Changeset e30ce8 for src/Actions/WorldAction

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/Actions/WorldAction/RepeatBoxAction.cpp (modified) (3 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -23 +23 @@
 #include "UIElements/Dialog.hpp"
 #include "Actions/MapOfActions.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
+#include "Descriptors/MoleculePtrDescriptor.hpp"
 
 const char WorldRepeatBoxAction::NAME[] = "repeat-box";
@@ -41 +43 @@
   int j = 0;
   atom *Walker = NULL;
+  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
   dialog->queryVector(NAME, &Repeater, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryMolecule("molecule-by-id", &mol,MapOfActions::getInstance().getDescription("molecule-by-id"));
+  //dialog->queryMolecule("molecule-by-id", &mol,MapOfActions::getInstance().getDescription("molecule-by-id"));
+  vector<molecule *> AllMolecules;
+  if (mol != NULL) {
+    DoLog(0) && (Log() << Verbose(0) << "Using molecule " << mol->name << "." << endl);
+    AllMolecules = World::getInstance().getAllMolecules(MoleculeByPtr(mol));
+  } else {
+    DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
+    AllMolecules = World::getInstance().getAllMolecules();
+  }
 
   if(dialog->display()) {
+    (cout << "Repeating box " << Repeater << " times for (x,y,z) axis." << endl);
     double * const cell_size = World::getInstance().getDomain();
+    double *M = ReturnFullMatrixforSymmetric(cell_size);
     Vector x,y;
-    for (int axis = 1; axis <= NDIM; axis++) {
-      Vector ** vectors;
+    int n[NDIM];
+    for (int axis = 0; axis < NDIM; axis++) {
       Repeater[axis] = floor(Repeater[axis]);
       if (Repeater[axis] < 1) {
@@ -55 +68 @@
         Repeater[axis] = 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 AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
-          Elements[j] = (*AtomRunner)->type;
-          vectors[j] = &(*AtomRunner)->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<Repeater[axis];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
-            Walker = World::getInstance().createAtom(); // create a new body
-            Walker->x = (*vectors[k]) + x;
-            Walker->type = Elements[k];  // insert original element
-            mol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
+      cell_size[(abs(axis+1) == 2) ? 2 : ((abs(axis+2) == 3) ? 5 : 0)] *= Repeater[axis];
+    }
+
+    molecule *newmol = NULL;
+    Vector ** vectors = NULL;
+    for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
+      y[0] = n[0];
+      for (n[1] = 0; n[1] < Repeater[1]; n[1]++) {
+        y[1] = n[1];
+        for (n[2] = 0; n[2] < Repeater[2]; n[2]++) {
+          y[2] = n[2];
+          if (n[0] == n[1] == n[2] == 0)
+            continue;
+          for (vector<molecule *>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
+            mol = *MolRunner;
+            DoLog(1) && (Log() << Verbose(1) << "Current mol is " << mol->name << "." << endl);
+            count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
+            if (count != 0) {  // if there is more than none
+              Elements = new const element *[count];
+              vectors = new Vector *[count];
+              j = 0;
+              for(molecule::iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
+                Elements[j] = (*AtomRunner)->type;
+                vectors[j] = &(*AtomRunner)->x;
+                j++;
+              }
+              if (count != j)
+                DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
+              x = y;
+              x.MatrixMultiplication(M);
+              newmol = World::getInstance().createMolecule();
+              molecules->insert(newmol);
+              for (int k=count;k--;) { // go through every atom of the original cell
+                Walker = World::getInstance().createAtom(); // create a new body
+                Walker->x = (*vectors[k]) + x;
+                Walker->type = Elements[k];  // insert original element
+                cout << "new atom is " << *Walker << endl;
+                newmol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
+              }
+              // free memory
+              delete[](Elements);
+              delete[](vectors);
+            } else {
+              DoLog(1) && (Log() << Verbose(1) << "\t ... is empty." << endl);
+            }
           }
         }
-        // free memory
-        delete[](Elements);
-        delete[](vectors);
-        // correct cell size
-        if (axis < 0) { // if sign was negative, we have to translate everything
-          x =(-(Repeater[axis]-1)) * y;
-          mol->Translate(&x);
-        }
-        cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= Repeater[axis];
       }
     }
+    delete(M);
     delete dialog;
     return Action::success;