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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 1224 by gezelter, Wed Jun 2 18:27:52 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 15 | Line 15 | using namespace std;
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 25 | 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 39 | Line 53 | namespace TPE {  // restrict the access of the folowin
53    typedef struct{
54      char nameA[15];
55      char nameB[15];
42 –    char type[30];
56      double d0;
57 +    double k0;
58      int last;      //  0  -> default
59                     //  1  -> tells nodes to stop listening
60 +    int type;
61    } bondStruct;
62    
63    
# Line 101 | Line 116 | namespace TPE {  // restrict the access of the folowin
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 130 | 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 146 | 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 162 | 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 172 | Line 202 | namespace TPE {  // restrict the access of the folowin
202        next = NULL;
203        nameA[0] = '\0';
204        nameB[0] = '\0';
175 –      type[0] = '\0';
205      }
206      ~LinkedBondType(){ if( next != NULL ) delete next; }
207  
# Line 207 | Line 236 | namespace TPE {  // restrict the access of the folowin
236          next = new LinkedBondType();
237          strcpy(next->nameA, info.nameA);
238          strcpy(next->nameB, info.nameB);
239 <        strcpy(next->type,  info.type);
239 >        next->type = info.type;
240          next->d0 = info.d0;
241 +        next->k0 = info.k0;
242        }
243      }
244      
# Line 216 | Line 246 | namespace TPE {  // restrict the access of the folowin
246      void duplicate( bondStruct &info ){
247        strcpy(info.nameA, nameA);
248        strcpy(info.nameB, nameB);
249 <      strcpy(info.type,  type);
249 >      info.type = type;
250        info.d0   = d0;
251 +      info.k0   = k0;
252        info.last = 0;
253      }
254  
# Line 226 | Line 257 | namespace TPE {  // restrict the access of the folowin
257  
258      char nameA[15];
259      char nameB[15];
260 <    char type[30];
260 >    int type;
261      double d0;
262 +    double k0;
263  
264      LinkedBondType* next;
265    };
# Line 410 | Line 442 | namespace TPE {  // restrict the access of the folowin
442  
443   } // namespace
444  
445 < using namespace TPE;
445 > using namespace DUFF_NS;
446  
447  
448   //****************************************************************
# Line 424 | Line 456 | DUFF::DUFF(){
456    char* ffPath_env = "FORCE_PARAM_PATH";
457    char* ffPath;
458    char temp[200];
427 –  char errMsg[1000];
459  
460    headAtomType       = NULL;
461    currentAtomType    = NULL;
# Line 446 | 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 468 | Line 499 | DUFF::DUFF(){
499    // Init the bondStruct mpi type
500    
501    bondStruct bondProto; // mpiPrototype
502 <  int bondBC[3] = {60,1,1};  // block counts
502 >  int bondBC[3] = {30,2,2};  // block counts
503    MPI_Aint bondDspls[3];           // displacements
504    MPI_Datatype bondMbrTypes[3];    // member mpi types
505    
# Line 564 | 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 628 | Line 661 | void DUFF::readParams( void ){
661  
662   void DUFF::readParams( void ){
663  
631 –  int i, a, b, c, d;
664    int identNum;
633 –  char* atomA;
634 –  char* atomB;
635 –  char* atomC;
636 –  char* atomD;
665    
666    atomStruct atomInfo;
667    bondStruct bondInfo;
# Line 705 | Line 733 | void DUFF::readParams( void ){
733      while( currentAtomType != NULL ){
734        currentAtomType->duplicate( atomInfo );
735  
708 –
709 –
736        sendFrcStruct( &atomInfo, mpiAtomStructType );
737  
738        sprintf( checkPointMsg,
# Line 724 | Line 750 | void DUFF::readParams( void ){
750    else{
751      
752      // listen for node 0 to send out the force params
753 <    
753 >
754      MPIcheckPoint();
755  
756      headAtomType = new LinkedAtomType;
757 <    recieveFrcStruct( &atomInfo, mpiAtomStructType );
757 >    receiveFrcStruct( &atomInfo, mpiAtomStructType );
758      
759      while( !atomInfo.last ){
760  
735 –
736 –
761        headAtomType->add( atomInfo );
762        
763        MPIcheckPoint();
764  
765 <      recieveFrcStruct( &atomInfo, mpiAtomStructType );
765 >      receiveFrcStruct( &atomInfo, mpiAtomStructType );
766      }
767    }
768  
# Line 754 | Line 778 | void DUFF::readParams( void ){
778    
779    int isGB = 0;
780    int isLJ = 1;
781 <  double GB_dummy = 0.0;
782 <  
783 <  
781 >  int isEAM =0;
782 >  int isCharge = 0;
783 >  double charge=0.0;
784 >    
785    currentAtomType = headAtomType->next;;
786    while( currentAtomType != NULL ){
787      
788 <    if(currentAtomType->isDipole) entry_plug->useDipole = 1;
788 >    if(currentAtomType->isDipole) entry_plug->useDipoles = 1;
789      if(currentAtomType->isSSD) {
790        entry_plug->useSticky = 1;
791 <      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0));
791 >      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0),
792 >                         &(currentAtomType->v0p),
793 >                         &(currentAtomType->rl), &(currentAtomType->ru),
794 >                         &(currentAtomType->rlp), &(currentAtomType->rup));
795      }
796  
797      if( currentAtomType->name[0] != '\0' ){
# Line 773 | Line 801 | void DUFF::readParams( void ){
801                   &(currentAtomType->isSSD),
802                   &(currentAtomType->isDipole),
803                   &isGB,
804 +                 &isEAM,
805 +                 &isCharge,
806                   &(currentAtomType->epslon),
807                   &(currentAtomType->sigma),
808 +                 &charge,
809                   &(currentAtomType->dipole),
