Changeset 3fa16b

Timestamp:

Jun 12, 2015, 1:27:22 PM (10 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:

dbfb03

Parents:

08d042 (diff), 19dfdf (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'GUI_niceties' into Candidate_v1.4.11

Location:

src

Files:

• Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) (3 diffs)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) (1 diff)
• UIElements/Views/Qt4/QtInfoBox.cpp (modified) (3 diffs)
• UIElements/Views/Qt4/QtStatusBar.cpp (modified) (1 diff)

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp

@@ -62 +62 @@
   }
 
+  // check whether Axis is valid
+  if (params.Axis.get().IsZero()) {
+    STATUS("Rotation Axis must not be zero.");
+    return Action::failure;
+  }
+
+  // convert from degrees to radian
+  const double angle_radian = params.angle.get() * M_PI/180.;
+
   // go through all selected molecules
   BOOST_FOREACH(molecule *mol, selectedMolecules) {
-    // check whether Axis is valid
-    if (params.Axis.get().IsZero()) {
-      STATUS("Rotation Axis must not be zero.");
-      return Action::failure;
-    }
-
-    // convert from degrees to radian
-    params.angle.set(params.angle.get() * M_PI/180.);
-
     // Creation Line that is the rotation axis
     const Vector CenterOfGravity = mol->DetermineCenterOfGravity();
-    LOG(0,  "Center of gravity is " << CenterOfGravity << ".");
+    LOG(3, "DEBUG: Center of gravity is " << CenterOfGravity << ".");
     Line RotationAxis(CenterOfGravity, params.Axis.get());
-    LOG(0, "Rotate " << mol->getName() << " around self by " << params.angle.get() << " radian around axis " << RotationAxis << ".");
+    LOG(2, "DEBUG: Rotate " << mol->getName() << " around self by " << angle_radian << " radian around axis " << RotationAxis << ".");
 
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), params.angle.get()));
+      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), angle_radian));
     }
-    LOG(0, "done.");
+    LOG(2, "DEBUG: Rotatating of " << mol->getName() << " done.");
   }
 
@@ -91 +91 @@
   MoleculeRotateAroundSelfByAngleState *state = assert_cast<MoleculeRotateAroundSelfByAngleState*>(_state.get());
 
+  // convert from degrees to radian
+  const double angle_radian = -state->params.angle.get() * M_PI/180.;
+
   BOOST_FOREACH(molecule *mol, state->selectedMolecules) {
     const Vector CenterOfGravity = mol->DetermineCenterOfGravity();
     LOG(0,  "Center of gravity is " <<CenterOfGravity << ".");
     Line RotationAxis(CenterOfGravity, state->params.Axis.get());
-    LOG(0, "Rotate " << mol->getName() << " around self by " << -state->params.angle.get() << " radian around axis " << RotationAxis << ".");
+    LOG(0, "Rotate " << mol->getName() << " around self by " << angle_radian << " radian around axis " << RotationAxis << ".");
 
-    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), -state->params.angle.get()));
-    }
+    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter)
+      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), angle_radian));
   }
 
@@ -108 +110 @@
   MoleculeRotateAroundSelfByAngleState *state = assert_cast<MoleculeRotateAroundSelfByAngleState*>(_state.get());
 
+  // convert from degrees to radian
+  const double angle_radian = state->params.angle.get() * M_PI/180.;
+
   BOOST_FOREACH(molecule *mol, state->selectedMolecules) {
     const Vector CenterOfGravity = mol->DetermineCenterOfGravity();
     LOG(0,  "Center of gravity is " << CenterOfGravity << ".");
     Line RotationAxis(CenterOfGravity, state->params.Axis.get());
-    LOG(0, "Rotate " << mol->getName() << " around self by " << state->params.angle.get() << " radian around axis " << RotationAxis << ".");
+    LOG(0, "Rotate " << mol->getName() << " around self by " << angle_radian << " radian around axis " << RotationAxis << ".");
 
-    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), state->params.angle.get()));
-    }
+    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter)
+      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), angle_radian));
   }
 

src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp

@@ -464 +464 @@
       +" does not have a groupitem?");
   QList<QStandardItem *> mol_row = _molitem->parent()->takeRow(_molitem->index().row());
-  // call setOccurrence on the old group later
-  addToBeSetOccurrence(groupitem);
+  // call setOccurrence on the old group later, if it's not a removal candidate
+  if (groupitem->rowCount() != 0)
+    addToBeSetOccurrence(groupitem);
   // ..  and re-add where new formula fits
   const std::string molecule_formula = _molitem->getMolecule()->getFormula().toString();

src/UIElements/Views/Qt4/QtInfoBox.cpp

@@ -57 +57 @@
 
   setMinimumWidth(200);
-  setMinimumHeight(200);
+  setMinimumHeight(220);
   currentPage = 0;
 
@@ -178 +178 @@
   addInfo(this, "Mass", QString("%1").arg(atomRef->getMass()));
   addInfo(this, "Charge", QString("%1").arg(atomRef->getCharge()));
-  addInfo(this, "Position", QString(toString(atomRef->getPosition()).c_str()));
   addInfo(this, "Bonds", QString("%1").arg(atomRef->getListOfBonds().size()));
+  addInfo(this, "Position x", QString(toString(atomRef->getPosition()[0]).c_str()));
+  addInfo(this, "Position y", QString(toString(atomRef->getPosition()[1]).c_str()));
+  addInfo(this, "Position z", QString(toString(atomRef->getPosition()[2]).c_str()));
 }
 
@@ -218 +220 @@
   addInfo(this, "Formula", QString(mol->getFormula().toString().c_str()));
   addInfo(this, "Atoms", QString("%1").arg(mol->getAtomCount()));
+  addInfo(this, "NonHydrogens", QString("%1").arg(mol->getNoNonHydrogen()));
   addInfo(this, "Bonds", QString("%1").arg(mol->getBondCount()));
+  const Vector molCenter = mol->DetermineCenterOfAll();
+  addInfo(this, "Center x", QString("%1").arg(molCenter[0]));
+  addInfo(this, "Center y", QString("%1").arg(molCenter[1]));
+  addInfo(this, "Center z", QString("%1").arg(molCenter[2]));
 }
 

src/UIElements/Views/Qt4/QtStatusBar.cpp

@@ -65 +65 @@
   StatusList_signedOn(false),
   timer(NULL),
-  timer_interval(1500)
+  timer_interval(4000)
 {
   World::getInstance().signOn(this);