Changeset 056e70 for src/Parser

Timestamp:

Feb 24, 2011, 5:56:03 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:

6b020f

Parents:

6625c3

Message:

Suffixed getters and setters for AtomInfo trajecories with AtStep.

• AtomInfo:: getters are now const members
• added lots of ASSERTS to getters with time step to assure no out-of-bounds access.

File:

• src/Parser/TremoloParser.cpp (modified) (8 diffs)

src/Parser/TremoloParser.cpp

@@ -313 +313 @@
   ConvertTo<double> toDouble;
   ConvertTo<int> toInt;
+  Vector tempVector;
 
   // setup tokenizer, splitting up white-spaced entries
@@ -327 +328 @@
     currentField = knownKeys[keyName];
     const string word = *tok_iter;
-    //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with remaining data " << word << std::endl);
+    DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with remaining data " << word << std::endl);
     switch (currentField) {
       case TremoloKey::x :
@@ -333 +334 @@
         for (int i=0;i<NDIM;i++) {
           ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for x["+toString(i)+"]!");
-          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+          DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
           newAtom->set(i, toDouble(*tok_iter));
           tok_iter++;
@@ -342 +343 @@
         for (int i=0;i<NDIM;i++) {
           ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for u["+toString(i)+"]!");
-          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
-          newAtom->getAtomicVelocity()[i] = toDouble(*tok_iter);
+          DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+          tempVector[i] = toDouble(*tok_iter);
           tok_iter++;
         }
+        newAtom->setAtomicVelocity(tempVector);
         break;
       case TremoloKey::Type :
       {
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
-        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+        DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         std::string element(knownTypes[(*tok_iter)]);
         // put type name into container for later use
         atomInfo->set(currentField, *tok_iter);
-        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
+        DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
         tok_iter++;
         newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
@@ -362 +364 @@
       case TremoloKey::Id :
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
-        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+        DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         atomIdMap[toInt(*tok_iter)] = newAtom->getId();
         tok_iter++;
@@ -369 +371 @@
         for (int i=0;i<atoi(it->substr(it->find("=") + 1, 1).c_str());i++) {
           ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
-          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+          DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
           lineStream << *tok_iter << "\t";
           tok_iter++;
@@ -378 +380 @@
       default :
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
-        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+        DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         atomInfo->set(currentField, *tok_iter);
         tok_iter++;
@@ -403 +405 @@
     // 0 is used to fill empty neighbor positions in the tremolo file.
     if (neighborId > 0) {
-//      DoLog(1) && (Log() << Verbose(1)
-//          << "Atom with global id " << atomId
-//          << " has neighbour with serial " << neighborId
-//          << std::endl);
+      DoLog(4) && (Log() << Verbose(4)
+          << "Atom with global id " << atomId
+          << " has neighbour with serial " << neighborId
+          << std::endl);
       additionalAtomData[atomId].neighbors.push_back(neighborId);
     }