Changes in src/Parser/TremoloParser.cpp [acd638:72d108]

File:

• src/Parser/TremoloParser.cpp (modified) (10 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"
@@ -67 +66 @@
   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)
@@ -75 +72 @@
   // 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();
 }
 
@@ -140 +131 @@
   vector<string>::iterator it;
 
-  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
-
   *file << "# ATOMDATA";
   for (it=usedFields.begin(); it < usedFields.end(); it++) {
@@ -173 +162 @@
   vector<string>::iterator it;
   TremoloKey::atomDataKey currentField;
-
-  DoLog(4) && (Log() << Verbose(4) << "INFO: Saving atom " << *currentAtom << ", its father id is " << currentAtom->GetTrueFather()->getId() << std::endl);
 
   for (it = usedFields.begin(); it != usedFields.end(); it++) {
@@ -181 +168 @@
       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";
@@ -188 +174 @@
       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";
@@ -194 +179 @@
         break;
       case TremoloKey::Type :
-        if (additionalAtomData.count(currentAtom->getId())) {
-          if (additionalAtomData[currentAtom->getId()].get(currentField) != "-") {
-            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
-            *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
-          } else {
-            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
-            *file << currentAtom->getType()->getSymbol() << "\t";
-          }
-        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
-          if (additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) != "-") {
-            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) << "\t";
-          } else {
-            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value from father: " << currentAtom->GetTrueFather()->getType()->getSymbol() << std::endl);
-            *file << currentAtom->GetTrueFather()->getType()->getSymbol() << "\t";
-          }
-        } else {
-          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its default value: " << currentAtom->getType()->getSymbol() << std::endl);
-          *file << currentAtom->getType()->getSymbol() << "\t";
-        }
+        *file << currentAtom->getType()->getSymbol() << "\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.count(currentAtom->getId())) {
-          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
           *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.count(currentAtom->getId())) {
-          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
           *file << additionalAtomData[currentAtom->getId()].get(currentField);
-        } 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);
+        } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
           *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);
         }
@@ -348 +306 @@
         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);
-        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);
+        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
+        strncpy(type, (*tok_iter).c_str(), 3);
         tok_iter++;
-        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
+        //type[1]='\0'; // cutoff after first char, correct for ATOM entries
+        newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
         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+"!");
@@ -521 +476 @@
 }
 
-/** 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);
-      }
-    }
-  }
-
-}