--- trunk/OOPSE/libmdtools/DUFF.cpp 2003/08/20 19:11:51 704 +++ trunk/OOPSE/libmdtools/DUFF.cpp 2004/04/12 20:32:20 1097 @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include using namespace std; @@ -32,6 +32,7 @@ namespace DUFF_NS { // restrict the access of the fol double mass; double epslon; double sigma; + double charge; double dipole; double w0; double v0; @@ -41,6 +42,7 @@ namespace DUFF_NS { // restrict the access of the fol double rlp; double rup; int isSSD; + int isCharge; int isDipole; int ident; int last; // 0 -> default @@ -114,7 +116,7 @@ namespace DUFF_NS { // restrict the access of the fol void printMe( void ){ std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; - if( next != NULL ) next->printMe(); + // if( next != NULL ) next->printMe(); } @@ -454,7 +456,6 @@ DUFF::DUFF(){ char* ffPath_env = "FORCE_PARAM_PATH"; char* ffPath; char temp[200]; - char errMsg[1000]; headAtomType = NULL; currentAtomType = NULL; @@ -476,7 +477,7 @@ DUFF::DUFF(){ // Init the atomStruct mpi type atomStruct atomProto; // mpiPrototype - int atomBC[3] = {15,6,4}; // block counts + int atomBC[3] = {15,12,5}; // block counts MPI_Aint atomDspls[3]; // displacements MPI_Datatype atomMbrTypes[3]; // member mpi types @@ -658,12 +659,7 @@ void DUFF::readParams( void ){ void DUFF::readParams( void ){ - int i, a, b, c, d; int identNum; - char* atomA; - char* atomB; - char* atomC; - char* atomD; atomStruct atomInfo; bondStruct bondInfo; @@ -734,8 +730,6 @@ void DUFF::readParams( void ){ currentAtomType = headAtomType->next; //skip the first element who is a place holder. while( currentAtomType != NULL ){ currentAtomType->duplicate( atomInfo ); - - sendFrcStruct( &atomInfo, mpiAtomStructType ); @@ -754,21 +748,19 @@ void DUFF::readParams( void ){ else{ // listen for node 0 to send out the force params - + MPIcheckPoint(); headAtomType = new LinkedAtomType; - recieveFrcStruct( &atomInfo, mpiAtomStructType ); + receiveFrcStruct( &atomInfo, mpiAtomStructType ); while( !atomInfo.last ){ - - headAtomType->add( atomInfo ); MPIcheckPoint(); - recieveFrcStruct( &atomInfo, mpiAtomStructType ); + receiveFrcStruct( &atomInfo, mpiAtomStructType ); } } @@ -785,13 +777,13 @@ void DUFF::readParams( void ){ int isGB = 0; int isLJ = 1; int isEAM =0; - double GB_dummy = 0.0; - - + int isCharge = 0; + double charge=0.0; + currentAtomType = headAtomType->next;; while( currentAtomType != NULL ){ - if(currentAtomType->isDipole) entry_plug->useDipole = 1; + if(currentAtomType->isDipole) entry_plug->useDipoles = 1; if(currentAtomType->isSSD) { entry_plug->useSticky = 1; set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), @@ -808,8 +800,10 @@ void DUFF::readParams( void ){ &(currentAtomType->isDipole), &isGB, &isEAM, + &isCharge, &(currentAtomType->epslon), &(currentAtomType->sigma), + &charge, &(currentAtomType->dipole), &isError ); if( isError ){ @@ -900,11 +894,11 @@ void DUFF::readParams( void ){ MPIcheckPoint(); headBondType = new LinkedBondType; - recieveFrcStruct( &bondInfo, mpiBondStructType ); + receiveFrcStruct( &bondInfo, mpiBondStructType ); while( !bondInfo.last ){ headBondType->add( bondInfo ); - recieveFrcStruct( &bondInfo, mpiBondStructType ); + receiveFrcStruct( &bondInfo, mpiBondStructType ); } } @@ -928,7 +922,7 @@ void DUFF::readParams( void ){ fastForward( "BendTypes", "initializeBends" ); // we are now at the bendTypes section - + eof_test = fgets( readLine, sizeof(readLine), frcFile ); lineNum++; @@ -983,11 +977,11 @@ void DUFF::readParams( void ){ MPIcheckPoint(); headBendType = new LinkedBendType; - recieveFrcStruct( &bendInfo, mpiBendStructType ); + receiveFrcStruct( &bendInfo, mpiBendStructType ); while( !bendInfo.last ){ headBendType->add( bendInfo ); - recieveFrcStruct( &bendInfo, mpiBendStructType ); + receiveFrcStruct( &bendInfo, mpiBendStructType ); } } @@ -1068,11 +1062,11 @@ void DUFF::readParams( void ){ MPIcheckPoint(); headTorsionType = new LinkedTorsionType; - recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); + receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); while( !torsionInfo.last ){ headTorsionType->add( torsionInfo ); - recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); + receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); } } @@ -1126,6 +1120,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato // initialize the atoms DirectionalAtom* dAtom; + double ji[3]; for(int i=0; isetMass( currentAtomType->mass ); - the_atoms[i]->setEpslon( currentAtomType->epslon ); - the_atoms[i]->setSigma( currentAtomType->sigma ); the_atoms[i]->setIdent( currentAtomType->ident ); - the_atoms[i]->setLJ(); if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; @@ -1150,19 +1142,19 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato if( the_atoms[i]->isDirectional() ){ dAtom = (DirectionalAtom *) the_atoms[i]; - dAtom->setMu( currentAtomType->dipole ); dAtom->setHasDipole( 1 ); - dAtom->setJx( 0.0 ); - dAtom->setJy( 0.0 ); - dAtom->setJz( 0.0 ); + + ji[0] = 0.0; + ji[1] = 0.0; + ji[2] = 0.0; + + dAtom->setJ( ji ); if(!strcmp("SSD",the_atoms[i]->getType())){ dAtom->setI( waterI ); - dAtom->setSSD( 1 ); } else if(!strcmp("HEAD",the_atoms[i]->getType())){ dAtom->setI( headI ); - dAtom->setSSD( 0 ); } else{ sprintf(painCave.errMsg, @@ -1186,7 +1178,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato else{ if( the_atoms[i]->isDirectional() ){ sprintf( painCave.errMsg, - "DUFF error: Atom \"%s\" was given a standard" + "DUFF error: Atom \"%s\" was given a standard " "orientation in the BASS file, yet it is not a dipole.\n", currentAtomType->name); painCave.isFatal = 1; @@ -1310,8 +1302,7 @@ void DUFF::initializeBends( int nBends, Bend** bendArr } gBend = new GhostBend( *the_atoms[a], - *the_atoms[b], - *the_atoms[c] ); + *the_atoms[b]); gBend->setConstants( currentBendType->k1, currentBendType->k2, @@ -1640,7 +1631,7 @@ int DUFF_NS::parseBond( char *lineBuffer, int lineNum, else{ sprintf( painCave.errMsg, "Unknown DUFF bond type \"%s\" at line %d\n", - info.type, + bondType, lineNum ); painCave.isFatal = 1; simError();