Changeset ccb487

Timestamp:

Apr 3, 2012, 7:58:43 AM (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:

08a0f52

Parents:

a275b3

git-author:

Frederik Heber <heber@…> (03/15/12 17:29:54)

git-committer:

Frederik Heber <heber@…> (04/03/12 07:58:43)

Message:

TremoloParser now always writes current domain as "# Box ..." into file.

• This is important, as format tremolo is essentially also a domain preserving type (i.e. tremolo reads Box from .data file).
• TESTFIX: The following regression tests have a "' Box ..." line added to their .data files: Domain/RepeatBox, Filling/FillVoidWithMolecule, Molecules/Copy, Molecules/CreateMicelle, Parser/Tremolo-SetAtomdata.
• FIX: Forgot to add testsuite-fill-void-with-tenside-molecule.at to Makefile.am

Files:

• src/Parser/TremoloParser.cpp (modified) (3 diffs)
• src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) (6 diffs)
• tests/regression/Domain/RepeatBox/post/ec.data (modified) (1 diff)
• tests/regression/Domain/RepeatBox/pre/ec.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/testsuite-fill-void-with-tenside-molecule.at (modified) (2 diffs)
• tests/regression/Makefile.am (modified) (1 diff)
• tests/regression/Molecules/Copy/post/tensid-undo.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/Molecules/CreateMicelle/post/tensid.data (modified) (1 diff)
• tests/regression/Molecules/CreateMicelle/pre/tensid.data (modified) (1 diff)
• tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) (1 diff)

src/Parser/TremoloParser.cpp

@@ -29 +29 @@
 #include "Atom/atom.hpp"
 #include "Bond/bond.hpp"
+#include "Box.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
@@ -171 +173 @@
   }
 
-  // store
+  // store Atomdata line
   *file << "# ATOMDATA";
   for (it=usedFields.begin(); it < usedFields.end(); it++) {
@@ -177 +179 @@
   }
   *file << endl;
+
+  // store Box info
+  *file << "# Box";
+  const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
+  for (size_t i=0; i<NDIM;++i)
+    for (size_t j=0; j<NDIM;++j)
+      *file << "\t" << M.at(i,j);
+  *file << std::endl;
+
+  // store particles
   for (atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
     saveLine(file, *atomIt);

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -43 +43 @@
 
 static string Tremolo_Atomdata1 = "\
-# ATOMDATA\tId\tname\ttype\tx=3\n";
+# ATOMDATA\tId\tname\ttype\tx=3\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n";
 static string Tremolo_Atomdata2 = "\
 #\n\
 #ATOMDATA Id name type x=3\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 1 hydrogen H 3.0 4.5 0.1\n\
 \n";
@@ -52 +54 @@
 #\n\
 #ATOMDATA Id name foo type x=3\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 \n\n";
 static string Tremolo_velocity = "\
 #\n\
 #ATOMDATA Id name type u=3\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 1 hydrogen H 3.0 4.5 0.1\n\
 \n";
 static string Tremolo_neighbours = "#\n\
 #ATOMDATA Id type neighbors=2\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 1 H 3 0\n\
 2 H 3 0\n\
@@ -66 +71 @@
 #\n\
 #ATOMDATA Id type imprData\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 8 H 9-10\n\
 9 H 10-8,8-10\n\
@@ -72 +78 @@
 #\n\
 #ATOMDATA Id type torsion\n\
+# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
 8 H 9-10\n\
 9 H 10-8,8-10\n\
@@ -77 +84 @@
 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";
 
@@ -211 +219 @@
     std::vector<atom *> atoms = World::getInstance().getAllAtoms();
     parser->save(&output, atoms);
+//    std::cout << output.str() << std::endl;
+//    std::cout << Tremolo_full << std::endl;
     CPPUNIT_ASSERT(output.str() == Tremolo_full);
   }

tests/regression/Domain/RepeatBox/post/ec.data

@@ -1 +1 @@
 # ATOMDATA      Id      type    x=3     u=3     neighbors=4
+# Box   40      0       0       0       40      0       0       0       40
 1       O       7.36404 5       5.01    0       0       0       4       0       0       0       
 2       OS      5.50419 6.07129 5       0       0       0       4       5       0       0       

tests/regression/Domain/RepeatBox/pre/ec.data

@@ -1 +1 @@
 # ATOMDATA      Id      type    x=3     u=3     neighbors=4
+# Box   20      0       0       0       20      0       0       0       20
 1       O       7.36404 5       5.01    0       0       0       4       0       0       0       
 2       OS      5.50419 6.07129 5       0       0       0       4       5       0       0       

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

@@ -1 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   30      0       0       0       30      0       0       0       30
 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 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   30      0       0       0       30      0       0       0       30
 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/testsuite-fill-void-with-tenside-molecule.at

@@ -15 +15 @@
 
 AT_SETUP([Filling - filling void space besides tenside micelle in box with Undo])
-AT_XFAIL_IF([/bin/true])
 AT_KEYWORDS([filling fill-void undo])
 
@@ -23 +22 @@
 AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -B "30,0,30,0,0,30" --fill-void water.data --distances "3.1, 3.1, 3.1" --distance-to-molecule "2.1" --DoRotate 0 --undo], 0, [stdout], [stderr])
-AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/FillVoidWithMolecule/post/tensid.data], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data], 0, [ignore], [ignore])
 
 AT_CLEANUP

tests/regression/Makefile.am

@@ -61 +61 @@
         $(srcdir)/Filling/SuspendInWater/testsuite-suspend-in-water.at \
         $(srcdir)/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at \
+        $(srcdir)/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at \
         $(srcdir)/Fragmentation/testsuite-fragmentation.at \
         $(srcdir)/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at \

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

@@ -1 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   20      0       0       0       20      0       0       0       20
 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/post/tensid.data

@@ -1 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   20      0       0       0       20      0       0       0       20
 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 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   20      0       0       0       20      0       0       0       20
 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/CreateMicelle/post/tensid.data

@@ -1 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   20      0       0       0       20      0       0       0       20
 1       NA      SLES    1       -4.78921        -8.81932        -49.4988        NA      0       0       0       0       1.000000e+00    
 2       S       SLES    1       -3.65465        -6.08892        -48.8416        SL      3       4       5       6       1.330000e+00    

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

@@ -1 +1 @@
 # ATOMDATA      Id      name    resName chainID x=3     type    neighbors=4     charge
+# Box   20      0       0       0       20      0       0       0       20
 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-SetAtomdata/post/argon.data

@@ -1 +1 @@
 # ATOMDATA      type    x=3
+# Box   20      0       0       0       20      0       0       0       20
 Ar      4.72977 8       8       
 Ar      7.3     8       8