Changeset e6e4a0 for src/Parser

Timestamp:

Sep 26, 2012, 5:24:47 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:

158c3d9

Parents:

5d4179f

git-author:

Frederik Heber <heber@…> (07/13/12 09:36:24)

git-committer:

Frederik Heber <heber@…> (09/26/12 17:24:47)

Message:

FIX: TremoloParser did not treat key F properly in saveLine() and readAtomDataLine().

• did not write/load all three components.
• TESTFIX: ParserTremoloUnitTest due to key F changes.
• TESTFIX: regression tests Atoms/Add and Parser/Tremolo and Tremolo-Potentials neded their .data files adapted (F was so far stored with just one component and not three).

Location:

src/Parser

Files:

• TremoloParser.cpp (modified) (2 diffs)
• unittests/ParserTremoloUnitTest.cpp (modified) (2 diffs)

src/Parser/TremoloParser.cpp

@@ -372 +372 @@
         *file << currentAtom->getAtomicVelocity()[2] << "\t";
         break;
+      case TremoloKey::F :
+        // for the moment, assume there are always three dimensions
+        LOG(3, "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getAtomicForce());
+        *file << currentAtom->getAtomicForce()[0] << "\t";
+        *file << currentAtom->getAtomicForce()[1] << "\t";
+        *file << currentAtom->getAtomicForce()[2] << "\t";
+        break;
       case TremoloKey::type :
         if (additionalAtomData.count(currentAtom->getId())) {
@@ -621 +628 @@
         newAtom->setAtomicVelocity(tempVector);
         break;
+      case TremoloKey::F :
+        // for the moment, assume there are always three dimensions
+        for (int i=0;i<NDIM;i++) {
+          ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for F["+toString(i)+"]!");
+          LOG(4, "INFO: Parsing key " << keyName << " with next token " << *tok_iter);
+          tempVector[i] = toDouble(*tok_iter);
+          tok_iter++;
+        }
+        newAtom->setAtomicForce(tempVector);
+        break;
       case TremoloKey::type :
       {

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -86 +86 @@
 10 O -\n";
 static string Tremolo_full = "\
-# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\ttype\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n\
-# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
-0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
+# ATOMDATA\tx=3\tu=3\tF=3\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\ttype\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
+0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
 
 void ParserTremoloUnitTest::setUp() {
@@ -245 +245 @@
     atom* newAtom = World::getInstance().createAtom();
     newAtom->setType(1);
-    parser->setAtomData("x=3 u=3 F stress Id neighbors=5 imprData GroupMeasureTypeNo type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
+    parser->setAtomData("x=3 u=3 F=3 stress Id neighbors=5 imprData GroupMeasureTypeNo type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
     std::vector<atom *> atoms = World::getInstance().getAllAtoms();
     parser->save(&output, atoms);