Changeset eddea2

Timestamp:

May 30, 2010, 5:29:38 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:

8048a4

Parents:

5d12d2

git-author:

Frederik Heber <heber@…> (05/30/10 17:03:25)

git-committer:

Frederik Heber <heber@…> (05/30/10 17:29:38)

Message:

Added case '-T' (periodic translation) to testsuite.

• BUGFIX: Vector::WrapPeriodically() added half of the box on top which is not as intended.
  • this broke testcase '-b', which relied on the half of the box adding.
  • new function molecule::DetermineCenterOfBox()
  • is used instead to additionally add this center in molecule::CenterInBox()
• BUGFIX: molecule::TranslatePeriodically() subtracted vector instead of adding.

Files:

• src/molecule.hpp (modified) (1 diff)
• src/molecule_geometry.cpp (modified) (4 diffs)
• src/vector.cpp (modified) (1 diff)
• tests/regression/Molecules/7/post/test.conf (added)
• tests/regression/Molecules/7/pre/test.conf (added)
• tests/regression/testsuite.at (modified) (1 diff)

src/molecule.hpp

@@ -249 +249 @@
   Vector * DetermineCenterOfGravity();
   Vector * DetermineCenterOfAll() const;
+  Vector * DetermineCenterOfBox() const;
   void SetNameFromFilename(const char *filename);
   void SetBoxDimension(Vector *dim);

src/molecule_geometry.cpp

@@ -27 +27 @@
   bool status = true;
   const Vector *Center = DetermineCenterOfAll();
+  const Vector *CenterBox = DetermineCenterOfBox();
   double * const cell_size = World::getInstance().getDomain();
   double *M = ReturnFullMatrixforSymmetric(cell_size);
@@ -33 +34 @@
   // go through all atoms
   ActOnAllVectors( &Vector::SubtractVector, *Center);
+  ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
   ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
 
@@ -142 +144 @@
 };
 
+/** Returns vector pointing to center of the domain.
+ * \return pointer to center of the domain
+ */
+Vector * molecule::DetermineCenterOfBox() const
+{
+  Vector *a = new Vector(0.5,0.5,0.5);
+
+  const double *cell_size = World::getInstance().getDomain();
+  double *M = ReturnFullMatrixforSymmetric(cell_size);
+  a->MatrixMultiplication(M);
+  Free(&M);
+
+  return a;
+};
+
 /** Returns vector pointing to center of gravity.
  * \param *out output stream for debugging
@@ -236 +253 @@
 
   // go through all atoms
-  ActOnAllVectors( &Vector::SubtractVector, *trans);
+  ActOnAllVectors( &Vector::AddVector, *trans);
   ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
 

src/vector.cpp

@@ -543 +543 @@
   // truncate to [0,1] for each axis
   for (int i=0;i<NDIM;i++) {
-    x[i] += 0.5;  // set to center of box
+    //x[i] += 0.5;  // set to center of box
     while (x[i] >= 1.)
       x[i] -= 1.;

tests/regression/testsuite.at

@@ -267 +267 @@
 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t 1. 1. 1.], 0, [stdout], [stderr])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+
+# 6. Periodic translation
+AT_SETUP([Molecules - Periodic translation])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/pre/test.* .], 0)
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T 12. 12. 12.], 0, [stdout], [stderr])
+AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP