Changeset 305e7e

Timestamp:

Apr 18, 2011, 12:45:06 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:

4fdc65

Parents:

4217e7

git-author:

Frederik Heber <heber@…> (04/18/11 12:43:30)

git-committer:

Frederik Heber <heber@…> (04/18/11 12:45:06)

Message:

FIX: Type is actually spelled type with TREMOLO.

• corrected in TremoloParser.
• TESTFIX: the following tests has to be changed accordingly:
  • Parser/Tremolo
  • Parser/Tremolo-Potentials
  • Atoms/Add
  • Filling/FillVoidWithMolecule
  • Molecule/Copy

Files:

• src/Parser/TremoloAtomInfoContainer.cpp (modified) (4 diffs)
• src/Parser/TremoloAtomInfoContainer.hpp (modified) (1 diff)
• src/Parser/TremoloKey.hpp (modified) (1 diff)
• src/Parser/TremoloParser.cpp (modified) (3 diffs)
• src/Parser/TremoloParser.hpp (modified) (1 diff)
• src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) (4 diffs)
• tests/regression/Atoms/Add/post/test.data (modified) (1 diff)
• tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) (1 diff)
• tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) (1 diff)
• tests/regression/Filling/FillVoidWithMolecule/pre/water.data (modified) (1 diff)
• tests/regression/Molecules/Copy/post/tensid.data (modified) (1 diff)
• tests/regression/Molecules/Copy/pre/tensid.data (modified) (1 diff)
• tests/regression/Parser/Tremolo-Potentials/post/argon.data (modified) (1 diff)
• tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) (1 diff)
• tests/regression/Parser/Tremolo-Potentials/pre/argon.data (modified) (1 diff)
• tests/regression/Parser/Tremolo/post/argon.data (modified) (1 diff)
• tests/regression/Parser/Tremolo/post/test.data (modified) (1 diff)
• tests/regression/Parser/Tremolo/pre/argon.data (modified) (1 diff)
• tests/regression/Parser/Tremolo/pre/test.data (modified) (1 diff)

src/Parser/TremoloAtomInfoContainer.cpp

@@ -32 +32 @@
   imprData("-"),
   GroupMeasureTypeNo("0"),
-  Type("-"),
+  type("-"),
   extType("-"),
   name("-"),
@@ -63 +63 @@
       GroupMeasureTypeNo = value;
       break;
-    case TremoloKey::Type :
-      Type = value;
+    case TremoloKey::type :
+      type = value;
       break;
     case TremoloKey::extType :
@@ -121 +121 @@
     case TremoloKey::GroupMeasureTypeNo :
       return GroupMeasureTypeNo;
-    case TremoloKey::Type :
-      return Type;
+    case TremoloKey::type :
+      return type;
     case TremoloKey::extType :
       return extType;
@@ -161 +161 @@
   out << info.get(TremoloKey::imprData) << "\t";
   out << info.get(TremoloKey::GroupMeasureTypeNo) << "\t";
-  out << info.get(TremoloKey::Type) << "\t";
+  out << info.get(TremoloKey::type) << "\t";
   out << info.get(TremoloKey::extType) << "\t";
   out << info.get(TremoloKey::name) << "\t";

src/Parser/TremoloAtomInfoContainer.hpp

@@ -32 +32 @@
   std::string imprData;
   std::string GroupMeasureTypeNo;
-  std::string Type;
+  std::string type;
   std::string extType;
   std::string name;

src/Parser/TremoloKey.hpp

@@ -30 +30 @@
     imprData,
     GroupMeasureTypeNo,
-    Type,
+    type,
     extType,
     name,

