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root/group/trunk/OOPSE/libmdtools/DUFF.cpp
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Comparing trunk/OOPSE/libmdtools/DUFF.cpp (file contents):
Revision 976 by chrisfen, Thu Jan 22 17:34:20 2004 UTC vs.
Revision 1224 by gezelter, Wed Jun 2 18:27:52 2004 UTC

# Line 116 | Line 116 | namespace DUFF_NS {  // restrict the access of the fol
116      void printMe( void ){
117        
118        std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
119 <      if( next != NULL ) next->printMe();
119 >      //      if( next != NULL ) next->printMe();
120  
121      }
122  
# Line 595 | Line 595 | DUFF::DUFF(){
595        if( frcFile == NULL ){
596          
597          sprintf( painCave.errMsg,
598 <                 "Error opening the force field parameter file: %s\n"
599 <                 "Have you tried setting the FORCE_PARAM_PATH environment "
600 <                 "vairable?\n",
598 >                 "Error opening the force field parameter file:\n"
599 >                 "\t%s\n"
600 >                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
601 >                 "variable?\n",
602                   fileName );
603 +        painCave.severity = OOPSE_ERROR;
604          painCave.isFatal = 1;
605          simError();
606        }
# Line 922 | Line 924 | void DUFF::readParams( void ){
924      fastForward( "BendTypes", "initializeBends" );
925  
926      // we are now at the bendTypes section
927 <
927 >    
928      eof_test =  fgets( readLine, sizeof(readLine), frcFile );
929      lineNum++;
930          
# Line 1120 | Line 1122 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1122    // initialize the atoms
1123    
1124    DirectionalAtom* dAtom;
1125 +  double ji[3];
1126  
1127    for(int i=0; i<nAtoms; i++ ){
1128  
# Line 1133 | Line 1136 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1136      }
1137      
1138      the_atoms[i]->setMass( currentAtomType->mass );
1136 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
1137 –    the_atoms[i]->setSigma( currentAtomType->sigma );
1139      the_atoms[i]->setIdent( currentAtomType->ident );
1139 –    the_atoms[i]->setLJ();
1140  
1141      if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
1142  
# Line 1144 | Line 1144 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1144        if( the_atoms[i]->isDirectional() ){
1145          
1146          dAtom = (DirectionalAtom *) the_atoms[i];
1147 –        dAtom->setMu( currentAtomType->dipole );
1147          dAtom->setHasDipole( 1 );
1148 <        dAtom->setJx( 0.0 );
1149 <        dAtom->setJy( 0.0 );
1150 <        dAtom->setJz( 0.0 );
1148 >
1149 >        ji[0] = 0.0;
1150 >        ji[1] = 0.0;
1151 >        ji[2] = 0.0;
1152 >
1153 >        dAtom->setJ( ji );
1154          
1155          if(!strcmp("SSD",the_atoms[i]->getType())){
1156            dAtom->setI( waterI );
1155 –          dAtom->setSSD( 1 );
1157          }
1158          else if(!strcmp("HEAD",the_atoms[i]->getType())){
1159            dAtom->setI( headI );
1159 –          dAtom->setSSD( 0 );
1160          }
1161          else{
1162            sprintf(painCave.errMsg,
# Line 1180 | Line 1180 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1180      else{
1181        if( the_atoms[i]->isDirectional() ){
1182          sprintf( painCave.errMsg,
1183 <                 "DUFF error: Atom \"%s\" was given a standard"
1183 >                 "DUFF error: Atom \"%s\" was given a standard "
1184                   "orientation in the BASS file, yet it is not a dipole.\n",
1185                   currentAtomType->name);
1186          painCave.isFatal = 1;

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