810                   &isError );
811        if( isError ){
# Line 865 | Line 896 | void DUFF::readParams( void ){
896      MPIcheckPoint();
897  
898      headBondType = new LinkedBondType;
899 <    recieveFrcStruct( &bondInfo, mpiBondStructType );
899 >    receiveFrcStruct( &bondInfo, mpiBondStructType );
900      while( !bondInfo.last ){
901  
902        headBondType->add( bondInfo );
903 <      recieveFrcStruct( &bondInfo, mpiBondStructType );
903 >      receiveFrcStruct( &bondInfo, mpiBondStructType );
904      }
905    }
906  
# Line 893 | 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 948 | Line 979 | void DUFF::readParams( void ){
979      MPIcheckPoint();
980  
981      headBendType = new LinkedBendType;
982 <    recieveFrcStruct( &bendInfo, mpiBendStructType );
982 >    receiveFrcStruct( &bendInfo, mpiBendStructType );
983      while( !bendInfo.last ){
984  
985        headBendType->add( bendInfo );
986 <      recieveFrcStruct( &bendInfo, mpiBendStructType );
986 >      receiveFrcStruct( &bendInfo, mpiBendStructType );
987      }
988    }
989  
# Line 1033 | Line 1064 | void DUFF::readParams( void ){
1064      MPIcheckPoint();
1065  
1066      headTorsionType = new LinkedTorsionType;
1067 <    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1067 >    receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1068      while( !torsionInfo.last ){
1069  
1070        headTorsionType->add( torsionInfo );
1071 <      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1071 >      receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1072      }
1073    }
1074  
# Line 1091 | 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 1104 | Line 1136 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1136      }
1137      
1138      the_atoms[i]->setMass( currentAtomType->mass );
1107 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
1108 –    the_atoms[i]->setSigma( currentAtomType->sigma );
1139      the_atoms[i]->setIdent( currentAtomType->ident );
1110 –    the_atoms[i]->setLJ();
1140  
1141      if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
1142  
# Line 1115 | Line 1144 | void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
1144        if( the_atoms[i]->isDirectional() ){
1145          
1146          dAtom = (DirectionalAtom *) the_atoms[i];
1118 –        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 );
1126 –          dAtom->setSSD( 1 );
1157          }
1158          else if(!strcmp("HEAD",the_atoms[i]->getType())){
1159            dAtom->setI( headI );
1130 –          dAtom->setSSD( 0 );
1160          }
1161          else{
1162            sprintf(painCave.errMsg,
# Line 1151 | 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;
# Line 1189 | Line 1218 | void DUFF::initializeBonds( int nBonds, Bond** bondArr
1218        simError();
1219      }
1220      
1221 <    if( !strcmp( currentBondType->type, "fixed" ) ){
1222 <      
1221 >    switch( currentBondType->type ){
1222 >
1223 >    case FIXED_BOND:
1224 >            
1225        bondArray[i] = new ConstrainedBond( *the_atoms[a],
1226                                            *the_atoms[b],
1227                                            currentBondType->d0 );
1228        entry_plug->n_constraints++;
1229 +      break;
1230 +
1231 +    case HARMONIC_BOND:
1232 +      
1233 +      bondArray[i] = new HarmonicBond( *the_atoms[a],
1234 +                                       *the_atoms[b],
1235 +                                       currentBondType->d0,
1236 +                                       currentBondType->k0 );
1237 +      break;
1238 +      
1239 +    default:
1240 +
1241 +      break;
1242 +      // do nothing
1243      }
1244    }
1245   }
# Line 1259 | 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 1275 | 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 1382 | Line 1428 | void DUFF::fastForward( char* stopText, char* searchOw
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 1468 | 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];
1573    
1574    the_token = strtok( lineBuffer, " \n\t,;" );
1575    if( the_token != NULL ){
# Line 1501 | Line 1592 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1592        simError();
1593      }
1594      
1595 <    strcpy( info.type, the_token );
1595 >    strcpy( bondType, the_token );
1596      
1597 <    if( !strcmp( info.type, "fixed" ) ){
1597 >    if( !strcmp( bondType, "fixed" ) ){
1598 >      info.type = FIXED_BOND;
1599 >      
1600 >      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1601 >        sprintf( painCave.errMsg,
1602 >                 "Error parseing BondTypes: line %d\n", lineNum );
1603 >        painCave.isFatal = 1;
1604 >        simError();
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;
1613 >      
1614        if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1615          sprintf( painCave.errMsg,
1616                   "Error parseing BondTypes: line %d\n", lineNum );
# Line 1512 | Line 1619 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1619        }
1620        
1621        info.d0 = atof( the_token );
1622 +
1623 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1624 +        sprintf( painCave.errMsg,
1625 +                 "Error parseing BondTypes: line %d\n", lineNum );
1626 +        painCave.isFatal = 1;
1627 +        simError();
1628 +      }
1629 +      
1630 +      info.k0 = atof( the_token );
1631      }
1632 +
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 1528 | Line 1645 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
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 1616 | Line 1733 | int TPE::parseBend( char *lineBuffer, int lineNum, ben
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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