Changeset d6f886

Timestamp:

Feb 3, 2011, 9:51:18 AM (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, Candidate_v1.7.0, 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:

9df680

Parents:

66fd49

git-author:

Frederik Heber <heber@…> (01/10/11 10:55:48)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

changed stupid --lengths parameter of fill...-with-molecule into three distinct ones.

• in this Vector length three distinct things had been mixed, with --distance it made sense, with lengths this's been just nonsense.
• new parameters are --distance-to-molecule --random-atom-displacement and --random-molecule-displacement and all default to zero.
• moved files into regression/Filling and three files, one for each test case according to new scheme.

TESTFIXES:

• Filling/1-3: lengths mostly replaced by --distance-to-molecule

Files:

• src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (2 diffs)
• src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) (1 diff)
• src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (2 diffs)
• src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) (1 diff)
• tests/regression/Filling/testsuite-fill-void-with-molecule.at (moved) (moved from tests/regression/testsuite-filling.at ) (4 diffs)
• tests/regression/Filling/testsuite-fill-with-molecule.at (added)
• tests/regression/Filling/testsuite-filling.at (added)
• tests/regression/Filling/testsuite-suspend-in-water.at (added)
• tests/regression/Makefile.am (modified) (1 diff)
• tests/regression/testsuite.at (modified) (1 diff)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -57 +57 @@
   }
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << params.lengths[0] << "," << params.lengths[1] << "," << params.lengths[2] << "), distances (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2] << "), MinDistance " << params.MinDistance << ", DoRotate " << params.DoRotate << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
+      << " minimum distance to molecules" << params.boundary
+      << ", random atom displacement " << params.RandAtomDisplacement
+      << ", random molecule displacement " << params.RandMoleculeDisplacement
+      << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
+      << "), MinDistance " << params.MinDistance
+      << ", DoRotate " << params.DoRotate << "." << endl);
   // construct water molecule
   std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
@@ -113 +119 @@
   for (int i=0;i<NDIM;i++)
     distance[i] = params.distances[i];
-  FillVoidWithMolecule(filler, *(World::getInstance().getConfig()), distance, params.lengths[0], params.lengths[1], params.lengths[2], params.MinDistance, params.DoRotate);
+  FillVoidWithMolecule(
+      filler,
+      *(World::getInstance().getConfig()),
+      distance,
+      params.boundary,
+      params.RandAtomDisplacement,
+      params.RandMoleculeDisplacement,
+      params.MinDistance,
+      params.DoRotate);
 
   // generate list of newly created molecules

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def

@@ -13 +13 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(Vector)(Vector)(double)(bool)
-#define paramtokens ("fill-void")("distances")("lengths")("MinDistance")("DoRotate")
-#define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("list of three of lengths in space, one for each axis direction")("minimum distance to boundary")("whether to rotate or not")
-#define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("0.")("0")
-#define paramreferences (fillername)(distances)(lengths)(MinDistance)(DoRotate)
+#define paramtypes (boost::filesystem::path)(Vector)(double)(double)(double)(double)(bool)
+#define paramtokens ("fill-void")("distances")("distance-to-molecule")("random-atom-displacement")("random-molecule-displacement")("distance-to-boundary")("DoRotate")
+#define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("minimum distance to present molecules")("magnitude of random atom displacement")("magnitude of random molecule displacement")("minimum distance to boundary")("whether to rotate or not")
+#define paramdefaults (NODEFAULT)(NODEFAULT)("0.")("0.")("0.")("0.")("0")
+#define paramreferences (fillername)(distances)(boundary)(RandAtomDisplacement)(RandMoleculeDisplacement)(MinDistance)(DoRotate)
 
 #define statetypes (std::vector<molecule *>)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -45 +45 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << params.lengths[0] << "," << params.lengths[1] << "," << params.lengths[2] << "), distances (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2] << "), MaxDistance " << params.MaxDistance << ", DoRotate " << params.DoRotate << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
+      << " minimum distance to molecules" << params.boundary
+      << ", random atom displacement " << params.RandAtomDisplacement
+      << ", random molecule displacement " << params.RandMoleculeDisplacement
+      << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
+      << "), MinDistance " << params.MaxDistance
+      << ", DoRotate " << params.DoRotate << "." << endl);
   // construct water molecule
   molecule *filler = World::getInstance().createMolecule();
@@ -74 +80 @@
   for (int i=0;i<NDIM;i++)
     distance[i] = params.distances[i];
-  Filling = FillBoxWithMolecule(World::getInstance().getMolecules(), filler, *(World::getInstance().getConfig()), params.MaxDistance, distance, params.lengths[0], params.lengths[1], params.lengths[2], params.DoRotate);
+  Filling = FillBoxWithMolecule(
+      World::getInstance().getMolecules(),
+      filler, *(World::getInstance().getConfig()),
+      params.MaxDistance,
+      distance,
+      params.boundary,
+      params.RandAtomDisplacement,
+      params.RandMoleculeDisplacement,
+      params.DoRotate);
   if (Filling != NULL) {
     Filling->ActiveFlag = false;

