Changeset e30ce8 for src/builder.cpp

Timestamp:

Jun 2, 2010, 4:17:17 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:

3610bb

Parents:

584a2a

git-author:

Frederik Heber <heber@…> (06/02/10 15:41:52)

git-committer:

Frederik Heber <heber@…> (06/02/10 16:17:17)

Message:

Case 'd' is now handled by CommandLineUI (RepeatBoxAction).

• rewritten the RepeatBoxAction quite a bit by allowing to build (x,y,z) matrices out of single molecules.
• implemented bew MoleculePtrDescriptor, which accepts the pointer to a molecule (so far, CommandLineQuery is as of yet lacking maybes/default values).

Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (1 diff)

src/builder.cpp

@@ -2354 +2354 @@
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                double * const cell_size = World::getInstance().getDomain();
-                for (int axis = 1; axis <= NDIM; axis++) {
-                  int faktor = atoi(argv[argptr++]);
-                  int count;
-                  const element ** Elements;
-                  Vector ** vectors;
-                  if (faktor < 1) {
-                    DoeLog(1) && (eLog()<< Verbose(1) << "Repetition factor mus be greater than 1!" << endl);
-                    faktor = 1;
-                  }
-                  if (mol->getAtomCount() != 0) {  // if there is more than none
-                    count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
-                    Elements = new const element *[count];
-                    vectors = new Vector *[count];
-                    j = 0;
-                    for(molecule::iterator iter = mol->begin();iter!=mol->end();++iter){
-                      Elements[j] = (*iter)->type;
-                      vectors[j] = &(*iter)->x;
-                      j++;
-                    }
-                    if (count != j)
-                      DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
-                    x.Zero();
-                    y.Zero();
-                    y[abs(axis)-1] = cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
-                    for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
-                      x += y; // per factor one cell width further
-                      for (int k=count;k--;) { // go through every atom of the original cell
-                        first = World::getInstance().createAtom(); // create a new body
-                        first->x = (*vectors[k]) + x;
-                        first->type = Elements[k];  // insert original element
-                        mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
-                      }
-                    }
-                    // free memory
-                    delete[](Elements);
-                    delete[](vectors);
-                    // correct cell size
-                    if (axis < 0) { // if sign was negative, we have to translate everything
-                      x =(-(faktor-1)) * y;
-                      mol->Translate(&x);
-                    }
-                    cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
-                  }
-                }
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                argptr+=3;
               }
               break;