src/Parser/TremoloParser.cpp

@@ -54 +54 @@
   knownKeys["imprData"] = TremoloKey::imprData;
   knownKeys["GroupMeasureTypeNo"] = TremoloKey::GroupMeasureTypeNo;
-  knownKeys["Type"] = TremoloKey::Type;
+  knownKeys["type"] = TremoloKey::type;
   knownKeys["extType"] = TremoloKey::extType;
   knownKeys["name"] = TremoloKey::name;
@@ -196 +196 @@
         *file << currentAtom->getAtomicVelocity()[2] << "\t";
         break;
-      case TremoloKey::Type :
+      case TremoloKey::type :
         if (additionalAtomData.count(currentAtom->getId())) {
           if (additionalAtomData[currentAtom->getId()].get(currentField) != "-") {
@@ -361 +361 @@
         newAtom->setAtomicVelocity(tempVector);
         break;
-      case TremoloKey::Type :
+      case TremoloKey::type :
       {
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");

src/Parser/TremoloParser.hpp

@@ -53 +53 @@
 
   /**
-   * Map to associate the elements with stuff in "Type", e.g. OC2 -> O.
+   * Map to associate the elements with stuff in "type", e.g. OC2 -> O.
    */
   std::map<std::string, std::string> knownTypes;

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -46 +46 @@
 
 static string Tremolo_Atomdata1 = "\
-# ATOMDATA\tId\tname\tType\tx=3\n";
+# ATOMDATA\tId\tname\ttype\tx=3\n";
 static string Tremolo_Atomdata2 = "\
 #\n\
-#ATOMDATA Id name Type x=3\n\
+#ATOMDATA Id name type x=3\n\
 1 hydrogen H 3.0 4.5 0.1\n\
 \n";
 static string Tremolo_invalidkey = "\
 #\n\
-#ATOMDATA Id name foo Type x=3\n\
+#ATOMDATA Id name foo type x=3\n\
 \n\n";
 static string Tremolo_velocity = "\
 #\n\
-#ATOMDATA Id name Type u=3\n\
+#ATOMDATA Id name type u=3\n\
 1 hydrogen H 3.0 4.5 0.1\n\
 \n";
 static string Tremolo_neighbours = "#\n\
-#ATOMDATA Id Type neighbors=2\n\
+#ATOMDATA Id type neighbors=2\n\
 1 H 3 0\n\
 2 H 3 0\n\
@@ -68 +68 @@
 static string Tremolo_improper = "\
 #\n\
-#ATOMDATA Id Type imprData\n\
+#ATOMDATA Id type imprData\n\
 8 H 9-10\n\
 9 H 10-8,8-10\n\
@@ -74 +74 @@
 static string Tremolo_torsion = "\
 #\n\
-#ATOMDATA Id Type torsion\n\
+#ATOMDATA Id type torsion\n\
 8 H 9-10\n\
 9 H 10-8,8-10\n\
 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\
+# 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\
 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";
 
@@ -214 +214 @@
     atom* newAtom = World::getInstance().createAtom();
     newAtom->setType(1);
-    testParser->setFieldsForSave("x=3 u=3 F stress Id neighbors=5 imprData GroupMeasureTypeNo Type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
+    testParser->setFieldsForSave("x=3 u=3 F 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();
     testParser->save(&output, atoms);

tests/regression/Atoms/Add/post/test.data

@@ -1 @@
-# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      Type    chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion u       x
-0       0       0       0       1       H       0       0       -       -       -       0       -       0       0       0       0       -       0       0       0       10      10      10      
+# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion type    u       x
+0       0       0       0       1       0       0       -       -       -       0       -       0       0       0       0       -       H       0       0       0       10      10      10      

tests/regression/Filling/FillVoidWithMolecule/post/tensid.data

@@ -1 @@
-# ATOMDATA      Id      name    resName chainID x=3     Type    neighbors=4     charge
+# ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
 1       NA      SLES    1       17.397  20.231  11.737  Na      0       0       0       0       1.000000e+00    
 2       S       SLES    1       16.282  18.88   14.208  S       3       4       5       6       1.330000e+00    

tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data

@@ -1 @@
-# ATOMDATA      Id      name    resName chainID x=3     Type    neighbors=4     charge
+# ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
 1       NA      SLES    1       17.397  20.231  11.737  Na      0       0       0       0       1.000000e+00    
 2       S       SLES    1       16.282  18.88   14.208  S       3       4       5       6       1.330000e+00    

