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root/group/trunk/OOPSE/libmdtools/DUFF.cpp
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Comparing trunk/OOPSE/libmdtools/DUFF.cpp (file contents):
Revision 635 by gezelter, Thu Jul 17 20:32:24 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstdio>
3 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <stdio.h>
3 > #include <string.h>
4  
5   #include <iostream>
6   using namespace std;
# Line 32 | Line 32 | namespace DUFF_NS {  // restrict the access of the fol
32      double mass;
33      double epslon;
34      double sigma;
35 +    double charge;
36      double dipole;
37      double w0;
38      double v0;
# Line 41 | Line 42 | namespace DUFF_NS {  // restrict the access of the fol
42      double rlp;
43      double rup;
44      int isSSD;
45 +    int isCharge;
46      int isDipole;
47      int ident;
48      int last;      //  0  -> default
# Line 114 | 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 454 | Line 456 | DUFF::DUFF(){
456    char* ffPath_env = "FORCE_PARAM_PATH";
457    char* ffPath;
458    char temp[200];
457 –  char errMsg[1000];
459  
460    headAtomType       = NULL;
461    currentAtomType    = NULL;
# Line 476 | Line 477 | DUFF::DUFF(){
477    // Init the atomStruct mpi type
478  
479    atomStruct atomProto; // mpiPrototype
480 <  int atomBC[3] = {15,6,4};  // block counts
480 >  int atomBC[3] = {15,12,5};  // block counts
481    MPI_Aint atomDspls[3];           // displacements
482    MPI_Datatype atomMbrTypes[3];    // member mpi types
483  
# Line 658 | Line 659 | void DUFF::readParams( void ){
659  
660   void DUFF::readParams( void ){
661  
661 –  int i, a, b, c, d;
662    int identNum;
663 –  char* atomA;
664 –  char* atomB;
665 –  char* atomC;
666 –  char* atomD;
663    
664    atomStruct atomInfo;
665    bondStruct bondInfo;
# Line 734 | Line 730 | void DUFF::readParams( void ){
730      currentAtomType = headAtomType->next; //skip the first element who is a place holder.
731      while( currentAtomType != NULL ){
732        currentAtomType->duplicate( atomInfo );
737 –
738 –
733  
734        sendFrcStruct( &atomInfo, mpiAtomStructType );
735  
# Line 754 | Line 748 | void DUFF::readParams( void ){
748    else{
749      
750      // listen for node 0 to send out the force params
751 <    
751 >
752      MPIcheckPoint();
753  
754      headAtomType = new LinkedAtomType;
755 <    recieveFrcStruct( &atomInfo, mpiAtomStructType );
755 >    receiveFrcStruct( &atomInfo, mpiAtomStructType );
756      
757      while( !atomInfo.last ){
758  
765 –
766 –
759        headAtomType->add( atomInfo );
760        
761        MPIcheckPoint();
762  
763 <      recieveFrcStruct( &atomInfo, mpiAtomStructType );
763 >      receiveFrcStruct( &atomInfo, mpiAtomStructType );
764      }
765    }
766  
# Line 785 | Line 777 | void DUFF::readParams( void ){
777    int isGB = 0;
778    int isLJ = 1;
779    int isEAM =0;
780 <  double GB_dummy = 0.0;
781 <  
782 <  
780 >  int isCharge = 0;
781 >  double charge=0.0;
782 >    
783    currentAtomType = headAtomType->next;;
784    while( currentAtomType != NULL ){
785      
786 <    if(currentAtomType->isDipole) entry_plug->useDipole = 1;
786 >    if(currentAtomType->isDipole) entry_plug->useDipoles = 1;
787      if(currentAtomType->isSSD) {
788        entry_plug->useSticky = 1;
789        set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0),
# Line 808 | Line 800 | void DUFF::readParams( void ){
800                   &(currentAtomType->isDipole),
801                   &isGB,
802                   &isEAM,
803 +                 &isCharge,
804                   &(currentAtomType->epslon),
805                   &(currentAtomType->sigma),
806 +                 &charge,
807                   &(currentAtomType->dipole),
808                   &isError );
809        if( isError ){
# Line 900 | Line 894 | void DUFF::readParams( void ){
894      MPIcheckPoint();
895  
896      headBondType = new LinkedBondType;
897 <    recieveFrcStruct( &bondInfo, mpiBondStructType );
897 >    receiveFrcStruct( &bondInfo, mpiBondStructType );
898      while( !bondInfo.last ){
899  
900        headBondType->add( bondInfo );
901 <      recieveFrcStruct( &bondInfo, mpiBondStructType );
901 >      receiveFrcStruct( &bondInfo, mpiBondStructType );
902      }
903    }
904  
# Line 928 | Line 922 | void DUFF::readParams( void ){
922      fastForward( "BendTypes", "initializeBends" );
923  
924      // we are now at the bendTypes section
925 <
925 >    
926      eof_test =  fgets( readLine, sizeof(readLine), frcFile );
927      lineNum++;
