--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/07/09 22:14:06 586 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2004/06/02 14:21:54 1218 @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include using namespace std; @@ -12,6 +12,8 @@ using namespace std; #include "fortranWrappers.hpp" +#include "MatVec3.h" + #ifdef IS_MPI #include "mpiSimulation.hpp" #endif @@ -20,269 +22,295 @@ inline double roundMe( double x ){ return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); } +inline double min( double a, double b ){ + return (a < b ) ? a : b; +} SimInfo* currentInfo; SimInfo::SimInfo(){ - excludes = NULL; + n_constraints = 0; + nZconstraints = 0; n_oriented = 0; n_dipoles = 0; ndf = 0; ndfRaw = 0; + nZconstraints = 0; the_integrator = NULL; setTemp = 0; thermalTime = 0.0; + currentTime = 0.0; rCut = 0.0; + rSw = 0.0; + haveRcut = 0; + haveRsw = 0; + boxIsInit = 0; + + resetTime = 1e99; + + orthoRhombic = 0; + orthoTolerance = 1E-6; + useInitXSstate = true; + usePBC = 0; useLJ = 0; useSticky = 0; - useDipole = 0; + useCharges = 0; + useDipoles = 0; useReactionField = 0; useGB = 0; useEAM = 0; + useSolidThermInt = 0; + useLiquidThermInt = 0; - wrapMeSimInfo( this ); -} + haveCutoffGroups = false; -void SimInfo::setBox(double newBox[3]) { - - int i; - double tempMat[9]; + excludes = Exclude::Instance(); - for(i=0; i<9; i++) tempMat[i] = 0.0;; + myConfiguration = new SimState(); - tempMat[0] = newBox[0]; - tempMat[4] = newBox[1]; - tempMat[8] = newBox[2]; + has_minimizer = false; + the_minimizer =NULL; - setBoxM( tempMat ); + ngroup = 0; + wrapMeSimInfo( this ); } -void SimInfo::setBoxM( double theBox[9] ){ - - int i, status; - double smallestBoxL, maxCutoff; - for(i=0; i<9; i++) Hmat[i] = theBox[i]; +SimInfo::~SimInfo(){ - cerr - << "setting Hmat ->\n" - << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n" - << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n" - << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n"; + delete myConfiguration; - calcHmatI(); - calcBoxL(); + map::iterator i; + + for(i = properties.begin(); i != properties.end(); i++) + delete (*i).second; + +} +void SimInfo::setBox(double newBox[3]) { + + int i, j; + double tempMat[3][3]; + for(i=0; i<3; i++) + for (j=0; j<3; j++) tempMat[i][j] = 0.0;; - setFortranBoxSize(Hmat, HmatI, &orthoRhombic); - - smallestBoxL = boxLx; - if (boxLy < smallestBoxL) smallestBoxL = boxLy; - if (boxLz < smallestBoxL) smallestBoxL = boxLz; + tempMat[0][0] = newBox[0]; + tempMat[1][1] = newBox[1]; + tempMat[2][2] = newBox[2]; - maxCutoff = smallestBoxL / 2.0; + setBoxM( tempMat ); - if (rList > maxCutoff) { - sprintf( painCave.errMsg, - "New Box size is forcing neighborlist radius down to %lf\n", - maxCutoff ); - painCave.isFatal = 0; - simError(); +} - rList = maxCutoff; +void SimInfo::setBoxM( double theBox[3][3] ){ + + int i, j; + double FortranHmat[9]; // to preserve compatibility with Fortran the + // ordering in the array is as follows: + // [ 0 3 6 ] + // [ 1 4 7 ] + // [ 2 5 8 ] + double FortranHmatInv[9]; // the inverted Hmat (for Fortran); - sprintf( painCave.errMsg, - "New Box size is forcing cutoff radius down to %lf\n", - maxCutoff - 1.0 ); - painCave.isFatal = 0; - simError(); + if( !boxIsInit ) boxIsInit = 1; - rCut = rList - 1.0; + for(i=0; i < 3; i++) + for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; + + calcBoxL(); + calcHmatInv(); - // list radius changed so we have to refresh the simulation structure. - refreshSim(); - } - - if (rCut > maxCutoff) { - sprintf( painCave.errMsg, - "New Box size is forcing cutoff radius down to %lf\n", - maxCutoff ); - painCave.isFatal = 0; - simError(); - - status = 0; - LJ_new_rcut(&rCut, &status); - if (status != 0) { - sprintf( painCave.errMsg, - "Error in recomputing LJ shifts based on new rcut\n"); - painCave.isFatal = 1; - simError(); + for(i=0; i < 3; i++) { + for (j=0; j < 3; j++) { + FortranHmat[3*j + i] = Hmat[i][j]; + FortranHmatInv[3*j + i] = HmatInv[i][j]; } } + + setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); + } -void SimInfo::getBoxM (double theBox[9]) { +void SimInfo::getBoxM (double theBox[3][3]) { - int i; - for(i=0; i<9; i++) theBox[i] = Hmat[i]; + int i, j; + for(i=0; i<3; i++) + for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; } void SimInfo::scaleBox(double scale) { - double theBox[9]; - int i; + double theBox[3][3]; + int i, j; - cerr << "Scaling box by " << scale << "\n"; + // cerr << "Scaling box by " << scale << "\n"; - for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; + for(i=0; i<3; i++) + for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; setBoxM(theBox); } -void SimInfo::calcHmatI( void ) { - - double C[3][3]; - double detHmat; - int i, j, k; +void SimInfo::calcHmatInv( void ) { + + int oldOrtho; + int i,j; double smallDiag; double tol; double sanity[3][3]; - // calculate the adjunct of Hmat; + invertMat3( Hmat, HmatInv ); - C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); - C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); - C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); - - C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); - C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); - C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); - - C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); - C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); - C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); - - // calcutlate the determinant of Hmat + // check to see if Hmat is orthorhombic - detHmat = 0.0; - for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; + oldOrtho = orthoRhombic; - - // H^-1 = C^T / det(H) - - i=0; - for(j=0; j<3; j++){ - for(k=0; k<3; k++){ + smallDiag = fabs(Hmat[0][0]); + if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); + if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); + tol = smallDiag * orthoTolerance; - HmatI[i] = C[j][k] / detHmat; - i++; - } - } - - // sanity check - - for(i=0; i<3; i++){ - for(j=0; j<3; j++){ - - sanity[i][j] = 0.0; - for(k=0; k<3; k++){ - sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; + orthoRhombic = 1; + + for (i = 0; i < 3; i++ ) { + for (j = 0 ; j < 3; j++) { + if (i != j) { + if (orthoRhombic) { + if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; + } } } } - cerr << "sanity => \n" - << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" - << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" - << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] - << "\n"; + if( oldOrtho != orthoRhombic ){ - - // check to see if Hmat is orthorhombic - - smallDiag = Hmat[0]; - if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; - if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; - tol = smallDiag * 1E-6; - - orthoRhombic = 1; - for(i=0; (i<9) && orthoRhombic; i++){ - - if( (i%4) ){ // ignore the diagonals (0, 4, and 8) - orthoRhombic = (Hmat[i] <= tol); + if( orthoRhombic ) { + sprintf( painCave.errMsg, + "\n\tOOPSE is switching from the default Non-Orthorhombic\n" + "\tto the faster Orthorhombic periodic boundary computations.\n" + "\tThis is usually a good thing, but if you wan't the\n" + "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" + "\tvariable ( currently set to %G ) smaller.\n", + orthoTolerance); + painCave.severity = OOPSE_INFO; + simError(); } + else { + sprintf( painCave.errMsg, + "\n\tOOPSE is switching from the faster Orthorhombic to the more\n" + "\tflexible Non-Orthorhombic periodic boundary computations.\n" + "\tThis is usually because the box has deformed under\n" + "\tNPTf integration. If you wan't to live on the edge with\n" + "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" + "\tvariable ( currently set to %G ) larger.\n", + orthoTolerance); + painCave.severity = OOPSE_WARNING; + simError(); + } } - } void SimInfo::calcBoxL( void ){ double dx, dy, dz, dsq; - int i; - // boxVol = h1 (dot) h2 (cross) h3 + // boxVol = Determinant of Hmat - boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) - + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) - + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); + boxVol = matDet3( Hmat ); - // boxLx - dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; + dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; dsq = dx*dx + dy*dy + dz*dz; - boxLx = sqrt( dsq ); + boxL[0] = sqrt( dsq ); + //maxCutoff = 0.5 * boxL[0]; // boxLy - dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; + dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; dsq = dx*dx + dy*dy + dz*dz; - boxLy = sqrt( dsq ); + boxL[1] = sqrt( dsq ); + //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; + // boxLz - dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; + dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; dsq = dx*dx + dy*dy + dz*dz; - boxLz = sqrt( dsq ); + boxL[2] = sqrt( dsq ); + //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; + + //calculate the max cutoff + maxCutoff = calcMaxCutOff(); + checkCutOffs(); + } + + +double SimInfo::calcMaxCutOff(){ + + double ri[3], rj[3], rk[3]; + double rij[3], rjk[3], rki[3]; + double minDist; + + ri[0] = Hmat[0][0]; + ri[1] = Hmat[1][0]; + ri[2] = Hmat[2][0]; + + rj[0] = Hmat[0][1]; + rj[1] = Hmat[1][1]; + rj[2] = Hmat[2][1]; + + rk[0] = Hmat[0][2]; + rk[1] = Hmat[1][2]; + rk[2] = Hmat[2][2]; + + crossProduct3(ri, rj, rij); + distXY = dotProduct3(rk,rij) / norm3(rij); + crossProduct3(rj,rk, rjk); + distYZ = dotProduct3(ri,rjk) / norm3(rjk); + crossProduct3(rk,ri, rki); + distZX = dotProduct3(rj,rki) / norm3(rki); + + minDist = min(min(distXY, distYZ), distZX); + return minDist/2; + +} + void SimInfo::wrapVector( double thePos[3] ){ - int i, j, k; + int i; double scaled[3]; if( !orthoRhombic ){ // calc the scaled coordinates. + + + matVecMul3(HmatInv, thePos, scaled); for(i=0; i<3; i++) - scaled[i] = - thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; - - // wrap the scaled coordinates - - for(i=0; i<3; i++) scaled[i] -= roundMe(scaled[i]); // calc the wrapped real coordinates from the wrapped scaled coordinates - for(i=0; i<3; i++) - thePos[i] = - scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; + matVecMul3(Hmat, scaled, thePos); + } else{ // calc the scaled coordinates. for(i=0; i<3; i++) - scaled[i] = thePos[i]*HmatI[i*4]; + scaled[i] = thePos[i]*HmatInv[i][i]; // wrap the scaled coordinates @@ -292,35 +320,61 @@ void SimInfo::wrapVector( double thePos[3] ){ // calc the wrapped real coordinates from the wrapped scaled coordinates for(i=0; i<3; i++) - thePos[i] = scaled[i]*Hmat[i*4]; + thePos[i] = scaled[i]*Hmat[i][i]; } - } int SimInfo::getNDF(){ - int ndf_local, ndf; + int ndf_local; + + ndf_local = 0; - ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; + for(int i = 0; i < integrableObjects.size(); i++){ + ndf_local += 3; + if (integrableObjects[i]->isDirectional()) { + if (integrableObjects[i]->isLinear()) + ndf_local += 2; + else + ndf_local += 3; + } + } + // n_constraints is local, so subtract them on each processor: + + ndf_local -= n_constraints; + #ifdef IS_MPI MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); #else ndf = ndf_local; #endif - ndf = ndf - 3; + // nZconstraints is global, as are the 3 COM translations for the + // entire system: + ndf = ndf - 3 - nZconstraints; + return ndf; } int SimInfo::getNDFraw() { - int ndfRaw_local, ndfRaw; + int ndfRaw_local; // Raw degrees of freedom that we have to set - ndfRaw_local = 3 * n_atoms + 3 * n_oriented; - + ndfRaw_local = 0; + + for(int i = 0; i < integrableObjects.size(); i++){ + ndfRaw_local += 3; + if (integrableObjects[i]->isDirectional()) { + if (integrableObjects[i]->isLinear()) + ndfRaw_local += 2; + else + ndfRaw_local += 3; + } + } + #ifdef IS_MPI MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); #else @@ -329,24 +383,51 @@ int SimInfo::getNDFraw() { return ndfRaw; } - + +int SimInfo::getNDFtranslational() { + int ndfTrans_local; + + ndfTrans_local = 3 * integrableObjects.size() - n_constraints; + + +#ifdef IS_MPI + MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); +#else + ndfTrans = ndfTrans_local; +#endif + + ndfTrans = ndfTrans - 3 - nZconstraints; + + return ndfTrans; +} + +int SimInfo::getTotIntegrableObjects() { + int nObjs_local; + int nObjs; + + nObjs_local = integrableObjects.size(); + + +#ifdef IS_MPI + MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); +#else + nObjs = nObjs_local; +#endif + + + return nObjs; +} + void SimInfo::refreshSim(){ simtype fInfo; int isError; int n_global; int* excl; - - fInfo.rrf = 0.0; - fInfo.rt = 0.0; + fInfo.dielect = 0.0; - fInfo.rlist = rList; - fInfo.rcut = rCut; - - if( useDipole ){ - fInfo.rrf = ecr; - fInfo.rt = ecr - est; + if( useDipoles ){ if( useReactionField )fInfo.dielect = dielectric; } @@ -355,43 +436,188 @@ void SimInfo::refreshSim(){ fInfo.SIM_uses_LJ = useLJ; fInfo.SIM_uses_sticky = useSticky; //fInfo.SIM_uses_sticky = 0; - fInfo.SIM_uses_dipoles = useDipole; + fInfo.SIM_uses_charges = useCharges; + fInfo.SIM_uses_dipoles = useDipoles; //fInfo.SIM_uses_dipoles = 0; - //fInfo.SIM_uses_RF = useReactionField; - fInfo.SIM_uses_RF = 0; + fInfo.SIM_uses_RF = useReactionField; + //fInfo.SIM_uses_RF = 0; fInfo.SIM_uses_GB = useGB; fInfo.SIM_uses_EAM = useEAM; - excl = Exclude::getArray(); - + n_exclude = excludes->getSize(); + excl = excludes->getFortranArray(); + #ifdef IS_MPI - n_global = mpiSim->getTotAtoms(); + n_global = mpiSim->getNAtomsGlobal(); #else n_global = n_atoms; #endif - + isError = 0; - + + getFortranGroupArrays(this, FglobalGroupMembership, mfact); + //it may not be a good idea to pass the address of first element in vector + //since c++ standard does not require vector to be stored continuously in meomory + //Most of the compilers will organize the memory of vector continuously setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, - &nGlobalExcludes, globalExcludes, molMembershipArray, - &isError ); + &nGlobalExcludes, globalExcludes, molMembershipArray, + &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); if( isError ){ - + sprintf( painCave.errMsg, - "There was an error setting the simulation information in fortran.\n" ); + "There was an error setting the simulation information in fortran.\n" ); painCave.isFatal = 1; simError(); } - + #ifdef IS_MPI sprintf( checkPointMsg, "succesfully sent the simulation information to fortran.\n"); MPIcheckPoint(); #endif // is_mpi - + this->ndf = this->getNDF(); this->ndfRaw = this->getNDFraw(); + this->ndfTrans = this->getNDFtranslational(); +} +void SimInfo::setDefaultRcut( double theRcut ){ + + haveRcut = 1; + rCut = theRcut; + rList = rCut + 1.0; + + notifyFortranCutOffs( &rCut, &rSw, &rList ); } +void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ + + rSw = theRsw; + setDefaultRcut( theRcut ); +} + + +void SimInfo::checkCutOffs( void ){ + + if( boxIsInit ){ + + //we need to check cutOffs against the box + + if( rCut > maxCutoff ){ + sprintf( painCave.errMsg, + "\n\tcutoffRadius is too large for the current periodic box.\n" + "\tCurrent Value of cutoffRadius = %G at time %G\n " + "\tThis is larger than half of at least one of the\n" + "\tperiodic box vectors. Right now, the Box matrix is:\n" + "\n" + "\t[ %G %G %G ]\n" + "\t[ %G %G %G ]\n" + "\t[ %G %G %G ]\n", + rCut, currentTime, + Hmat[0][0], Hmat[0][1], Hmat[0][2], + Hmat[1][0], Hmat[1][1], Hmat[1][2], + Hmat[2][0], Hmat[2][1], Hmat[2][2]); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); + } + } else { + // initialize this stuff before using it, OK? + sprintf( painCave.errMsg, + "\n\tTrying to check cutoffs without a box.\n" + "\tOOPSE should have better programmers than that.\n" ); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); + } + +} + +void SimInfo::addProperty(GenericData* prop){ + + map::iterator result; + result = properties.find(prop->getID()); + + //we can't simply use properties[prop->getID()] = prop, + //it will cause memory leak if we already contain a propery which has the same name of prop + + if(result != properties.end()){ + + delete (*result).second; + (*result).second = prop; + + } + else{ + + properties[prop->getID()] = prop; + + } + +} + +GenericData* SimInfo::getProperty(const string& propName){ + + map::iterator result; + + //string lowerCaseName = (); + + result = properties.find(propName); + + if(result != properties.end()) + return (*result).second; + else + return NULL; +} + + +void SimInfo::getFortranGroupArrays(SimInfo* info, + vector& FglobalGroupMembership, + vector& mfact){ + + Molecule* myMols; + Atom** myAtoms; + int numAtom; + double mtot; + int numMol; + int numCutoffGroups; + CutoffGroup* myCutoffGroup; + vector::iterator iterCutoff; + Atom* cutoffAtom; + vector::iterator iterAtom; + int atomIndex; + double totalMass; + + mfact.clear(); + FglobalGroupMembership.clear(); + + + // Fix the silly fortran indexing problem +#ifdef IS_MPI + numAtom = mpiSim->getNAtomsGlobal(); +#else + numAtom = n_atoms; +#endif + for (int i = 0; i < numAtom; i++) + FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); + + + myMols = info->molecules; + numMol = info->n_mol; + for(int i = 0; i < numMol; i++){ + numCutoffGroups = myMols[i].getNCutoffGroups(); + for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); + myCutoffGroup != NULL; + myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ + + totalMass = myCutoffGroup->getMass(); + + for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); + cutoffAtom != NULL; + cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ + mfact.push_back(cutoffAtom->getMass()/totalMass); + } + } + } + +}