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root/group/trunk/OOPSE/libmdtools/DUFF.cpp
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Comparing trunk/OOPSE/libmdtools/DUFF.cpp (file contents):
Revision 564 by mmeineke, Tue Jun 24 19:57:54 2003 UTC vs.
Revision 950 by mmeineke, Fri Jan 16 15:01:14 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 22 | Line 22 | namespace TPE {  // restrict the access of the folowin
22   #define HARMONIC_BOND 1
23  
24  
25 < namespace TPE {  // restrict the access of the folowing to this file only.
25 > namespace DUFF_NS {  // restrict the access of the folowing to this file only.
26  
27  
28    // Declare the structures that will be passed by MPI
# Line 32 | Line 32 | namespace TPE {  // restrict the access of the folowin
32      double mass;
33      double epslon;
34      double sigma;
35 +    double charge;
36      double dipole;
37      double w0;
38      double v0;
39 +    double v0p;
40 +    double rl;
41 +    double ru;
42 +    double rlp;
43 +    double rup;
44      int isSSD;
45 +    int isCharge;
46      int isDipole;
47      int ident;
48      int last;      //  0  -> default
# Line 138 | Line 145 | namespace TPE {  // restrict the access of the folowin
145          next->dipole   = info.dipole;
146          next->w0       = info.w0;
147          next->v0       = info.v0;
148 +        next->v0p      = info.v0p;
149 +        next->rl       = info.rl;
150 +        next->ru       = info.ru;
151 +        next->rlp      = info.rlp;
152 +        next->rup      = info.rup;
153          next->ident    = info.ident;
154        }
155      }
# Line 154 | Line 166 | namespace TPE {  // restrict the access of the folowin
166        info.dipole   = dipole;
167        info.w0       = w0;
168        info.v0       = v0;
169 +      info.v0p      = v0p;
170 +      info.rl       = rl;
171 +      info.ru       = ru;
172 +      info.rlp      = rlp;
173 +      info.rup      = rup;
174        info.ident    = ident;
175        info.last     = 0;
176      }
# Line 170 | Line 187 | namespace TPE {  // restrict the access of the folowin
187      double dipole;
188      double w0;
189      double v0;
190 +    double v0p;
191 +    double rl;
192 +    double ru;
193 +    double rlp;
194 +    double rup;
195      int ident;
196      LinkedAtomType* next;
197    };
# Line 420 | Line 442 | using namespace TPE;
442  
443   } // namespace
444  
445 < using namespace TPE;
445 > using namespace DUFF_NS;
446  
447  
448   //****************************************************************
# Line 434 | Line 456 | DUFF::DUFF(){
456    char* ffPath_env = "FORCE_PARAM_PATH";
457    char* ffPath;
458    char temp[200];
437 –  char errMsg[1000];
459  
460    headAtomType       = NULL;
461    currentAtomType    = NULL;
# Line 456 | 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 638 | Line 659 | void DUFF::readParams( void ){
659  
660   void DUFF::readParams( void ){
661  
641 –  int i, a, b, c, d;
662    int identNum;
643 –  char* atomA;
644 –  char* atomB;
645 –  char* atomC;
646 –  char* atomD;
663    
664    atomStruct atomInfo;
665    bondStruct bondInfo;
# Line 715 | Line 731 | void DUFF::readParams( void ){
731      while( currentAtomType != NULL ){
732        currentAtomType->duplicate( atomInfo );
733  
718 –
719 –
734        sendFrcStruct( &atomInfo, mpiAtomStructType );
735  
736        sprintf( checkPointMsg,
# Line 734 | 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;
# Line 742 | Line 756 | void DUFF::readParams( void ){
756      
757      while( !atomInfo.last ){
758  
745 –
746 –
759        headAtomType->add( atomInfo );
760        
761        MPIcheckPoint();
# Line 764 | Line 776 | void DUFF::readParams( void ){
776    
777    int isGB = 0;
778    int isLJ = 1;
779 <  double GB_dummy = 0.0;
780 <  
781 <  
779 >  int isEAM =0;
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));
789 >      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0),
790 >                         &(currentAtomType->v0p),
791 >                         &(currentAtomType->rl), &(currentAtomType->ru),
792 >                         &(currentAtomType->rlp), &(currentAtomType->rup));
793      }
794  
795      if( currentAtomType->name[0] != '\0' ){
# Line 783 | Line 799 | void DUFF::readParams( void ){
799                   &(currentAtomType->isSSD),
