Changeset 9907e7 for src

Timestamp:

Jun 7, 2010, 11:55:30 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:

4ed18b

Parents:

19c0e3

Message:

Case '-F' is now handled by CommandLineUI.

• FIX: FillWithMoleculeAction was still using internally created water instead of molecule parsed from xyz file.

Location:

src

Files:

• Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (1 diff)
• builder.cpp (modified) (1 diff)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -66 +66 @@
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << lengths[0] << "," << lengths[1] << "," << lengths[2] << "), distances (" << distances[0] << "," << distances[1] << "," << distances[2] << "), MaxDistance " << MaxDistance << ", DoRotate " << DoRotate << "." << endl);
     // construct water molecule
     molecule *filler = World::getInstance().createMolecule();
-//    if (!filler->AddXYZFile(filename)) {
-//      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << filename << "." << endl);
-//    }
-//    filler->SetNameFromFilename(filename);
+    if (!filler->AddXYZFile(filename)) {
+      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << filename << "." << endl);
+    }
+    filler->SetNameFromFilename(filename.c_str());
     molecule *Filling = NULL;
-    atom *first = NULL, *second = NULL, *third = NULL;
-    first = World::getInstance().createAtom();
-    first->type = World::getInstance().getPeriode()->FindElement(1);
-    first->x = Vector(0.441, -0.143, 0.);
-    filler->AddAtom(first);
-    second = World::getInstance().createAtom();
-    second->type = World::getInstance().getPeriode()->FindElement(1);
-    second->x = Vector(-0.464, 1.137, 0.0);
-    filler->AddAtom(second);
-    third = World::getInstance().createAtom();
-    third->type = World::getInstance().getPeriode()->FindElement(8);
-    third->x = Vector(-0.464, 0.177, 0.);
-    filler->AddAtom(third);
-    filler->AddBond(first, third, 1);
-    filler->AddBond(second, third, 1);
+//    atom *first = NULL, *second = NULL, *third = NULL;
+//    first = World::getInstance().createAtom();
+//    first->type = World::getInstance().getPeriode()->FindElement(1);
+//    first->x = Vector(0.441, -0.143, 0.);
+//    filler->AddAtom(first);
+//    second = World::getInstance().createAtom();
+//    second->type = World::getInstance().getPeriode()->FindElement(1);
+//    second->x = Vector(-0.464, 1.137, 0.0);
+//    filler->AddAtom(second);
+//    third = World::getInstance().createAtom();
+//    third->type = World::getInstance().getPeriode()->FindElement(8);
+//    third->x = Vector(-0.464, 0.177, 0.);
+//    filler->AddAtom(third);
+//    filler->AddBond(first, third, 1);
+//    filler->AddBond(second, third, 1);
     World::getInstance().getConfig()->BG->ConstructBondGraph(filler);
-    filler->SetNameFromFilename("water");
+//    filler->SetNameFromFilename("water");
     // call routine
     double distance[NDIM];

src/builder.cpp

@@ -1950 +1950 @@
             case 'F':
               if (ExitFlag == 0) ExitFlag = 1;
-              MaxDistance = -1;
-              if (argv[argptr-1][2] == 'F') { // option is -FF?
-                // fetch first argument as max distance to surface
-                MaxDistance = atof(argv[argptr++]);
-                DoLog(0) && (Log() << Verbose(0) << "Filling with maximum layer distance of " << MaxDistance << "." << endl);
-              }
-              if ((argptr+7 >=argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) || (!IsValidNumber(argv[argptr+6])) || (!IsValidNumber(argv[argptr+7]))) {
-                ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <xyz of filler> <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl);
-                performCriticalExit();
-              } else {
-                SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules." << endl);
-                // construct water molecule
-                molecule *filler = World::getInstance().createMolecule();
-                if (!filler->AddXYZFile(argv[argptr])) {
-                  DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << argv[argptr] << "." << endl);
-                }
-                filler->SetNameFromFilename(argv[argptr]);
-                configuration.BG->ConstructBondGraph(filler);
-                molecule *Filling = NULL;
-                // call routine
-                double distance[NDIM];
-                for (int i=0;i<NDIM;i++)
-                  distance[i] = atof(argv[argptr+i+1]);
-                Filling = FillBoxWithMolecule(molecules, filler, configuration, MaxDistance, distance, atof(argv[argptr+4]), atof(argv[argptr+5]), atof(argv[argptr+6]), atoi(argv[argptr+7]));
-                if (Filling != NULL) {
-                  Filling->ActiveFlag = false;
-                  molecules->insert(Filling);
-                }
-                World::getInstance().destroyMolecule(filler);
-                argptr+=6;
-              }
+              ArgcList.insert(argptr-1);
+              ArgcList.insert(argptr);
+              ArgcList.insert(argptr+1);
+              ArgcList.insert(argptr+2);
+              ArgcList.insert(argptr+3);
+              ArgcList.insert(argptr+4);
+              ArgcList.insert(argptr+5);
+              ArgcList.insert(argptr+6);
+              ArgcList.insert(argptr+7);
+              ArgcList.insert(argptr+8);
+              ArgcList.insert(argptr+9);
+              ArgcList.insert(argptr+10);
+              ArgcList.insert(argptr+11);
+              ArgcList.insert(argptr+12);
+              argptr+=13;
               break;
             case 'A':