Changeset acd638

Timestamp:

Feb 9, 2011, 8:04:56 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:

0bfe73

Parents:

4d4d33

git-author:

Frederik Heber <heber@…> (02/09/11 20:03:34)

git-committer:

Frederik Heber <heber@…> (02/09/11 20:04:56)

Message:

BUGFIX: copied atoms were not correctly stored with respect to Type, reported by Daniel Dueck.

• TremoloParser::saveLine() Father-check has been missing so far.
• TEST: Molecules/Copy - added test for copying from tremolo config.

Files:

• src/Parser/TremoloParser.cpp (modified) (3 diffs)
• tests/regression/Molecules/Copy/post/tensid.data (added)
• tests/regression/Molecules/Copy/pre/tensid.data (added)
• tests/regression/Molecules/Copy/pre/tensid.potentials (added)
• tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) (1 diff)

src/Parser/TremoloParser.cpp

@@ -140 +140 @@
   vector<string>::iterator it;
 
+  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
+
   *file << "# ATOMDATA";
   for (it=usedFields.begin(); it < usedFields.end(); it++) {
@@ -172 +174 @@
   TremoloKey::atomDataKey currentField;
 
-  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
+  DoLog(4) && (Log() << Verbose(4) << "INFO: Saving atom " << *currentAtom << ", its father id is " << currentAtom->GetTrueFather()->getId() << std::endl);
 
   for (it = usedFields.begin(); it != usedFields.end(); it++) {
@@ -192 +194 @@
         break;
       case TremoloKey::Type :
-        if ((!additionalAtomData.count(currentAtom->getId())) || (additionalAtomData[currentAtom->getId()].get(currentField) == "-")) {
-          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
+        if (additionalAtomData.count(currentAtom->getId())) {
+          if (additionalAtomData[currentAtom->getId()].get(currentField) != "-") {
+            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
+            *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
+          } else {
+            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
+            *file << currentAtom->getType()->getSymbol() << "\t";
+          }
+        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
+          if (additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) != "-") {
+            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
+            *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << "\t";
+          } else {
+            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value from father: " << currentAtom->GetTrueFather()->getType()->getSymbol() << std::endl);
+            *file << currentAtom->GetTrueFather()->getType()->getSymbol() << "\t";
+          }
+        } else {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its default value: " << currentAtom->getType()->getSymbol() << std::endl);
           *file << currentAtom->getType()->getSymbol() << "\t";
-        } else {
-          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
-          *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
         }
         break;

tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at

@@ -12 +12 @@
 AT_CHECK([../../molecuilder -i test-copy.xyz  --copy-molecule 0 --position "0,0,10" --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/tensid.* .], 0)
+AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i tensid.data  --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' tensid.data ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/tensid.data], 0, [ignore], [ignore])
 AT_CLEANUP