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root/group/trunk/OOPSE/libmdtools/DUFF.cpp
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Comparing trunk/OOPSE/libmdtools/DUFF.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 15 | Line 15 | namespace TPE {  // restrict the access of the folowin
15   #include "mpiForceField.h"
16   #endif // is_mpi
17  
18 – namespace TPE {  // restrict the access of the folowing to this file only.
18  
19 + // define some bond Types
20  
21 + #define FIXED_BOND    0
22 + #define HARMONIC_BOND 1
23 +
24 +
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
29    
30    typedef struct{
# Line 28 | Line 35 | namespace TPE {  // restrict the access of the folowin
35      double dipole;
36      double w0;
37      double v0;
38 +    double v0p;
39 +    double rl;
40 +    double ru;
41 +    double rlp;
42 +    double rup;
43      int isSSD;
44      int isDipole;
45      int ident;
# Line 39 | Line 51 | namespace TPE {  // restrict the access of the folowin
51    typedef struct{
52      char nameA[15];
53      char nameB[15];
42 –    char type[30];
54      double d0;
55 +    double k0;
56      int last;      //  0  -> default
57                     //  1  -> tells nodes to stop listening
58 +    int type;
59    } bondStruct;
60    
61    
# Line 130 | Line 143 | namespace TPE {  // restrict the access of the folowin
143          next->dipole   = info.dipole;
144          next->w0       = info.w0;
145          next->v0       = info.v0;
146 +        next->v0p      = info.v0p;
147 +        next->rl       = info.rl;
148 +        next->ru       = info.ru;
149 +        next->rlp      = info.rlp;
150 +        next->rup      = info.rup;
151          next->ident    = info.ident;
152        }
153      }
# Line 146 | Line 164 | namespace TPE {  // restrict the access of the folowin
164        info.dipole   = dipole;
165        info.w0       = w0;
166        info.v0       = v0;
167 +      info.v0p      = v0p;
168 +      info.rl       = rl;
169 +      info.ru       = ru;
170 +      info.rlp      = rlp;
171 +      info.rup      = rup;
172        info.ident    = ident;
173        info.last     = 0;
174      }
# Line 162 | Line 185 | namespace TPE {  // restrict the access of the folowin
185      double dipole;
186      double w0;
187      double v0;
188 +    double v0p;
189 +    double rl;
190 +    double ru;
191 +    double rlp;
192 +    double rup;
193      int ident;
194      LinkedAtomType* next;
195    };
# Line 172 | Line 200 | namespace TPE {  // restrict the access of the folowin
200        next = NULL;
201        nameA[0] = '\0';
202        nameB[0] = '\0';
175 –      type[0] = '\0';
203      }
204      ~LinkedBondType(){ if( next != NULL ) delete next; }
205  
# Line 207 | Line 234 | namespace TPE {  // restrict the access of the folowin
234          next = new LinkedBondType();
235          strcpy(next->nameA, info.nameA);
236          strcpy(next->nameB, info.nameB);
237 <        strcpy(next->type,  info.type);
237 >        next->type = info.type;
238          next->d0 = info.d0;
239 +        next->k0 = info.k0;
240        }
241      }
242      
# Line 216 | Line 244 | namespace TPE {  // restrict the access of the folowin
244      void duplicate( bondStruct &info ){
245        strcpy(info.nameA, nameA);
246        strcpy(info.nameB, nameB);
247 <      strcpy(info.type,  type);
247 >      info.type = type;
248        info.d0   = d0;
249 +      info.k0   = k0;
250        info.last = 0;
251      }
252  
# Line 226 | Line 255 | namespace TPE {  // restrict the access of the folowin
255  
256      char nameA[15];
257      char nameB[15];
258 <    char type[30];
258 >    int type;
259      double d0;
260 +    double k0;
261  
262      LinkedBondType* next;
263    };
# Line 410 | Line 440 | using namespace TPE;
440  
441   } // namespace
442  
443 < using namespace TPE;
443 > using namespace DUFF_NS;
444  
445  
446   //****************************************************************
# Line 424 | Line 454 | DUFF::DUFF(){
454    char* ffPath_env = "FORCE_PARAM_PATH";
455    char* ffPath;
456    char temp[200];
427 –  char errMsg[1000];
457  
458    headAtomType       = NULL;
459    currentAtomType    = NULL;
# Line 446 | Line 475 | DUFF::DUFF(){
475    // Init the atomStruct mpi type
476  
477    atomStruct atomProto; // mpiPrototype
478 <  int atomBC[3] = {15,6,4};  // block counts
478 >  int atomBC[3] = {15,11,4};  // block counts
479    MPI_Aint atomDspls[3];           // displacements
480    MPI_Datatype atomMbrTypes[3];    // member mpi types
481  
# Line 468 | Line 497 | DUFF::DUFF(){
497    // Init the bondStruct mpi type
498    
499    bondStruct bondProto; // mpiPrototype
500 <  int bondBC[3] = {60,1,1};  // block counts
500 >  int bondBC[3] = {30,2,2};  // block counts
501    MPI_Aint bondDspls[3];           // displacements
502    MPI_Datatype bondMbrTypes[3];    // member mpi types
503    
# Line 628 | Line 657 | void DUFF::readParams( void ){
657  
658   void DUFF::readParams( void ){
659  
631 –  int i, a, b, c, d;
660    int identNum;
633 –  char* atomA;
634 –  char* atomB;
635 –  char* atomC;
636 –  char* atomD;
661    
662    atomStruct atomInfo;
663    bondStruct bondInfo;
# Line 754 | Line 778 | void DUFF::readParams( void ){
778    
779    int isGB = 0;
780    int isLJ = 1;
781 <  double GB_dummy = 0.0;
782 <  
759 <  
781 >  int isEAM =0;
782 >    
783    currentAtomType = headAtomType->next;;
784    while( currentAtomType != NULL ){
785      
786      if(currentAtomType->isDipole) entry_plug->useDipole = 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 773 | Line 799 | void DUFF::readParams( void ){
799                   &(currentAtomType->isSSD),