tests/regression/Filling/FillVoidWithMolecule/pre/water.data

@@ -1 @@
-# ATOMDATA      Id      name    resName chainID x=3     Type    neighbors=4     charge
+# ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
 1       -       -       0       0.      0.      0.      O       2       3       0       0       0
 2       -       -       0       0.758602        0.      0.504284        H       1       0       0       0       0

tests/regression/Molecules/Copy/post/tensid.data

@@ -1 @@
-# ATOMDATA      Id      name    resName chainID x=3     Type    neighbors=4     charge
+# ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
 1       NA      SLES    1       32.397  35.231  26.737  NA      0       0       0       0       1.000000e+00    
 2       S       SLES    1       31.282  33.88   29.208  SL      3       4       5       6       1.330000e+00    

tests/regression/Molecules/Copy/pre/tensid.data

@@ -1 @@
-# ATOMDATA      Id      name    resName chainID x=3     Type    neighbors=4     charge
+# ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
 1       NA      SLES    1       32.397  35.231  26.737  NA      0       0       0       0       1.000000e+00    
 2       S       SLES    1       31.282  33.88   29.208  SL      3       4       5       6       1.330000e+00    

tests/regression/Parser/Tremolo-Potentials/post/argon.data

@@ -1 @@
-# ATOMDATA      Id      name    Type    x=3
+# ATOMDATA      Id      name    type    x=3
 1       Ar1     Argon   4.72977 8       8       
 2       Ar2     Argon   7.3     8       8       

tests/regression/Parser/Tremolo-Potentials/post/test.data

@@ -1 @@
-# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      Type    chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion u       x
-0       0       0       0       1       Ar      0       0       -       -       -       0       -          1    0       0       0       -       0       0       0       4.72977 8       8       
-0       0       0       0       2       Ar      0       0       -       -       -       0       -          1    0       0       0       -       0       0       0       7.3     8       8       
+# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion type    u       x
+0       0       0       0       1       0       0       -       -       -       0       -          1    0       0       0       -       Ar      0       0       0       4.72977 8       8       
+0       0       0       0       2       0       0       -       -       -       0       -          1    0       0       0       -       Ar      0       0       0       7.3     8       8       

tests/regression/Parser/Tremolo-Potentials/pre/argon.data

@@ -1 @@
-# ATOMDATA Id name Type x=3
+# ATOMDATA Id name type x=3
 1       Ar1     Argon   4.72977074      8.      8.      
 2       Ar2     Argon   7.3             8.              8.              

tests/regression/Parser/Tremolo/post/argon.data

@@ -1 @@
-# ATOMDATA      Id      name    Type    x=3
+# ATOMDATA      Id      name    type    x=3
 1       Ar1     Ar      4.72977 8       8       
 2       Ar2     Ar      7.3     8       8       

tests/regression/Parser/Tremolo/post/test.data

@@ -1 @@
-# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      Type    chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion u       x
-0       0       0       0       1       H       0       0       -       -       -       0       -          1    0       0       0       -       0       0       0       10      10      10      
+# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion type    u       x
+0       0       0       0       1       0       0       -       -       -       0       -          1    0       0       0       -       H       0       0       0       10      10      10      

tests/regression/Parser/Tremolo/pre/argon.data

@@ -1 @@
-# ATOMDATA Id name Type x=3
+# ATOMDATA Id name type x=3
 1       Ar1     Ar      4.72977074      8.      8.      
 ###2    3       4       5

tests/regression/Parser/Tremolo/pre/test.data

@@ -1 @@
-# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      Type    chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion u       x
-0       0       0       0       1       H       0       0       -       -       -       0       -          1    0       0       0       -       0       0       0       10      10      10      
+# ATOMDATA      Charge  F       GroupMeasureTypeNo      GrpTypeNo       Id      chainID charge  extType imprData        name    neighbors       occupancy       resName resSeq  segID   stress  tempFactor      torsion type    u       x
+0       0       0       0       1       0       0       -       -       -       0       -          1    0       0       0       -       H       0       0       0       10      10      10