--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/07/09 22:14:06 586 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2004/01/13 23:01:43 941 @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include using namespace std; @@ -20,269 +20,396 @@ 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; + ecr = 0.0; + est = 0.0; + haveRcut = 0; + haveEcr = 0; + boxIsInit = 0; + + resetTime = 1e99; + + orthoTolerance = 1E-6; + useInitXSstate = true; + usePBC = 0; useLJ = 0; useSticky = 0; - useDipole = 0; + useCharges = 0; + useDipoles = 0; useReactionField = 0; useGB = 0; useEAM = 0; + myConfiguration = new SimState(); + wrapMeSimInfo( this ); } + +SimInfo::~SimInfo(){ + + delete myConfiguration; + + map::iterator i; + + for(i = properties.begin(); i != properties.end(); i++) + delete (*i).second; + +} + void SimInfo::setBox(double newBox[3]) { - int i; - double tempMat[9]; + int i, j; + double tempMat[3][3]; - for(i=0; i<9; i++) tempMat[i] = 0.0;; + for(i=0; i<3; i++) + for (j=0; j<3; j++) tempMat[i][j] = 0.0;; - tempMat[0] = newBox[0]; - tempMat[4] = newBox[1]; - tempMat[8] = newBox[2]; + tempMat[0][0] = newBox[0]; + tempMat[1][1] = newBox[1]; + tempMat[2][2] = newBox[2]; setBoxM( tempMat ); } -void SimInfo::setBoxM( double theBox[9] ){ +void SimInfo::setBoxM( double theBox[3][3] ){ - int i, status; - double smallestBoxL, maxCutoff; + 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); - for(i=0; i<9; i++) Hmat[i] = theBox[i]; + if( !boxIsInit ) boxIsInit = 1; - 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"; - - calcHmatI(); + for(i=0; i < 3; i++) + for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; + calcBoxL(); + calcHmatInv(); - - - setFortranBoxSize(Hmat, HmatI, &orthoRhombic); - - smallestBoxL = boxLx; - if (boxLy < smallestBoxL) smallestBoxL = boxLy; - if (boxLz < smallestBoxL) smallestBoxL = boxLz; - - maxCutoff = smallestBoxL / 2.0; - - if (rList > maxCutoff) { - sprintf( painCave.errMsg, - "New Box size is forcing neighborlist radius down to %lf\n", - maxCutoff ); - painCave.isFatal = 0; - simError(); - - rList = maxCutoff; - - sprintf( painCave.errMsg, - "New Box size is forcing cutoff radius down to %lf\n", - maxCutoff - 1.0 ); - painCave.isFatal = 0; - simError(); - - rCut = rList - 1.0; - - // 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]); + // check to see if Hmat is orthorhombic + + oldOrtho = orthoRhombic; - 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]); + 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; - 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 + orthoRhombic = 1; - detHmat = 0.0; - for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; + 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; + } + } + } + } - - // H^-1 = C^T / det(H) - - i=0; - for(j=0; j<3; j++){ - for(k=0; k<3; k++){ - - HmatI[i] = C[j][k] / detHmat; - i++; + if( oldOrtho != orthoRhombic ){ + + if( orthoRhombic ){ + sprintf( painCave.errMsg, + "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" + " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", + orthoTolerance); + simError(); } + else { + sprintf( painCave.errMsg, + "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" + " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", + orthoTolerance); + simError(); + } } +} - // sanity check +double SimInfo::matDet3(double a[3][3]) { + int i, j, k; + double determinant; - 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]; - } - } + determinant = 0.0; + + for(i = 0; i < 3; i++) { + j = (i+1)%3; + k = (i+2)%3; + + determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); } - 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"; - + return determinant; +} - // check to see if Hmat is orthorhombic +void SimInfo::invertMat3(double a[3][3], double b[3][3]) { - smallDiag = Hmat[0]; - if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; - if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; - tol = smallDiag * 1E-6; + int i, j, k, l, m, n; + double determinant; - orthoRhombic = 1; - for(i=0; (i<9) && orthoRhombic; i++){ - - if( (i%4) ){ // ignore the diagonals (0, 4, and 8) - orthoRhombic = (Hmat[i] <= tol); + determinant = matDet3( a ); + + if (determinant == 0.0) { + sprintf( painCave.errMsg, + "Can't invert a matrix with a zero determinant!