800                   &(currentAtomType->isDipole),
801                   &isGB,
802 +                 &isEAM,
803                   &(currentAtomType->epslon),
804                   &(currentAtomType->sigma),
805                   &(currentAtomType->dipole),
# Line 1189 | Line 1216 | void DUFF::initializeBonds( int nBonds, Bond** bondArr
1216        simError();
1217      }
1218      
1219 <    if( !strcmp( currentBondType->type, "fixed" ) ){
1220 <      
1219 >    switch( currentBondType->type ){
1220 >
1221 >    case FIXED_BOND:
1222 >            
1223        bondArray[i] = new ConstrainedBond( *the_atoms[a],
1224                                            *the_atoms[b],
1225                                            currentBondType->d0 );
1226        entry_plug->n_constraints++;
1227 +      break;
1228 +
1229 +    case HARMONIC_BOND:
1230 +      
1231 +      bondArray[i] = new HarmonicBond( *the_atoms[a],
1232 +                                       *the_atoms[b],
1233 +                                       currentBondType->d0,
1234 +                                       currentBondType->k0 );
1235 +      break;
1236 +      
1237 +    default:
1238 +
1239 +      break;
1240 +      // do nothing
1241      }
1242    }
1243   }
# Line 1259 | 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 1275 | 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 1382 | Line 1426 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1426   }
1427  
1428  
1429 < int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1429 > int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1430  
1431    char* the_token;
1432    
# Line 1468 | Line 1512 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1512        }
1513        
1514        info.v0 = atof( the_token );
1515 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1516 +        sprintf( painCave.errMsg,
1517 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1518 +        painCave.isFatal = 1;
1519 +        simError();
1520 +      }
1521 +      
1522 +      info.v0p = atof( the_token );
1523 +
1524 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1525 +        sprintf( painCave.errMsg,
1526 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1527 +        painCave.isFatal = 1;
1528 +        simError();
1529 +      }
1530 +      
1531 +      info.rl = atof( the_token );
1532 +
1533 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1534 +        sprintf( painCave.errMsg,
1535 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1536 +        painCave.isFatal = 1;
1537 +        simError();
1538 +      }
1539 +      
1540 +      info.ru = atof( the_token );
1541 +
1542 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1543 +        sprintf( painCave.errMsg,
1544 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1545 +        painCave.isFatal = 1;
1546 +        simError();
1547 +      }
1548 +      
1549 +      info.rlp = atof( the_token );
1550 +
1551 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1552 +        sprintf( painCave.errMsg,
1553 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1554 +        painCave.isFatal = 1;
1555 +        simError();
1556 +      }
1557 +      
1558 +      info.rup = atof( the_token );
1559      }
1560 <    else info.v0 = info.w0 = 0.0;
1560 >    else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0;
1561  
1562      return 1;
1563    }
1564    else return 0;
1565   }
1566  
1567 < int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1567 > int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1568  
1569    char* the_token;
1570 +  char bondType[30];
1571    
1572    the_token = strtok( lineBuffer, " \n\t,;" );
1573    if( the_token != NULL ){
# Line 1501 | Line 1590 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1590        simError();
1591      }
1592      
1593 <    strcpy( info.type, the_token );
1593 >    strcpy( bondType, the_token );
1594      
1595 <    if( !strcmp( info.type, "fixed" ) ){
1595 >    if( !strcmp( bondType, "fixed" ) ){
1596 >      info.type = FIXED_BOND;
1597 >      
1598 >      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1599 >        sprintf( painCave.errMsg,
1600 >                 "Error parseing BondTypes: line %d\n", lineNum );
1601 >        painCave.isFatal = 1;
1602 >        simError();
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;
1611 >      
1612        if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1613          sprintf( painCave.errMsg,
1614                   "Error parseing BondTypes: line %d\n", lineNum );
# Line 1512 | Line 1617 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1617        }
1618        
1619        info.d0 = atof( the_token );
1620 +
1621 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1622 +        sprintf( painCave.errMsg,
1623 +                 "Error parseing BondTypes: line %d\n", lineNum );
1624 +        painCave.isFatal = 1;
1625 +        simError();
1626 +      }
1627 +      
1628 +      info.k0 = atof( the_token );
1629      }
1630 +
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();
# Line 1528 | Line 1643 | int TPE::parseBend( char *lineBuffer, int lineNum, ben
1643   }
1644  
1645  
1646 < int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1646 > int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1647  
1648    char* the_token;
1649    
# Line 1616 | Line 1731 | int TPE::parseTorsion( char *lineBuffer, int lineNum,
1731    else return 0;
1732   }
1733  
1734 < int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1734 > int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1735    
1736    char*  the_token;
1737  

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