Changeset 03a589 for src/Analysis

Timestamp:

Apr 4, 2012, 11:30:11 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:

47ed3d

Parents:

ce7bfd

git-author:

Frederik Heber <heber@…> (03/26/12 07:44:19)

git-committer:

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

Message:

Removed lots of remnant output functions in atom and molecule that are not used anymore.

• Removed functions in atom: OutputMPQCLine(), OutputPsi3Line(), OutputXYZLine(), OutputTrajectories(), OutputTrajectoryXYZ()
• functionality of outputters has been shifted to Psi3Parser and MPQCParser.
• Removed functions in molecule: OutputTrajectories(), OutputTrajectoriesXYZ(), OutputXYZ()
• Removed in CounBondsUnitTest: OutputTestMolecule().

File:

• src/Analysis/unittests/CountBondsUnitTest.cpp (modified) (10 diffs)

src/Analysis/unittests/CountBondsUnitTest.cpp

@@ -129 +129 @@
 };
 
-void OutputTestMolecule1(molecule *mol, const char *name)
-{
-  ofstream output(name);
-  mol->OutputXYZ(&output);
-  output.close();
-}
-
 /** UnitTest for CountBondsTest::HydrogenBridgeBondsTest().
  */
@@ -146 +139 @@
   Vector Translator;
 
-  //OutputTestMolecule1(TestMolecule1, "testmolecule1.xyz");
-
   // create TestMolecule2 as copy
   TestMolecule2 = TestMolecule1->CopyMolecule();
@@ -158 +149 @@
   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-1.xyz");
   Translator = Vector(-3,0,0);
   TestMolecule1->Translate(&Translator);
@@ -166 +156 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-2.xyz");
   Translator = Vector(0,-3,0);
   TestMolecule1->Translate(&Translator);
@@ -175 +164 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-3.xyz");
   Translator = Vector(0,3,0);
   TestMolecule1->Translate(&Translator);
@@ -184 +172 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-4.xyz");
   Translator = Vector(-2,-1,0);
   TestMolecule1->Translate(&Translator);
@@ -192 +179 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-5.xyz");
   Translator = Vector(0,0,-3);
   TestMolecule1->Translate(&Translator);
@@ -201 +187 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-6.xyz");
   Translator = Vector(3,0,0);
   TestMolecule1->Translate(&Translator);
@@ -211 +196 @@
   TestMolecule1->Translate(&Translator);
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-7.xyz");
   Translator = Vector(-3,0,0);
   TestMolecule1->Translate(&Translator);
@@ -220 +204 @@
   TestMolecule1->Scale((const double ** const)&mirror);
   TestMolecule1->Translate(&Translator);
-  //OutputTestMolecule1(TestMolecule1, "testmolecule2-8.xyz");
   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   Translator = Vector(0,-3,0);