Changeset cb7676 for src

Timestamp:

Apr 6, 2012, 11:44:09 AM (13 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:

4187a7

Parents:

93eae36

git-author:

Frederik Heber <heber@…> (04/04/12 11:16:14)

git-committer:

Frederik Heber <heber@…> (04/06/12 11:44:09)

Message:

FillSphericalSurface now works on selected molecule and requires an alignment axis.

• the axis is used to perform the rotation assuming the filler molecule is oriented on this direction.
• also, it now uses CopyAtoms_withBonds.

Location:

src/Actions/FillAction

Files:

• FillSphericalSurfaceAction.cpp (modified) (3 diffs)
• FillSphericalSurfaceAction.def (modified) (2 diffs)

src/Actions/FillAction/FillSphericalSurfaceAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Atom/atom.hpp"
-#include "Atom/CopyAtoms/CopyAtoms_Simple.hpp"
+#include "Atom/CopyAtoms/CopyAtoms_withBonds.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Filling/Cluster.hpp"
 #include "Filling/Filler.hpp"
 #include "Filling/Inserter/Inserter.hpp"
-#include "Filling/Inserter/SimpleInserter.hpp"
+#include "Filling/Inserter/SurfaceInserter.hpp"
 #include "Filling/Mesh/MeshAdaptor.hpp"
 #include "Filling/Predicates/IsVoidNode_FillPredicate.hpp"
+#include "molecule.hpp"
 #include "Shapes/BaseShapes.hpp"
 #include "World.hpp"
@@ -49 +49 @@
 /** =========== define the function ====================== */
 Action::state_ptr FillSphericalSurfaceAction::performCall() {
-  typedef std::vector<atom*> AtomVector;
-
   // obtain information
   getParametersfromValueStorage();
 
   // check for selected atoms
-  std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
-  if (atoms.size() == 0) {
-    ELOG(1, "There are no atoms selected.");
+  // get the filler molecule and move to origin
+  const std::vector< molecule *> molecules = World::getInstance().getSelectedMolecules();
+  if (molecules.size() != 1) {
+    ELOG(1, "No exactly one molecule selected, aborting,");
     return Action::failure;
   }
-  AtomIdSet atomIds;
-  BOOST_FOREACH(atom * const _atom, atoms) {
-    atomIds.insert( _atom );
+  molecule *filler = *(molecules.begin());
+  LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
+
+  // center filler's tip at origin
+  Vector max;
+  filler->CenterEdge(&max);
+
+  // determine center with respect to alignment axis
+  Vector sum = zeroVec;
+  for (molecule::iterator it2=filler->begin();it2 !=filler->end();++it2) {
+    const Vector helper = (**it2).getPosition().partition(params.AlignedAxis).second;
+    sum += helper;
+  }
+  sum *= 1./filler->size();
+
+  // translate molecule's closest atom to origin (such that is resides on the filler spot)
+  LOG(1, "DEBUG: molecule is off Alignment axis by " << sum << ", shifting ...");
+  {
+    Vector translater = -1.*sum;
+    filler->Translate(&translater);
   }
 
@@ -78 +94 @@
     Mesh *mesh = new MeshAdaptor(func);
     Inserter *inserter = new Inserter(
-        Inserter::impl_ptr(new SimpleInserter));
+        Inserter::impl_ptr(new SurfaceInserter(s, params.AlignedAxis)));
 
     // fill
     {
       Filler *fillerFunction = new Filler(*mesh, *voidnode_predicate, *inserter);
-      ClusterInterface::Cluster_impl cluster( new Cluster( atomIds.getAtomIds(), Sphere()) ); //TODO: calculate true bounding box of atomIds
-      CopyAtoms_Simple copyMethod;
+      ClusterInterface::Cluster_impl cluster( new Cluster( filler->getAtomIds(), filler->getBoundingShape() ) );
+      CopyAtoms_withBonds copyMethod;
       successflag = (*fillerFunction)(copyMethod, cluster);
       delete fillerFunction;

src/Actions/FillAction/FillSphericalSurfaceAction.def

@@ -9 +9 @@
 class atom;
 
+#include "LinearAlgebra/Vector.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (Vector)(double)(int)(double)
-#define paramtokens ("center")("radius")("count")("min-distance")
-#define paramdescriptions ("center of the sphere")("sphere size")("number of instances to be added, changed according to geometric needs")("minimum distance between added instances")
-#define paramdefaults ("0.,0.,0.")(NODEFAULT)("12")("1.")
-#define paramreferences (center)(radius)(N)(mindistance)
+#define paramtypes (Vector)(double)(int)(double)(Vector)
+#define paramtokens ("center")("radius")("count")("min-distance")("Alignment-Axis")
+#define paramdescriptions ("center of the sphere")("sphere size")("number of instances to be added, changed according to geometric needs")("minimum distance between added instances")("The filler molecule is rotated relative to this alignment axis")
+#define paramdefaults ("0.,0.,0.")(NODEFAULT)("12")("1.")(NODEFAULT)
+#define paramreferences (center)(radius)(N)(mindistance)(AlignedAxis)
 
 #undef statetypes 
@@ -31 +33 @@
 // finally the information stored in the ActionTrait specialization
 #define DESCRIPTION "\
-fill homogenous points on a sphere surface with instances of the selected atoms."
+fill homogenous points on a sphere surface with instances of the selected molecule."
 #undef SHORTFORM