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root/group/branches/new_design/OOPSE-4/src/UseTheForce/DUFF.cpp
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Comparing branches/new_design/OOPSE-4/src/UseTheForce/DUFF.cpp (file contents):
Revision 1758 by tim, Fri Nov 19 17:56:32 2004 UTC vs.
Revision 1762 by tim, Fri Nov 19 21:38:22 2004 UTC

# Line 76 | Line 76 | void DUFF::parse(const std::string& filename) {
76      std::string line;
77      char buffer[bufferSize];
78      int lineNo = 0;
79 +    int atomIdent = getNAtomType() + 1;  //atom's indent begins from 1 (since only fortran's array begins from 1)
80      ParseState currentSection = DUFF::UnknownSection;
81      
82      while(ffStream.getline(buffer, bufferSize)){
# Line 89 | Line 90 | void DUFF::parse(const std::string& filename) {
90  
91              switch(currentSection) {
92                  case DUFF::AtomTypeSection :
93 <                    parseAtomType(line, lineNo);
93 >                    parseAtomType(line, lineNo, atomIdent);
94                      break;
95  
96 +                case DUFF::DirectionalAtomTypeSection :
97 +                    parseDirectionalAtomType(line, lineNo);
98 +                    break;
99 +                    
100                  case DUFF::BondTypeSection :
101                      parseBondType(line, lineNo);
102                      break;
# Line 141 | Line 146 | void DUFF::parse(const std::string& filename) {
146      delete ffStream;
147   }
148  
144 –
149   void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
150      StringTokenizer tokenizer(line);
151      int nTokens = tokenizer.countTokens();    
# Line 149 | Line 153 | void DUFF::parseAtomType(const std::string& line, int
153      //in AtomTypeSection, a line at least contains 5 tokens
154      //atomTypeName, is Directional, isLJ, isCharge and mass
155      if (nTokens < 5)  {
156 <        sprintf( painCave.errMsg,
153 <               "Not enough tokens when parsing DUFF Force Field : %s\n"
154 <               "in line %d : %s\n",
155 <               filename.c_str(), lineNo, line);
156 <        painCave.severity = OOPSE_ERROR;
157 <        painCave.isFatal = 1;
158 <        simError();                
159 <
160 <        
156 >                      
157      } else {
158  
159          std::string atomTypeName = tokenizer.nextToken();
# Line 201 | Line 197 | void DUFF::parseAtomType(const std::string& line, int
197          atomType->setName(atomTypeName);
198          atomType->setMass(mass);
199          
200 <        //by default, all of the properties in AtomTypeProperties is set to 0
201 <        //In  Lennard-Jones Force Field, we only need to set Lennard-Jones to true
202 <        atomType->setLennardJones();
200 >        if (isLJ) {
201 >            atomType->setLennardJones();
202 >        }
203  
204 +        if (isCharge) {
205 +            atomType->setCharge();
206 +        }
207 +        
208          atomType->setIdent(ident);
209          
210          atomType->complete();
# Line 264 | Line 264 | void DUFF::parseDirectionalAtomType(const std::string&
264  
265          }
266  
267 <        dAtomType->setDipole(isDipole);
268 <        dAtomType->setSticky(isSticky);
267 >        if (isDipole) {
268 >            dAtomType->setDipole();
269 >        }
270  
271 +        if (isSticky) {
272 +            dAtomType->setSticky();
273 +        }
274 +        
275          Mat3x3d inertialMat;
276          inertialMat(0, 0) = Ixx;
277          inertialMat(1, 1) = Ixx;

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