Changeset 4d4d33 for src/Parser/TremoloParser.cpp

Timestamp:

Feb 9, 2011, 5:25:13 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:

acd638

Parents:

1a6bda

git-author:

Frederik Heber <heber@…> (02/09/11 16:18:50)

git-committer:

Frederik Heber <heber@…> (02/09/11 17:25:13)

Message:

Added tremolo's potential file parsing, reported by Daniel Dueck.

TremoloParser cannot interpret Type with HLA2 because it lacks mapping of the
value to an element. Hence, ...

• new Action ParseTremoloPotentialsAction.
• TremoloParser::knownTypes new map to contain: HLA2 -> H, ... map.
• TremoloParser::createKnownTypesByIdentity() creates identity mapping.
• TremoloParser::parseKnownTypes() parses potentials file.

File:

• src/Parser/TremoloParser.cpp (modified) (9 diffs)

src/Parser/TremoloParser.cpp

@@ -22 +22 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "TremoloParser.hpp"
@@ -66 +67 @@
   knownKeys["torsion"] = TremoloKey::torsion;
 
+  createKnownTypesByIdentity();
+
   // default behavior: use all possible keys on output
   for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
@@ -72 +75 @@
   // and noKey afterwards(!) such that it is not used in usedFields
   knownKeys[" "] = TremoloKey::noKey; // with this we can detect invalid keys
+
+  // invert knownKeys for debug output
+  for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
+    knownKeyNames.insert( make_pair( iter->second, iter->first) );
+
+  additionalAtomData.clear();
 }
 
@@ -163 +172 @@
   TremoloKey::atomDataKey currentField;
 
+  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
+
   for (it = usedFields.begin(); it != usedFields.end(); it++) {
     currentField = knownKeys[it->substr(0, it->find("="))];
@@ -168 +179 @@
       case TremoloKey::x :
         // for the moment, assume there are always three dimensions
+        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getPosition() << std::endl);
         *file << currentAtom->at(0) << "\t";
         *file << currentAtom->at(1) << "\t";
@@ -174 +186 @@
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
+        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->AtomicVelocity << std::endl);
         *file << currentAtom->AtomicVelocity[0] << "\t";
         *file << currentAtom->AtomicVelocity[1] << "\t";
@@ -179 +192 @@
         break;
       case TremoloKey::Type :
-        *file << currentAtom->getType()->getSymbol() << "\t";
+        if ((!additionalAtomData.count(currentAtom->getId())) || (additionalAtomData[currentAtom->getId()].get(currentField) == "-")) {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
+          *file << currentAtom->getType()->getSymbol() << "\t";
+        } else {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
+          *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
+        }
         break;
       case TremoloKey::Id :
+        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1 << std::endl);
         *file << currentAtom->getId()+1 << "\t";
         break;
       case TremoloKey::neighbors :
+        DoLog(3) && (Log() << Verbose(3) << "Writing type " << knownKeyNames[currentField] << std::endl);
         writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
         break;
       case TremoloKey::resSeq :
-        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+        if (additionalAtomData.count(currentAtom->getId())) {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
           *file << additionalAtomData[currentAtom->getId()].get(currentField);
         } else if (currentAtom->getMolecule() != NULL) {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its own id: " << currentAtom->getMolecule()->getId()+1 << std::endl);
           *file << setw(4) << currentAtom->getMolecule()->getId()+1;
         } else {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << defaultAdditionalData.get(currentField) << std::endl);
           *file << defaultAdditionalData.get(currentField);
         }
         *file << "\t";
-      break;
+        break;
       default :
-        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+        if (additionalAtomData.count(currentAtom->getId())) {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
           *file << additionalAtomData[currentAtom->getId()].get(currentField);
-        } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
+        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
           *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
         } else {
+          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " the default: " << defaultAdditionalData.get(currentField) << std::endl);
           *file << defaultAdditionalData.get(currentField);
         }
@@ -306 +333 @@
         break;
       case TremoloKey::Type :
-        char type[3];
+      {
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
-        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
-        strncpy(type, (*tok_iter).c_str(), 3);
+        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+        std::string element(knownTypes[(*tok_iter)]);
+        // put type name into container for later use
+        atomInfo->set(currentField, *tok_iter);
+        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
         tok_iter++;
-        //type[1]='\0'; // cutoff after first char, correct for ATOM entries
-        newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
+        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
         ASSERT(newAtom->getType(), "Type was not set for this atom");
         break;
+      }
       case TremoloKey::Id :
         ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
@@ -476 +506 @@
 }
 