928          
# Line 983 | Line 977 | void DUFF::readParams( void ){
977      MPIcheckPoint();
978  
979      headBendType = new LinkedBendType;
980 <    recieveFrcStruct( &bendInfo, mpiBendStructType );
980 >    receiveFrcStruct( &bendInfo, mpiBendStructType );
981      while( !bendInfo.last ){
982  
983        headBendType->add( bendInfo );
984 <      recieveFrcStruct( &bendInfo, mpiBendStructType );
984 >      receiveFrcStruct( &bendInfo, mpiBendStructType );
985      }
986    }
987  
# Line 1068 | Line 1062 | void DUFF::readParams( void ){
1062      MPIcheckPoint();
1063  
1064      headTorsionType = new LinkedTorsionType;
1065 <    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1065 >    receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1066      while( !torsionInfo.last ){
1067  
1068        headTorsionType->add( torsionInfo );
1069 <      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1069 >      receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1070      }
1071    }
1072  
# Line 1126 | Line 1120 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1120    // initialize the atoms
1121    
1122    DirectionalAtom* dAtom;
1123 +  double ji[3];
1124  
1125    for(int i=0; i<nAtoms; i++ ){
1126  
# Line 1139 | Line 1134 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1134      }
1135      
1136      the_atoms[i]->setMass( currentAtomType->mass );
1142 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
1143 –    the_atoms[i]->setSigma( currentAtomType->sigma );
1137      the_atoms[i]->setIdent( currentAtomType->ident );
1145 –    the_atoms[i]->setLJ();
1138  
1139      if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
1140  
# Line 1150 | Line 1142 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1142        if( the_atoms[i]->isDirectional() ){
1143          
1144          dAtom = (DirectionalAtom *) the_atoms[i];
1153 –        dAtom->setMu( currentAtomType->dipole );
1145          dAtom->setHasDipole( 1 );
1146 <        dAtom->setJx( 0.0 );
1147 <        dAtom->setJy( 0.0 );
1148 <        dAtom->setJz( 0.0 );
1146 >
1147 >        ji[0] = 0.0;
1148 >        ji[1] = 0.0;
1149 >        ji[2] = 0.0;
1150 >
1151 >        dAtom->setJ( ji );
1152          
1153          if(!strcmp("SSD",the_atoms[i]->getType())){
1154            dAtom->setI( waterI );
1161 –          dAtom->setSSD( 1 );
1155          }
1156          else if(!strcmp("HEAD",the_atoms[i]->getType())){
1157            dAtom->setI( headI );
1165 –          dAtom->setSSD( 0 );
1158          }
1159          else{
1160            sprintf(painCave.errMsg,
# Line 1186 | Line 1178 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1178      else{
1179        if( the_atoms[i]->isDirectional() ){
1180          sprintf( painCave.errMsg,
1181 <                 "DUFF error: Atom \"%s\" was given a standard"
1181 >                 "DUFF error: Atom \"%s\" was given a standard "
1182                   "orientation in the BASS file, yet it is not a dipole.\n",
1183                   currentAtomType->name);
1184          painCave.isFatal = 1;
# Line 1310 | Line 1302 | void DUFF::initializeBends( int nBends, Bend** bendArr
1302          }
1303          
1304          gBend = new GhostBend( *the_atoms[a],
1305 <                               *the_atoms[b] );                        
1305 >                               *the_atoms[b]);
1306 >                                                                      
1307          gBend->setConstants( currentBendType->k1,
1308                               currentBendType->k2,
1309                               currentBendType->k3,
# Line 1326 | Line 1319 | void DUFF::initializeBends( int nBends, Bend** bendArr
1319                               currentBendType->k3,
1320                               currentBendType->t0 );
1321          bendArray[i] = qBend;
1322 <      }
1322 >      }      
1323      }
1324    }
1325   }
# Line 1610 | Line 1603 | int DUFF_NS::parseBond( char *lineBuffer, int lineNum,
1603        }
1604        
1605        info.d0 = atof( the_token );
1606 +      
1607 +      info.k0=0.0;
1608      }
1609      else if( !strcmp( bondType, "harmonic" ) ){
1610        info.type = HARMONIC_BOND;
# Line 1636 | Line 1631 | int DUFF_NS::parseBond( char *lineBuffer, int lineNum,
1631      else{
1632        sprintf( painCave.errMsg,
1633                 "Unknown DUFF bond type \"%s\" at line %d\n",
1634 <               info.type,
1634 >               bondType,
1635                 lineNum );
1636        painCave.isFatal = 1;
1637        simError();

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