Changeset f0a3ec for src

Timestamp:

Jun 11, 2010, 12:19:50 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:

54b953

Parents:

6c7352

git-author:

Frederik Heber <heber@…> (06/11/10 10:22:45)

git-committer:

Frederik Heber <heber@…> (06/11/10 12:19:50)

Message:

Case 'a' is now handled by CommandLineUI.

• NOTE: atom has still to be added to a molecule to get saved in the end, this is fixed with new parser and should be corrected then (TODO is in the code)
• TESTFIX: Scanning for "Not enough or invalid" for invalid commands test cases has been replaced by just "Not enough"

Location:

src

Files:

• Actions/AtomAction/AddAction.cpp (modified) (2 diffs)
• Actions/MapOfActions.cpp (modified) (4 diffs)
• builder.cpp (modified) (2 diffs)

src/Actions/AtomAction/AddAction.cpp

@@ -10 +10 @@
 #include "element.hpp"
 #include "log.hpp"
-#include "periodentafel.hpp"
+#include "molecule.hpp"
 #include "vector.hpp"
 #include "verbose.hpp"
@@ -35 +35 @@
 Action::state_ptr AtomAddAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  int Z = -1;
+  std::vector<element *> elements;
   Vector position;
 
-  dialog->queryInt(NAME, &Z, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
   dialog->queryVector("position", &position, World::getInstance().getDomain(), true, MapOfActions::getInstance().getDescription("position"));
+  cout << "pre-dialog" << endl;
 
   if(dialog->display()) {
+    cout << "post-dialog" << endl;
     delete dialog;
-    atom * first = World::getInstance().createAtom();
-    first->type = World::getInstance().getPeriode()->FindElement(Z);
-    first->x = position;
-    if (first->type != NULL) {
+    if (elements.size() == 1) {
+      atom * first = World::getInstance().createAtom();
+      first->type = *(elements.begin());
+      first->x = position;
       DoLog(1) && (Log() << Verbose(1) << "Adding new atom with element " << first->type->name << " at " << (first->x) << "." << endl);
+      // TODO: remove when all of World's atoms are stored.
+      std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+      if (!molecules.empty()) {
+        std::vector<molecule *>::iterator iter = molecules.begin();
+        (*iter)->AddAtom(first);
+      }
       return Action::success;
     } else {
       DoeLog(1) && (eLog()<< Verbose(1) << "Could not find the specified element." << endl);
-      World::getInstance().destroyAtom(first);
       return Action::failure;
     }

src/Actions/MapOfActions.cpp

@@ -164 +164 @@
 
   // value types for the actions
-  TypeMap["add-atom"] = Atom;
+  TypeMap["add-atom"] = Element;
   TypeMap["bond-file"] = String;
   TypeMap["bond-table"] = String;
@@ -210 +210 @@
   TypeMap["distances"] = Vector;
   TypeMap["DoRotate"] = Boolean;
-  TypeMap["elements"] = Element;
+  TypeMap["element"] = Element;
   TypeMap["elements"] = ListOfElements;
   TypeMap["length"] = Double;
@@ -230 +230 @@
 
   // list of generic actions
-//      generic.insert("add-atom");
+        generic.insert("add-atom");
 //  generic.insert("bond-file");
         generic.insert("bond-table");
@@ -434 +434 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  DefaultValue.find(*OptionRunner) != DefaultValue.end() ?
-                        po::value< int >()->default_value(atoi(DefaultValue[*OptionRunner].c_str())) :
-                        po::value< int >(),
+                  po::value< vector<int> >(),
                   getDescription(*OptionRunner).c_str())
               ;

src/builder.cpp

@@ -1681 +1681 @@
             case 'a':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3]))) {
+              if ((argptr+4 >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for adding atom: -a <element> <x> <y> <z>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough arguments for adding atom: -a <Z> --position <x> <y> <z>" << endl);
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                Log() << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ";
-                first = World::getInstance().createAtom();
-                first->type = periode->FindElement(atoi(argv[argptr]));
-                if (first->type != NULL)
-                  DoLog(2) && (Log() << Verbose(2) << "found element " << first->type->name << endl);
-                for (int i=NDIM;i--;)
-                  first->x[i] = atof(argv[argptr+1+i]);
-                if (first->type != NULL) {
-                  mol->AddAtom(first);  // add to molecule
-                  if ((configPresent == empty) && (mol->getAtomCount() != 0))
-                    configPresent = present;
-                } else
-                  DoeLog(1) && (eLog()<< Verbose(1) << "Could not find the specified element." << endl);
-                argptr+=4;
+                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;
@@ -1738 +1730 @@
                 bool periodic = (argv[argptr-1][2] =='p');
                 if (ExitFlag == 0) ExitFlag = 1;
-                if ((argptr >= argc)) {
+                if ((argptr+11 >= argc)) {
                   ExitFlag = 255;
                   DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C[p] <type: E/P/S> [more params] <output> <bin output> <BinStart> <BinEnd>" << endl);