+/** Creates knownTypes as the identity, e.g. H -> H, He -> He, ... .
+ *
+ */
+void TremoloParser::createKnownTypesByIdentity()
+{
+  // remove old mapping
+  knownTypes.clear();
+  // make knownTypes the identity mapping
+  const periodentafel *periode = World::getInstance().getPeriode();
+  for (periodentafel::const_iterator iter = periode->begin();
+      iter != periode->end();
+      ++iter) {
+    knownTypes.insert( make_pair(iter->second->getSymbol(), iter->second->getSymbol()) );
+  }
+}
+
+/** Parses a .potentials file and creates from it the knownTypes file.
+ *
+ * @param file input stream of .potentials file
+ */
+void TremoloParser::parseKnownTypes(std::istream &file)
+{
+  const periodentafel *periode = World::getInstance().getPeriode();
+  // remove old mapping
+  knownTypes.clear();
+
+  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
+
+  // parse in file
+  typedef boost::tokenizer<boost::char_separator<char> >
+      tokenizer;
+  boost::char_separator<char> tokensep(":\t ,;");
+  boost::char_separator<char> equalitysep("\t =");
+  std::string line;
+  while (file.good()) {
+    std::getline( file, line );
+    DoLog(4) && (Log() << Verbose(4) << "INFO: full line of parameters is '" << line << "'" << std::endl);
+    if (line.find("particle:") != string::npos) {
+      DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle:'." << std::endl);
+      tokenizer tokens(line, tokensep);
+      ASSERT(tokens.begin() != tokens.end(),
+          "TremoloParser::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
+      // look for particle_type
+      std::string particle_type("NULL");
+      std::string element_type("NULL");
+      for (tokenizer::iterator tok_iter = tokens.begin();
+          tok_iter != tokens.end();
+          ++tok_iter) {
+        if ((*tok_iter).find("particle_type") != string::npos) {
+          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle_type'." << std::endl);
+          tokenizer token((*tok_iter), equalitysep);
+          ASSERT(token.begin() != token.end(),
+                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
+          tokenizer::iterator particle_iter = token.begin();
+          particle_iter++;
+          particle_type = *particle_iter;
+        }
+        if ((*tok_iter).find("element_name") != string::npos) {
+          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'element_name'." << std::endl);
+          tokenizer token((*tok_iter), equalitysep);
+          ASSERT(token.begin() != token.end(),
+                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
+          tokenizer::iterator element_iter = token.begin();
+          element_iter++;
+          element_type = *element_iter;
+        }
+      }
+      if ((particle_type != "NULL") && (element_type != "NULL")) {
+        if (periode->FindElement(element_type) != NULL) {
+          DoLog(1) && (Log() << Verbose(1) << "INFO: Added Type " << particle_type << " as reference to element " << element_type << "." << std::endl);
+          knownTypes.insert( make_pair (particle_type, element_type) );
+        } else {
+          DoeLog(1) && (Log() << Verbose(1) << "INFO: Either Type " << particle_type << " or " << element_type << " could not be recognized." << std::endl);
+        }
+      } else {
+        DoeLog(1) && (Log() << Verbose(1) << "INFO: Desired element " << element_type << " is not known." << std::endl);
+      }
+    }
+  }
+
+}