Changeset 2fd80b5

Timestamp:

Jun 22, 2010, 3:33:06 PM (15 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:

df481f

Parents:

52baf9

Message:

FIXES: ParserUnitTest was broken

• XyzParser: ctime returns endline, has to be cut away as variable comment is without.
• TESTFIX: ParserUnitTest had 0.00000 instead of 0 (noshowpoint is in action).
• TESTFIX: MpqcParser: due to newly used center, ParserUnitTest had wrong coordinates.
• PcpParser::CalculateOrbitals() - used Valence instead of NoValenceOrbitals
• PcpParser::Load() - PsiType changes parsing of PsiMaxNoUp/Down in place for MaxPsiDouble, but the others should be parsed optionally to ensure the taking over of the values if present.
• BUGFIX: MpqcParser::MpqcParser() - HessianPresent was not initialized, causing failures when ParserUnitTest is run with gdb and none without

Location:

src

Files:

• Parser/MpqcParser.cpp (modified) (1 diff)
• Parser/PcpParser.cpp (modified) (2 diffs)
• Parser/XyzParser.cpp (modified) (1 diff)
• unittests/ParserUnitTest.cpp (modified) (6 diffs)

src/Parser/MpqcParser.cpp

@@ -21 +21 @@
  *
  */
-MpqcParser::MpqcParser()
+MpqcParser::MpqcParser() : HessianPresent(false)
 {
 

src/Parser/PcpParser.cpp

@@ -282 +282 @@
   case 0: // SpinDouble
     ParseForParameter(verbose,FileBuffer,"MaxPsiDouble", 0, 1, 1, int_type, &(PlaneWaveSpecifics.MaxPsiDouble), 1, critical);
+    ParseForParameter(verbose,FileBuffer,"PsiMaxNoUp", 0, 1, 1, int_type, &(PlaneWaveSpecifics.PsiMaxNoUp), 1, optional);
+    ParseForParameter(verbose,FileBuffer,"PsiMaxNoDown", 0, 1, 1, int_type, &(PlaneWaveSpecifics.PsiMaxNoDown), 1, optional);
     ParseForParameter(verbose,FileBuffer,"AddPsis", 0, 1, 1, int_type, &(PlaneWaveSpecifics.AddPsis), 1, optional);
     break;
   case 1: // SpinUpDown
     if (Parallelization.ProcPEGamma % 2) Parallelization.ProcPEGamma*=2;
+    ParseForParameter(verbose,FileBuffer,"MaxPsiDouble", 0, 1, 1, int_type, &(PlaneWaveSpecifics.MaxPsiDouble), 1, optional);
     ParseForParameter(verbose,FileBuffer,"PsiMaxNoUp", 0, 1, 1, int_type, &(PlaneWaveSpecifics.PsiMaxNoUp), 1, critical);
     ParseForParameter(verbose,FileBuffer,"PsiMaxNoDown", 0, 1, 1, int_type, &(PlaneWaveSpecifics.PsiMaxNoDown), 1, critical);
@@ -450 +453 @@
   PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
   for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
-    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->type->Valence;
+    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->type->NoValenceOrbitals;
   }
   cout << PlaneWaveSpecifics.MaxPsiDouble << endl;

src/Parser/XyzParser.cpp

@@ -60 +60 @@
     time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     comment = "\tCreated by molecuilder on ";
-    comment += ctime(&now);
+    // ctime ends in \n\0, we have to cut away the newline
+    std::string time(ctime(&now));
+    comment += time.substr(time.find('\n'));
   }
-  *file << World::getInstance().numAtoms() << endl << comment;
+  *file << World::getInstance().numAtoms() << endl << comment << endl;
 
   vector<atom*> atoms = World::getInstance().getAllAtoms();

src/unittests/ParserUnitTest.cpp

@@ -66 +66 @@
 RelEpsTotalE\t1e-07\t# relative change in total energy\n\
 RelEpsKineticE\t1e-05\t# relative change in kinetic energy\n\
-MaxMinStopStep\t0\t# check every ..th steps\n\
+MaxMinStopStep\t2\t# check every ..th steps\n\
 MaxMinGapStopStep\t1\t# check every ..th steps\n\
 \n\
@@ -73 +73 @@
 InitRelEpsTotalE\t1e-05\t# relative change in total energy\n\
 InitRelEpsKineticE\t0.0001\t# relative change in kinetic energy\n\
-InitMaxMinStopStep\t0\t# check every ..th steps\n\
+InitMaxMinStopStep\t2\t# check every ..th steps\n\
 InitMaxMinGapStopStep\t1\t# check every ..th steps\n\
 \n\
@@ -86 +86 @@
 RiemannTensor\t0\t# (Use metric)\n\
 PsiType\t0\t# 0 - doubly occupied, 1 - SpinUp,SpinDown\n\
-MaxPsiDouble\t0\t# here: specifying both maximum number of SpinUp- and -Down-states\n\
-PsiMaxNoUp\t0\t# here: specifying maximum number of SpinUp-states\n\
-PsiMaxNoDown\t0\t# here: specifying maximum number of SpinDown-states\n\
+MaxPsiDouble\t2\t# here: specifying both maximum number of SpinUp- and -Down-states\n\
+PsiMaxNoUp\t2\t# here: specifying maximum number of SpinUp-states\n\
+PsiMaxNoDown\t2\t# here: specifying maximum number of SpinDown-states\n\
 AddPsis\t0\t# Additional unoccupied Psis for bandgap determination\n\
 \n\
@@ -122 +122 @@
 \tunit = angstrom\n\
 \t{ atoms geometry } = {\n\
-\t\tO [ 0\t0\t0 ]\n\
-\t\tH [ 0.758602\t0\t0.504284 ]\n\
-\t\tH [ 0.758602\t0\t-0.504284 ]\n\
+\t\tO [ -0.505735\t0\t0 ]\n\
+\t\tH [ 0.252867\t0\t0.504284 ]\n\
+\t\tH [ 0.252867\t0\t-0.504284 ]\n\
 \t}\n\
 )\n\
@@ -131 +131 @@
 \tmolecule = $:molecule\n\
 )\n";
-static string waterXyz = "3\nH2O: water molecule\nO\t0.000000\t0.000000\t0.000000\nH\t0.758602\t0.000000\t0.504284\nH\t0.758602\t0.000000\t-0.504284\n";
+static string waterXyz = "3\nH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
 static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
 static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
@@ -321 +321 @@
 
   // compare both configs
-  CPPUNIT_ASSERT(input.str() == output.str());
-}
+  string first = input.str();
+  string second = output.str();
+  CPPUNIT_ASSERT(first == second);
+}