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 1285 | Line 1304 | void DUFF::initializeBends( int nBends, Bend** bendArr
1304          }
1305          
1306          gBend = new GhostBend( *the_atoms[a],
1307 <                               *the_atoms[b] );                        
1307 >                               *the_atoms[b]);
1308 >                                                                      
1309          gBend->setConstants( currentBendType->k1,
1310                               currentBendType->k2,
1311                               currentBendType->k3,
# Line 1301 | Line 1321 | void DUFF::initializeBends( int nBends, Bend** bendArr
1321                               currentBendType->k3,
1322                               currentBendType->t0 );
1323          bendArray[i] = qBend;
1324 <      }
1324 >      }      
1325      }
1326    }
1327   }
# Line 1408 | Line 1428 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1428   }
1429  
1430  
1431 < int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1431 > int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1432  
1433    char* the_token;
1434    
# Line 1494 | Line 1514 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1514        }
1515        
1516        info.v0 = atof( the_token );
1517 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1518 +        sprintf( painCave.errMsg,
1519 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1520 +        painCave.isFatal = 1;
1521 +        simError();
1522 +      }
1523 +      
1524 +      info.v0p = atof( the_token );
1525 +
1526 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1527 +        sprintf( painCave.errMsg,
1528 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1529 +        painCave.isFatal = 1;
1530 +        simError();
1531 +      }
1532 +      
1533 +      info.rl = atof( the_token );
1534 +
1535 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1536 +        sprintf( painCave.errMsg,
1537 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1538 +        painCave.isFatal = 1;
1539 +        simError();
1540 +      }
1541 +      
1542 +      info.ru = atof( the_token );
1543 +
1544 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1545 +        sprintf( painCave.errMsg,
1546 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1547 +        painCave.isFatal = 1;
1548 +        simError();
1549 +      }
1550 +      
1551 +      info.rlp = atof( the_token );
1552 +
1553 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1554 +        sprintf( painCave.errMsg,
1555 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1556 +        painCave.isFatal = 1;
1557 +        simError();
1558 +      }
1559 +      
1560 +      info.rup = atof( the_token );
1561      }
1562 <    else info.v0 = info.w0 = 0.0;
1562 >    else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0;
1563  
1564      return 1;
1565    }
1566    else return 0;
1567   }
1568  
1569 < int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1569 > int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1570  
1571    char* the_token;
1572    char bondType[30];
# Line 1541 | Line 1605 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1605        }
1606        
1607        info.d0 = atof( the_token );
1608 +      
1609 +      info.k0=0.0;
1610      }
1611      else if( !strcmp( bondType, "harmonic" ) ){
1612        info.type = HARMONIC_BOND;
# Line 1567 | Line 1633 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1633      else{
1634        sprintf( painCave.errMsg,
1635                 "Unknown DUFF bond type \"%s\" at line %d\n",
1636 <               info.type,
1636 >               bondType,
1637                 lineNum );
1638        painCave.isFatal = 1;
1639        simError();
# Line 1579 | Line 1645 | int TPE::parseBend( char *lineBuffer, int lineNum, ben
1645   }
1646  
1647  
1648 < int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1648 > int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1649  
1650    char* the_token;
1651    
# Line 1667 | Line 1733 | int TPE::parseTorsion( char *lineBuffer, int lineNum,
1733    else return 0;
1734   }
1735  
1736 < int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1736 > int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1737    
1738    char*  the_token;
1739  

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