Changeset 8b58ac for src

Timestamp:

Nov 16, 2012, 2:03:40 PM (12 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:

a67a04

Parents:

fb69e9

git-author:

Frederik Heber <heber@…> (11/16/12 14:01:22)

git-committer:

Frederik Heber <heber@…> (11/16/12 14:03:40)

Message:

KeySetsContainer::ParseKeySets() may now parse arbitrary files.

• ParseKeySets() can now be given filename to parse, also ACounter is no longer required.
• changed joiner, analyzer, FragmentationAutomationAction and controller_MPQCCommandJob due to changed signature.
• FIX: KeySetsContainer would not correctly parse keys but often one too many.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (4 diffs)
• Fragmentation/KeySetsContainer.cpp (modified) (3 diffs)
• Fragmentation/KeySetsContainer.hpp (modified) (1 diff)
• Fragmentation/analyzer.cpp (modified) (1 diff)
• Fragmentation/joiner.cpp (modified) (1 diff)
• controller_MPQCCommandJob.cpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -38 +38 @@
 
 #include "CodePatterns/MemDebug.hpp"
-
-#include <boost/assign.hpp>
 
 #include "CodePatterns/Assert.hpp"
@@ -60 +58 @@
 #include "Fragmentation/Summation/printSum.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
+#include "Helpers/defs.hpp"
 #include "Jobs/MPQCJob.hpp"
 #include "Jobs/MPQCData.hpp"
@@ -79 +78 @@
 
 using namespace MoleCuilder;
-
-using namespace boost::assign;
 
 // and construct the stuff
@@ -282 +279 @@
   // initialise indices
   KeySetsContainer KeySet;
+  KeySetsContainer ForceKeySet;
   if (!Energy.InitialiseIndices()) return false;
 
   if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
 
-  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
-
-  /// prepare for OrthogonalSummation
+  {
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << KEYSETFILE;
+    if (!KeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter)) return false;
+  }
+
+  {
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << FORCESFILE;
+    if (!ForceKeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter)) return false;
+  }
 
   // forces need different keysets: they must include hydrogen

src/Fragmentation/KeySetsContainer.cpp

@@ -37 +37 @@
 #include <fstream>
 #include <sstream>
+
+#include <boost/lexical_cast.hpp>
+#include <boost/tokenizer.hpp>
 
 #include "CodePatterns/Log.hpp"
@@ -72 +75 @@
  * \return parsing succesful
  */
-bool KeySetsContainer::ParseKeySets(const std::string name, const IntVector ACounter, const int FCounter) {
+bool KeySetsContainer::ParseKeySets(const std::string path, const std::string name, const int FCounter) {
   ifstream input;
-  char *FragmentNumber = NULL;
+  //char *FragmentNumber = NULL;
   stringstream file;
   char filename[1023];
 
   FragmentCounter = FCounter;
-  LOG(0, "Parsing key sets.");
   KeySets.resize(FragmentCounter);
-  file << name << FRAGMENTPREFIX << KEYSETFILE;
+  AtomCounter.resize(FragmentCounter);
+
+  // open file
+  file << path << "/" << name;
   input.open(file.str().c_str(), ios::in);
   if (input.fail()) {
@@ -88 +93 @@
   }
 
-  AtomCounter.resize(FragmentCounter);
+  // parse each line, i.e. get the index set per fragment
+  LOG(0, "Parsing key sets.");
   for(int i=0;(i<FragmentCounter) && (!input.eof());i++) {
-    stringstream line;
-    AtomCounter[i] = ACounter[i];
-    // parse the values
-    KeySets[i].resize(AtomCounter[i]);
-    for(int j=AtomCounter[i];j--;)
-      KeySets[i][j] = -1;
-    FragmentNumber = FixedDigitNumber(FragmentCounter, i);
-    //std::stringstream output;
-    //output << FRAGMENTPREFIX << FragmentNumber << "[" << AtomCounter[i] << "]:";
-    delete[](FragmentNumber);
     input.getline(filename, 1023);
-    line.str(filename);
-    for(int j=0;(j<AtomCounter[i]) && (!line.eof());j++) {
-      line >> KeySets[i][j];
-      //output << " " << KeySets[i][j];
+    string line(filename);
+//    LOG(2, "DEBUG: line is " << line << ".");
+    std::stringstream set_output;
+    typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
+    boost::char_separator<char> sep(" \t");
+    tokenizer tok(line, sep);
+    for(tokenizer::iterator beg=tok.begin();
+        beg != tok.end();++beg){
+      const int tempvalue = boost::lexical_cast<int>(*beg);
+      KeySets[i].push_back(tempvalue);
+//      set_output << " " << KeySets[i].back();
     }
-    //LOG(0, output.str());
+//    LOG(2, "DEBUG: Scanned keys are '" << set_output.str() << "'.");
+    AtomCounter[i] = KeySets[i].size();
+//    {
+//      std::stringstream output;
+//      FragmentNumber = FixedDigitNumber(FragmentCounter, i);
+//      output << FRAGMENTPREFIX << FragmentNumber << "[" << AtomCounter[i] << "]:" << set_output.str();
+//      delete[](FragmentNumber);
+//      LOG(0, output.str());
+//    }
   }
   input.close();

src/Fragmentation/KeySetsContainer.hpp

@@ -35 +35 @@
   ~KeySetsContainer();
 
-  bool ParseKeySets(const std::string name, const std::vector<int> ACounter, const int FCounter);
+  bool ParseKeySets(const std::string path, const std::string name, const int FCounter);
   bool ParseManyBodyTerms();
   bool Contains(const int GreaterSet, const int SmallerSet);

src/Fragmentation/analyzer.cpp

@@ -182 +182 @@
 
   // ---------- Parse the KeySets into an array ---------------
-  if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
+  {
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << KEYSETFILE;
+    if (!KeySet.ParseKeySets(argv[1], filename.str(), Force.MatrixCounter)) return 1;
+  }
   if (!KeySet.ParseManyBodyTerms()) return 1;
 

src/Fragmentation/joiner.cpp

@@ -147 +147 @@
 
   // ---------- Parse the KeySets into an array ---------------
-  if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
+  {
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << KEYSETFILE;
+    if (!KeySet.ParseKeySets(argv[1], filename.str(), Force.MatrixCounter)) return 1;
+  }
 
   if (!KeySet.ParseManyBodyTerms()) return 1;

src/controller_MPQCCommandJob.cpp

@@ -217 +217 @@
   if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
 
-  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
+  {
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << KEYSETFILE;
+    if (!KeySet.ParseKeySets(KeySetFilename.c_str(), filename.str(), Force.MatrixCounter)) return 1;
+  }
 
   if (!KeySet.ParseManyBodyTerms()) return false;