Changeset 4e855e for src/Actions

Timestamp:

Feb 4, 2011, 6:56:38 PM (14 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:

febef3

Parents:

fd3788

git-author:

Frederik Heber <heber@…> (02/04/11 18:54:12)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

BondGraph::LoadBondLengthTable() now accepts istream instead of const char *.

• This has been quite a lot of work because the matrix parsing is involved.
• Hence, the fix is not really clean, this should get fixed as soon as we deal with the BondGraph implementation.
• This fixes ticket #130.

Location:

src/Actions

Files:

• CommandAction/BondLengthTableAction.cpp (modified) (2 diffs)
• CommandAction/BondLengthTableAction.def (modified) (2 diffs)
• FragmentationAction/DepthFirstSearchAction.cpp (modified) (1 diff)

src/Actions/CommandAction/BondLengthTableAction.cpp

@@ -45 +45 @@
   DoLog(0) && (Log() << Verbose(0) << "Using " << params.BondGraphFileName << " as bond length table." << endl);
   config *configuration = World::getInstance().getConfig();
-  if (configuration->BG == NULL) {
-    configuration->BG = new BondGraph(configuration->GetIsAngstroem());
-    if ((!params.BondGraphFileName.empty())
-        && boost::filesystem::exists(params.BondGraphFileName)
-        && (configuration->BG->LoadBondLengthTable(params.BondGraphFileName.string()))) {
-      DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
-      return Action::success;
+  BondGraph *OldBG;
+  if (configuration->BG != NULL) {
+    OldBG = configuration->BG;
+    DoLog(0) && (Log() << Verbose(0) << "There is a bond length table already present." << endl);
+  }
+  configuration->BG = new BondGraph(configuration->GetIsAngstroem());
+  if ((!params.BondGraphFileName.empty())
+      && boost::filesystem::exists(params.BondGraphFileName)) {
+    std::ifstream input(params.BondGraphFileName.string().c_str());
+    if ((input.good()) && (configuration->BG->LoadBondLengthTable(input))) {
+      DoLog(0) && (Log() << Verbose(0) << "Bond length table parsed successfully." << endl);
+      input.close();
+      return Action::state_ptr(new CommandBondLengthTableState(*OldBG, params));
     } else {
-      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
+      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table parsing failed." << endl);
+      input.close();
+      configuration->BG = new BondGraph(*OldBG);
       return Action::failure;
     }
   } else {
-    DoLog(0) && (Log() << Verbose(0) << "Bond length table already present." << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
+    configuration->BG = new BondGraph(*OldBG);
     return Action::failure;
   }
@@ -63 +72 @@
 
 Action::state_ptr CommandBondLengthTableAction::performUndo(Action::state_ptr _state) {
-//  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
+  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
 
-  return Action::failure;
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
-//
-//  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
+  config *configuration = World::getInstance().getConfig();
+  BondGraph *OldBG = new BondGraph(*configuration->BG);
+  configuration->BG = new BondGraph(state->OldBG);
+
+  return Action::state_ptr(new CommandBondLengthTableState(*OldBG,params));
 }
 
 Action::state_ptr CommandBondLengthTableAction::performRedo(Action::state_ptr _state){
-  return Action::failure;
+  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
+
+  config *configuration = World::getInstance().getConfig();
+  BondGraph *OldBG = new BondGraph(*configuration->BG);
+  configuration->BG = new BondGraph(state->OldBG);
+
+  return Action::state_ptr(new CommandBondLengthTableState(*OldBG,params));
 }
 

src/Actions/CommandAction/BondLengthTableAction.def

@@ -8 +8 @@
 // all includes and forward declarations necessary for non-integral types below
 
+#include "bondgraph.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -18 +19 @@
 #define paramreferences (BondGraphFileName)
 
-#undef statetypes
-#undef statereferences
+#define statetypes (BondGraph)
+#define statereferences (OldBG)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -52 +52 @@
   std::deque<bond *> *BackEdgeStack = NULL;
   std::deque<bond *> *LocalBackEdgeStack = NULL;
-  mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+  BondGraph *BG = World::getInstance().getConfig()->BG;
+  if (BG != NULL)
+    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::BondLengthMatrixMinMaxDistance, BG);
+  else
+    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, BG);
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   if (Subgraphs != NULL) {