Changeset f10b0c for src/Actions/AtomAction

Timestamp:

Jun 11, 2012, 9:53:19 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:

95f965

Parents:

b9c69d

git-author:

Michael Ankele <ankele@…> (04/24/12 13:55:16)

git-committer:

Frederik Heber <heber@…> (06/11/12 09:53:19)

Message:

disastrously big and ugly commit

• using new Parameter<T> classes:
  • Actions
  • Queries (all UIs)

• TODO:
  • actions crash cause Value is unset
  • no query<BoxVector>

Location:

src/Actions/AtomAction

Files:

• AddAction.cpp (modified) (2 diffs)
• AddAction.def (modified) (2 diffs)
• ChangeElementAction.cpp (modified) (2 diffs)
• RotateAroundOriginByAngleAction.cpp (modified) (3 diffs)
• SaveSelectedAtomsAction.cpp (modified) (2 diffs)
• TranslateAction.cpp (modified) (3 diffs)

src/Actions/AtomAction/AddAction.cpp

@@ -43 +43 @@
   // execute action
   atom * first = World::getInstance().createAtom();
-  first->setType(params.elemental);
-  first->setPosition(params.position);
+  first->setType(params.elemental.get());
+  first->setPosition(params.position.get());
   LOG(1, "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << ".");
   // TODO: remove when all of World's atoms are stored.
@@ -68 +68 @@
 
   atom * first = World::getInstance().createAtom();
-  first->setType(state->params.elemental);
-  first->setPosition(state->params.position);
-  LOG(1, "Re-adding new atom with element " << state->params.elemental->getName() << " at " << state->params.position << ".");
+  first->setType(state->params.elemental.get());
+  first->setPosition(state->params.position.get());
+  LOG(1, "Re-adding new atom with element " << state->params.elemental.get()->getName() << " at " << state->params.position.get() << ".");
   // TODO: remove when all of World's atoms are stored.
   std::vector<molecule *> molecules = World::getInstance().getAllMolecules();

src/Actions/AtomAction/AddAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-#include "LinearAlgebra/BoxVector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
 class element;
@@ -14 +14 @@
 // 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 (const element *)(BoxVector)
+//#define paramtypes (const element *)(BoxVector) TODO: use a validator
+#define paramtypes (const element *)(Vector)
 #define paramtokens ("add-atom")("domain-position")
 #define paramdescriptions ("element of new atom")("position within current domain")

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -54 +54 @@
   for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
     first = iter->second;
-    LOG(1, "Changing atom " << *first << " to element " << *params.elemental << ".");
+    LOG(1, "Changing atom " << *first << " to element " << *params.elemental.get() << ".");
     mol = first->getMolecule();
     first->removeFromMolecule(); // remove atom
-    first->setType(params.elemental);
+    first->setType(params.elemental.get());
     mol->AddAtom(first);  // add atom to ensure correctness of formula
   }
@@ -88 +88 @@
     mol = first->getMolecule();
     first->removeFromMolecule(); // remove atom
-    first->setType(state->params.elemental);
+    first->setType(state->params.elemental.get());
     mol->AddAtom(first);  // add atom to ensure correctness of formula
   }

src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp

@@ -44 +44 @@
 
   // check whether Axis is valid
-  if (params.Axis.IsZero())
+  if (params.Axis.get().IsZero())
     return Action::failure;
 
   // convert from degrees to radian
-  params.angle *= M_PI/180.;
+  params.angle.set(params.angle.get() * M_PI/180.);
 
   // Creation Line that is the rotation axis
-  Line RotationAxis(Vector(0.,0.,0.), params.Axis);
+  Line RotationAxis(Vector(0.,0.,0.), params.Axis.get());
 
-  LOG(0, "Rotate around origin by " << params.angle << " radian, axis from origin to " << params.Axis << ".");
+  LOG(0, "Rotate around origin by " << params.angle.get() << " radian, axis from origin to " << params.Axis.get() << ".");
   // TODO: use AtomSet::rotate?
   for (std::vector<atom *>::iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter) {
-    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), params.angle));
+    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), params.angle.get()));
   }
   LOG(0, "done.");
@@ -66 +66 @@
 