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -13 +13 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(Vector)(Vector)(double)(bool)
-#define paramtokens ("fill-molecule")("distances")("lengths")("MaxDistance")("DoRotate")
-#define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("list of three of lengths in space, one for each axis direction")("maximum spatial distance")("whether to rotate or not")
-#undef paramdefaults
-#define paramreferences (fillername)(distances)(lengths)(MaxDistance)(DoRotate)
+#define paramtypes (boost::filesystem::path)(Vector)(double)(double)(double)(double)(bool)
+#define paramtokens ("fill-molecule")("distances")("distance-to-molecule")("random-atom-displacement")("random-molecule-displacement")("MaxDistance")("DoRotate")
+#define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("minimum distance to present molecules")("magnitude of random atom displacement")("magnitude of random molecule displacement")("maximum spatial distance")("whether to rotate or not")
+#define paramdefaults (NODEFAULT)(NODEFAULT)("0.")("0.")("0.")("0.")("0")
+#define paramreferences (fillername)(distances)(boundary)(RandAtomDisplacement)(RandMoleculeDisplacement)(MaxDistance)(DoRotate)
 
 #undef statetypes

tests/regression/Filling/testsuite-fill-void-with-molecule.at

@@ -1 @@
-AT_BANNER([MoleCuilder - Filling in molecules])
-# 1. filling box
-AT_SETUP([Filling - filling box around molecule's surface])
-AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/pre/test.conf .], 0)
-AT_DATA([water.xyz], [[3
- # test configuration, created by molecuilder test suite
-O       0.      0.      0.
-H       0.758602 0.     0.504284 
-H       0.758602 0.     -0.504284 
-]])
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -F water.xyz --MaxDistance -1 --distances "3.1, 3.1, 3.1"  --lengths "2.1, 0., 0." --DoRotate 0], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/post/$file], 0, [ignore], [ignore])
-AT_CLEANUP
+### 3. filling box
 
-# 2. suspend in water with certain density
-AT_SETUP([Filling - BROKEN: suspend in water])
-AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-molecule-by-id 0 -u 1.3], 0, [stdout], [stderr])
-#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/post/$file], 0, [ignore], [ignore])
-AT_CLEANUP
-
-# 3. filling box
 AT_SETUP([Filling - filling void space in box])
 AT_KEYWORDS([filling])
@@ -32 +10 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i test.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --lengths "1.5, 0., 0." --DoRotate 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0], 0, [stdout], [stderr])
 AT_CHECK([file=test.xyz; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/3/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
@@ -45 +23 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i empty.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --lengths "1.5, 0., 0." --DoRotate 0 --undo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i empty.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0 --undo], 0, [stdout], [stderr])
 AT_CHECK([file=empty.xyz; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/3/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
@@ -52 +30 @@
 AT_KEYWORDS([filling])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/3/pre/*.data .], 0)
-AT_CHECK([../../molecuilder -i tensid.data  -B "30,0,30,0,0,30" --fill-void water.data --distances "3.1, 3.1, 3.1"  --lengths "2.1, 0., 0." --DoRotate 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i tensid.data  -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], 0, [stdout], [stderr])
 AT_CHECK([file=tensid.data; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/3/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP

tests/regression/Makefile.am

@@ -19 +19 @@
         $(srcdir)/testsuite-analysis.at \
         $(srcdir)/testsuite-domain.at \
-        $(srcdir)/testsuite-filling.at \
+        $(srcdir)/Filling/testsuite-filling.at \
+        $(srcdir)/Filling/testsuite-fill-with-molecule.at \
+        $(srcdir)/Filling/testsuite-suspend-in-water.at \
+        $(srcdir)/Filling/testsuite-fill-void-with-molecule.at \
         $(srcdir)/testsuite-fragmentation.at \
         $(srcdir)/testsuite-graph.at \

tests/regression/testsuite.at

@@ -28 +28 @@
 m4_include(testsuite-tesselation.at)
 
-m4_include(testsuite-filling.at)
+m4_include(Filling/testsuite-filling.at)
 
 m4_include(testsuite-analysis.at)