoms);
-  adaptImprData();
-  adaptTorsion();
+  adaptImprData(atoms);
+  adaptTorsion(atoms);
 
   // append usedFields to global usedFields, is made unique on save, clear after use
@@ -424 +427 @@
         writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
         break;
+      case TremoloKey::imprData :
+      case TremoloKey::torsion :
+        LOG(3, "Writing type " << knownKeyNames[currentField]);
+        *file << adaptIdDependentDataString(
+            additionalAtomData[currentAtom->getId()].get(currentField),
+            idlocalizer)
+            << "\t";
+        break;
       case TremoloKey::resSeq :
         if (additionalAtomData.count(currentAtom->getId())) {
@@ -810 +821 @@
  *
  * \param string in which atom IDs should be adapted
+ * \param idgetter function pointer to change the id
  *
  * \return input string with modified atom IDs
  */
-std::string FormatParser< tremolo >::adaptIdDependentDataString(std::string data) {
+std::string FormatParser< tremolo >::adaptIdDependentDataString(
+    const std::string &data,
+    const boost::function<int (const int)> &idgetter
+    ) {
   // there might be no IDs
   if (data == "-") {
@@ -825 +840 @@
 
   line >> id;
-  result << getGlobalId(id);
+  result << idgetter(id);
   while (line.good()) {
     line >> separator >> id;
-    result << separator << getGlobalId(id);
+    result << separator << idgetter(id);
   }
 
@@ -834 +849 @@
 }
 
-/**
- * Corrects the atom IDs in each imprData entry to the corresponding world IDs
+/** Corrects the atom IDs in each imprData entry to the corresponding world IDs
  * as they might differ from the originally read IDs.
- */
-void FormatParser< tremolo >::adaptImprData() {
+ *
+ * \param atoms currently parsed in atoms
+ */
+void FormatParser< tremolo >::adaptImprData(const std::vector<atomId_t> &atoms) {
   if (!isUsedField(usedFields_load, "imprData")) {
     return;
   }
 
-  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
-    currentInfo != additionalAtomData.end(); currentInfo++
-  ) {
-    currentInfo->second.imprData = adaptIdDependentDataString(currentInfo->second.imprData);
-  }
-}
-
-/**
- * Corrects the atom IDs in each torsion entry to the corresponding world IDs
+  for (std::vector<atomId_t>::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+    ASSERT(additionalAtomData.count(*iter) != 0,
+        "FormatParser< tremolo >::processNeighborInformation() - global id "
+        +toString(*iter)+" unknown in additionalAtomData.");
+    TremoloAtomInfoContainer &currentInfo = additionalAtomData[*iter];
+    currentInfo.imprData = adaptIdDependentDataString(currentInfo.imprData, idglobalizer);
+  }
+}
+
+/** Corrects the atom IDs in each torsion entry to the corresponding world IDs
  * as they might differ from the originally read IDs.
- */
-void FormatParser< tremolo >::adaptTorsion() {
+ *
+ * \param atoms currently parsed in atoms
+ */
+void FormatParser< tremolo >::adaptTorsion(const std::vector<atomId_t> &atoms) {
   if (!isUsedField(usedFields_load, "torsion")) {
     return;
   }
 
-  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
-    currentInfo != additionalAtomData.end(); currentInfo++
-  ) {
-    currentInfo->second.torsion = adaptIdDependentDataString(currentInfo->second.torsion);
-  }
-}
-
+  for (std::vector<atomId_t>::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+    ASSERT(additionalAtomData.count(*iter) != 0,
+        "FormatParser< tremolo >::processNeighborInformation() - global id "
+        +toString(*iter)+" unknown in additionalAtomData.");
+    TremoloAtomInfoContainer &currentInfo = additionalAtomData[*iter];
+    currentInfo.torsion = adaptIdDependentDataString(currentInfo.torsion, idglobalizer);
+  }
+}
+

src/Parser/TremoloParser.hpp

@@ -14 +14 @@
 #endif
 
+#include <boost/function.hpp>
 #include <string>
 
@@ -99 +100 @@
   void readNeighbors(std::stringstream* line, const int numberOfNeighbors, const int atomId);
   void processNeighborInformation(const std::vector<atomId_t> &atoms);
-  void adaptImprData();
-  void adaptTorsion();
-  std::string adaptIdDependentDataString(std::string data);
+  void adaptImprData(const std::vector<atomId_t> &atoms);
+  void adaptTorsion(const std::vector<atomId_t> &atoms);
+  std::string adaptIdDependentDataString(const std::string &data, const boost::function<int (const int)> &idgetter);
   bool isUsedField(const usedFields_t &fields, const std::string &fieldName) const;
   void writeNeighbors(std::ostream* file, const int numberOfNeighbors, const atom* currentAtom);
@@ -140 +141 @@
    */
   TremoloAtomInfoContainer defaultAdditionalData;
+
+  //!> bound function to convert id to global id, stored to avoid creation many times
+  const boost::function<int (const int)> idglobalizer;
+
+  //!> bound function to convert id to local id, stored to avoid creation many times
+  const boost::function<int (const int)> idlocalizer;
 };
 

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -108 +108 @@
   World::getInstance();
 
-  setVerbosity(5);
+  setVerbosity(2);
 
   parser = new FormatParser<tremolo>();
@@ -128 +128 @@
 
 void ParserTremoloUnitTest::readTremoloPreliminaryCommentsTest() {
-  cout << "Testing the tremolo parser." << endl;
+//  cout << "Testing the tremolo parser." << endl;
   stringstream input, output;
 
@@ -150 +150 @@
     std::vector<atom *> atoms = World::getInstance().getAllAtoms();
     parser->save(&output, atoms);
-    std::cout << output.str() << std::endl;
+//    std::cout << output.str() << std::endl;
     CPPUNIT_ASSERT(output.str().find("hydrogen") != string::npos);
     input.clear();
@@ -229 +229 @@
     parser->save(&output, atoms);
     CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-    std::cout << output.str() << std::endl;
-    CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
+//    std::cout << output.str() << std::endl;
+    CPPUNIT_ASSERT(output.str().find("3-1,1-3") != string::npos);
     input.clear();
     output.clear();
@@ -246 +246 @@
     parser->save(&output, atoms);
     CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-    std::cout << output.str() << std::endl;
-    CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
+//    std::cout << output.str() << std::endl;
+    CPPUNIT_ASSERT(output.str().find("3-1,1-3") != string::npos);
     input.clear();
     output.clear();
@@ -268 +268 @@
   }
 
-  cout << "testing the tremolo parser is done" << endl;
-}
-
+//  cout << "testing the tremolo parser is done" << endl;
+}
+