   // Creation Line that is the rotation axis
-  Line RotationAxis(Vector(0.,0.,0.), state->params.Axis);
+  Line RotationAxis(Vector(0.,0.,0.), state->params.Axis.get());
 
   for (std::vector<atom *>::iterator iter = state->selectedAtoms.begin(); iter != state->selectedAtoms.end(); ++iter) {
-    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), -state->params.angle));
+    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), -state->params.angle.get()));
   }
 
@@ -79 +79 @@
 
   // Creation Line that is the rotation axis
-  Line RotationAxis(Vector(0.,0.,0.), state->params.Axis);
+  Line RotationAxis(Vector(0.,0.,0.), state->params.Axis.get());
 
   for (std::vector<atom *>::iterator iter = state->selectedAtoms.begin(); iter != state->selectedAtoms.end(); ++iter) {
-    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), state->params.angle));
+    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), state->params.angle.get()));
   }
 

src/Actions/AtomAction/SaveSelectedAtomsAction.cpp

@@ -38 +38 @@
 /** =========== define the function ====================== */
 Action::state_ptr AtomSaveSelectedAtomsAction::performCall() {
-  LOG(1, "Storing selected atoms to file " << params.filename << ".");
+  LOG(1, "Storing selected atoms to file " << params.filename.get() << ".");
 
   // extract suffix
   std::string FilenameSuffix;
   std::string FilenamePrefix;
-  if (params.filename.has_filename()) {
+  if (params.filename.get().has_filename()) {
     // get suffix
 #if BOOST_VERSION >= 104600
-      FilenameSuffix = params.filename.extension().string().substr(1); // remove the prefixed "."
-      FilenamePrefix = params.filename.stem().string();
+      FilenameSuffix = params.filename.get().extension().string().substr(1); // remove the prefixed "."
+      FilenamePrefix = params.filename.get().stem().string();
 #else
-      FilenameSuffix = params.filename.extension().substr(1); // remove the prefixed "."
-      FilenamePrefix = params.filename.stem();
+      FilenameSuffix = params.filename.get().extension().substr(1); // remove the prefixed "."
+      FilenamePrefix = params.filename.get().stem();
 #endif
   } else {
@@ -60 +60 @@
   // parse the file
   boost::filesystem::ofstream output;
-  output.open(params.filename);
+  output.open(params.filename.get());
   if (!output.fail()) {
     FormatParserStorage::getInstance().saveSelectedAtoms(output, FilenameSuffix);
   } else {
-    ELOG(1, "Could not open file " << params.filename << ".");
+    ELOG(1, "Could not open file " << params.filename.get() << ".");
   }
   output.close();

src/Actions/AtomAction/TranslateAction.cpp

@@ -44 +44 @@
   // TODO: use AtomSet::translate
   for (std::vector<atom *>::iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter) {
-    *(*iter) += params.x;
-    if (params.periodic)
+    *(*iter) += params.x.get();
+    if (params.periodic.get())
       (*iter)->setPosition(domain.enforceBoundaryConditions((*iter)->getPosition()));
   }
@@ -57 +57 @@
 
   for (std::vector<atom *>::iterator iter = state->selectedAtoms.begin(); iter != state->selectedAtoms.end(); ++iter) {
-    *(*iter) -= state->params.x;
-    if (state->params.periodic)
+    *(*iter) -= state->params.x.get();
+    if (state->params.periodic.get())
       (*iter)->setPosition(domain.enforceBoundaryConditions((*iter)->getPosition()));
   }
@@ -70 +70 @@
 
   for (std::vector<atom *>::iterator iter = state->selectedAtoms.begin(); iter != state->selectedAtoms.end(); ++iter) {
-    *(*iter) += state->params.x;
-    if (state->params.periodic)
+    *(*iter) += state->params.x.get();
+    if (state->params.periodic.get())
       (*iter)->setPosition(domain.enforceBoundaryConditions((*iter)->getPosition()));
   }