Changeset 980dd6

Timestamp:

Jun 12, 2010, 10:34:14 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, 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:

88104f, e6317b

Parents:

f6bd32

git-author:

Frederik Heber <heber@…> (06/11/10 19:41:45)

git-committer:

Frederik Heber <heber@…> (06/12/10 10:34:14)

Message:

Case 'N' is now handled by CommandLineUI.

• TESTFIX: Tesselation/1 and Tesselation/3 molecuilder calls have been changed.
• TESTFIX: Tesselation/defs.in call of molecuilder has been changed.

Files:

• src/Actions/MapOfActions.cpp (modified) (4 diffs)
• src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) (1 diff)
• src/builder.cpp (modified) (1 diff)
• tests/Tesselations/defs.in (modified) (1 diff)
• tests/regression/testsuite-tesselation.at (modified) (2 diffs)

src/Actions/MapOfActions.cpp

@@ -127 +127 @@
   DescriptionMap["periodic"] = "system is constraint to periodic boundary conditions (y/n)";
   DescriptionMap["position"] = "position in R^3 space";
+  DescriptionMap["sphere-radius"] = "radius of tesselation sphere";
   DescriptionMap["start-step"] = "first or start step";
 
@@ -229 +230 @@
   TypeMap["periodic"] = Boolean;
   TypeMap["position"] = Vector;
+  TypeMap["sphere-radius"] = Double;
   TypeMap["start-step"] = Integer;
 
@@ -260 +262 @@
         generic.insert("linear-interpolate");
 //  generic.insert("molecular-volume");
-//  generic.insert("nonconvex-envelope");
+  generic.insert("nonconvex-envelope");
         generic.insert("pair-correlation");
 //      generic.insert("parse-xyz");
@@ -307 +309 @@
   generic.insert("periodic");
   generic.insert("position");
+  generic.insert("sphere-radius");
   generic.insert("start-step");
 }

src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

@@ -56 +56 @@
   clock_t start,end;
 
-  dialog->queryDouble(NAME, &SphereRadius, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryString("output", &filename, MapOfActions::getInstance().getDescription("output"));
-  dialog->queryMolecule("molecule-by-id", &Boundary, MapOfActions::getInstance().getDescription("molecule-by-id"));
+  dialog->queryMolecule(NAME, &Boundary, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryString("nonconvex-file", &filename, MapOfActions::getInstance().getDescription("nonconvex-file"));
+  dialog->queryDouble("sphere-radius", &SphereRadius, MapOfActions::getInstance().getDescription("sphere-radius"));
 
   if(dialog->display()) {

src/builder.cpp

@@ -1900 +1900 @@
             case 'N':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-')){
+              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')){
                 ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for non-convex envelope: -o <radius> <tecplot output file>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for non-convex envelope: -N <molecule_id> --sphere-radius <radius> --nonconvex-file <output prefix>" << endl);
                 performCriticalExit();
               } else {
-                class Tesselation *T = NULL;
-                const LinkedCell *LCList = NULL;
-                molecule * Boundary = NULL;
-                //string filename(argv[argptr+1]);
-                //filename.append(".csv");
-                DoLog(0) && (Log() << Verbose(0) << "Evaluating non-convex envelope of biggest molecule.");
-                DoLog(1) && (Log() << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl);
-                // find biggest molecule
-                int counter  = 0;
-                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-                  if ((Boundary == NULL) || (Boundary->getAtomCount() < (*BigFinder)->getAtomCount())) {
-                    Boundary = *BigFinder;
-                  }
-                  counter++;
-                }
-                DoLog(1) && (Log() << Verbose(1) << "Biggest molecule has " << Boundary->getAtomCount() << " atoms." << endl);
-                start = clock();
-                LCList = new LinkedCell(Boundary, atof(argv[argptr])*2.);
-                if (!FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]))
-                  ExitFlag = 255;
-                //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
-                end = clock();
-                DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
-                delete(LCList);
-                delete(T);
-                argptr+=2;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                argptr+=5;
               }
               break;

tests/Tesselations/defs.in

@@ -54 +54 @@
         #echo "Current dir is `pwd`, calling $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -N $RADIUS $FILENAME."
         if [ -e $mol.dbond ]; then
-                $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -A $mol.dbond -N $RADIUS $FILENAME 2>stderr >stdout || exitcode=$?
+                $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -A $mol.dbond -N 0 --sphere-radius $RADIUS --nonconvex-file $FILENAME 2>stderr >stdout || exitcode=$?
         else
-                $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -N $RADIUS $FILENAME 2>stderr >stdout || exitcode=$?
+                $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -N 0 --sphere-radius $RADIUS --nonconvex-file $FILENAME 2>stderr >stdout || exitcode=$?
         fi
         #echo "Molecuilder done with exitcode $exitcode."

tests/regression/testsuite-tesselation.at

@@ -4 +4 @@
 AT_KEYWORDS([Tesselation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 0 --sphere-radius 4. --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
 AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
@@ -22 +22 @@
 AT_SETUP([Tesselation - Big non-Convex Envelope])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 0 --sphere-radius 4. --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
 AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])