\n"); + painCave.isFatal = 1; + simError(); + } + + for (i=0; i < 3; i++) { + j = (i+1)%3; + k = (i+2)%3; + for(l = 0; l < 3; l++) { + m = (l+1)%3; + n = (l+2)%3; + + b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; } } - } -void SimInfo::calcBoxL( void ){ +void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { + double r00, r01, r02, r10, r11, r12, r20, r21, r22; - double dx, dy, dz, dsq; - int i; + r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; + r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; + r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; + + r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; + r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; + r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; + + r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; + r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; + r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; + + c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; + c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; + c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; +} - // boxVol = h1 (dot) h2 (cross) h3 +void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { + double a0, a1, a2; - 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]) ); + a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; + outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; + outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; + outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; +} - // boxLx - - dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; +void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { + double temp[3][3]; + int i, j; + + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + temp[j][i] = in[i][j]; + } + } + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + out[i][j] = temp[i][j]; + } + } +} + +void SimInfo::printMat3(double A[3][3] ){ + + std::cerr + << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" + << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" + << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; +} + +void SimInfo::printMat9(double A[9] ){ + + std::cerr + << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" + << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" + << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; +} + + +void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ + + out[0] = a[1] * b[2] - a[2] * b[1]; + out[1] = a[2] * b[0] - a[0] * b[2] ; + out[2] = a[0] * b[1] - a[1] * b[0]; + +} + +double SimInfo::dotProduct3(double a[3], double b[3]){ + return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; +} + +double SimInfo::length3(double a[3]){ + return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); +} + +void SimInfo::calcBoxL( void ){ + + double dx, dy, dz, dsq; + + // boxVol = Determinant of Hmat + + boxVol = matDet3( Hmat ); + + // boxLx + + 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) / length3(rij); + + crossProduct3(rj,rk, rjk); + distYZ = dotProduct3(ri,rjk) / length3(rjk); + + crossProduct3(rk,ri, rki); + distZX = dotProduct3(rj,rki) / length3(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 @@ -292,15 +419,14 @@ 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 = 3 * n_atoms + 3 * n_oriented - n_constraints; @@ -310,13 +436,13 @@ int SimInfo::getNDF(){ ndf = ndf_local; #endif - ndf = ndf - 3; + 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; @@ -329,24 +455,33 @@ int SimInfo::getNDFraw() { return ndfRaw; } - + +int SimInfo::getNDFtranslational() { + int ndfTrans_local; + + ndfTrans_local = 3 * n_atoms - 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; +} + 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; } @@ -355,7 +490,8 @@ 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; @@ -392,6 +528,133 @@ void SimInfo::refreshSim(){ this->ndf = this->getNDF(); this->ndfRaw = this->getNDFraw(); + this->ndfTrans = this->getNDFtranslational(); +} +void SimInfo::setDefaultRcut( double theRcut ){ + + haveRcut = 1; + rCut = theRcut; + + ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; + + notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); } +void SimInfo::setDefaultEcr( double theEcr ){ + + haveEcr = 1; + ecr = theEcr; + + ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; + + notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); +} + +void SimInfo::setDefaultEcr( double theEcr, double theEst ){ + + est = theEst; + setDefaultEcr( theEcr ); +} + + +void SimInfo::checkCutOffs( void ){ + + if( boxIsInit ){ + + //we need to check cutOffs against the box + + if( rCut > maxCutoff ){ + sprintf( painCave.errMsg, + "Box size is too small for the long range cutoff radius, " + "%G, at time %G\n" + " [ %G %G %G ]\n" + " [ %G %G %G ]\n" + " [ %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.isFatal = 1; + simError(); + } + + if( haveEcr ){ + if( ecr > maxCutoff ){ + sprintf( painCave.errMsg, + "Box size is too small for the electrostatic cutoff radius, " + "%G, at time %G\n" + " [ %G %G %G ]\n" + " [ %G %G %G ]\n" + " [ %G %G %G ]\n", + ecr, 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.isFatal = 1; + simError(); + } + } + } else { + // initialize this stuff before using it, OK? + sprintf( painCave.errMsg, + "Trying to check cutoffs without a box. Be smarter.\n" ); + 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; +} + +vector SimInfo::getProperties(){ + + vector result; + map::iterator i; + + for(i = properties.begin(); i != properties.end(); i++) + result.push_back((*i).second); + + return result; +} + +double SimInfo::matTrace3(double m[3][3]){ + double trace; + trace = m[0][0] + m[1][1] + m[2][2]; + + return trace; +}