Changeset 2034f3 for src/Parser

Timestamp:

Apr 5, 2012, 3:55:48 PM (13 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:

259887

Parents:

3d0892

git-author:

Frederik Heber <heber@…> (03/27/12 12:37:05)

git-committer:

Frederik Heber <heber@…> (04/05/12 15:55:48)

Message:

Added AtomInfo::charge along with getter and setter.

• charge is used by both TremoloParser and XmlParser, hence needs to be exchanged.
• Added charge to state info in AtomicInfo.
• TESTFIX: regression tests Molecules/Copy, Molecules/CreateMicelle, and Filling/FillVoidWithMolecule's tensid.data file had to be changed due to present Charge info with precision different to the one arising from new AtomInfo::Charge.
• removed ParserXmlUnitTest from XFAIL_TESTS.

Location:

src/Parser

Files:

• TremoloParser.cpp (modified) (3 diffs)
• XmlParser.cpp (modified) (2 diffs)
• unittests/Makefile.am (modified) (1 diff)
• unittests/ParserXmlUnitTest.cpp (modified) (1 diff)

src/Parser/TremoloParser.cpp

@@ -41 +41 @@
 
 #include <algorithm>
+#include <boost/lexical_cast.hpp>
 #include <boost/tokenizer.hpp>
 #include <iostream>
@@ -308 +309 @@
         *file << "\t";
         break;
+      case TremoloKey::charge :
+        if (currentAtom->getCharge() == 0.) {
+          if (additionalAtomData.count(currentAtom->getId())) {
+            LOG(3, "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField));
+            *file << additionalAtomData[currentAtom->getId()].get(currentField);
+          } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
+            LOG(3, "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField));
+            *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
+          } else {
+            LOG(3, "Writing for type " << knownKeyNames[currentField] << " AtomInfo::charge : " << currentAtom->getCharge());
+            *file << currentAtom->getCharge();
+          }
+        } else {
+          LOG(3, "Writing for type " << knownKeyNames[currentField] << " AtomInfo::charge : " << currentAtom->getCharge());
+          *file << currentAtom->getCharge();
+        }
+        *file << "\t";
+        break;
       default :
         if (additionalAtomData.count(currentAtom->getId())) {
@@ -482 +501 @@
             atoi(it->substr(it->find("=") + 1, 1).c_str()), atomid);
         break;
+      case TremoloKey::charge :
+        ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
+        LOG(4, "INFO: Parsing key " << keyName << " with next token " << *tok_iter);
+        atomInfo->set(currentField, *tok_iter);
+        newAtom->setCharge(boost::lexical_cast<double>(*tok_iter));
+        tok_iter++;
+        break;
       default :
         ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");

src/Parser/XmlParser.cpp

@@ -164 +164 @@
     newAtom->setType(World::getInstance().getPeriode()->FindElement((atomicNumber_t)1));
     newAtom->setPosition(p.position);
+    newAtom->setCharge(p.q);
     newmol->AddAtom(newAtom);
     additionalAtomInfo atomInfo(p.q, p.potential, p.field);
@@ -201 +202 @@
     const additionalAtomInfo &atomInfo = getAtomData(*(*it));
     p.position = (*it)->getPosition();
-    p.q = atomInfo.charge;
+    p.q = (*it)->getCharge();
     p.potential = atomInfo.potential;
     p.field = atomInfo.field;

src/Parser/unittests/Makefile.am

@@ -33 +33 @@
   ParserXmlUnitTest \
   ParserXyzUnitTest
-
-XFAIL_TESTS += \
-        ParserXmlUnitTest 
 
 TESTS += $(PARSERTESTS)

src/Parser/unittests/ParserXmlUnitTest.cpp

@@ -104 +104 @@
     CPPUNIT_ASSERT( parser->data == parser_control->data );
     delete parser_control;
-//    // check for non-empty streams
-//    input.peek();
-//    output.peek();
-//    CPPUNIT_ASSERT(input.good() && output.good());
-//    // check equality of streams per line (for debugging)
-//    for (; std::getline(input, first) && std::getline(output, second); ) {
-//      std::cout << "Comparing '" << first << "' to '" << second << "'" << std::endl;
-//      CPPUNIT_ASSERT(first == second);
-//    }
   }
 }