--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/06/30 22:04:01 568 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2003/07/14 21:28:54 597 @@ -2,6 +2,8 @@ #include #include +#include +using namespace std; #include "SimInfo.hpp" #define __C @@ -14,6 +16,11 @@ #include "mpiSimulation.hpp" #endif +inline double roundMe( double x ){ + return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); +} + + SimInfo* currentInfo; SimInfo::SimInfo(){ @@ -40,77 +47,53 @@ void SimInfo::setBox(double newBox[3]) { } void SimInfo::setBox(double newBox[3]) { + + int i, j; + double tempMat[3][3]; - double smallestBoxL, maxCutoff; - int status; - int i; + for(i=0; i<3; i++) + for (j=0; j<3; j++) tempMat[i][j] = 0.0;; - for(i=0; i<9; i++) Hmat[i] = 0.0;; + tempMat[0][0] = newBox[0]; + tempMat[1][1] = newBox[1]; + tempMat[2][2] = newBox[2]; - Hmat[0] = newBox[0]; - Hmat[4] = newBox[1]; - Hmat[8] = newBox[2]; + setBoxM( tempMat ); - calcHmatI(); - calcBoxL(); +} - setFortranBoxSize(Hmat); +void SimInfo::setBoxM( double theBox[3][3] ){ + + int i, j, status; + double smallestBoxL, maxCutoff; + 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); - smallestBoxL = boxLx; - if (boxLy < smallestBoxL) smallestBoxL = boxLy; - if (boxLz < smallestBoxL) smallestBoxL = boxLz; - maxCutoff = smallestBoxL / 2.0; + for(i=0; i < 3; i++) + for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; + + cerr + << "setting Hmat ->\n" + << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" + << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" + << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; - if (rList > maxCutoff) { - sprintf( painCave.errMsg, - "New Box size is forcing neighborlist radius down to %lf\n", - maxCutoff ); - painCave.isFatal = 0; - simError(); + calcBoxL(); + calcHmatInv(); - 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]; } } -} -void SimInfo::setBoxM( double theBox[9] ){ - - int i, status; - double smallestBoxL, maxCutoff; - - for(i=0; i<9; i++) Hmat[i] = theBox[i]; - calcHmatI(); - calcBoxL(); - - setFortranBoxSize(Hmat); + setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); smallestBoxL = boxLx; if (boxLy < smallestBoxL) smallestBoxL = boxLy; @@ -158,78 +141,188 @@ void SimInfo::setBoxM( double theBox[9] ){ } -void SimInfo::getBox(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::calcHmatI( void ) { - double C[3][3]; - double detHmat; - int i, j, k; +void SimInfo::scaleBox(double scale) { + double theBox[3][3]; + int i, j; - // calculate the adjunct of Hmat; + cerr << "Scaling box by " << scale << "\n"; - 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]); + for(i=0; i<3; i++) + for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; - 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]); + setBoxM(theBox); - 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 +void SimInfo::calcHmatInv( void ) { - detHmat = 0.0; - for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; + int i,j; + double smallDiag; + double tol; + double sanity[3][3]; + invertMat3( Hmat, HmatInv ); + + // Check the inverse to make sure it is sane: + + matMul3( Hmat, HmatInv, sanity ); + + // check to see if Hmat is orthorhombic - // H^-1 = C^T / det(H) + smallDiag = Hmat[0][0]; + if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; + if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; + tol = smallDiag * 1E-6; + + orthoRhombic = 1; - i=0; - for(j=0; j<3; j++){ - for(k=0; k<3; k++){ + for (i = 0; i < 3; i++ ) { + for (j = 0 ; j < 3; j++) { + if (i != j) { + if (orthoRhombic) { + if (Hmat[i][j] >= tol) orthoRhombic = 0; + } + } + } + } +} - HmatI[i] = C[j][k] / detHmat; - i++; +double SimInfo::matDet3(double a[3][3]) { + int i, j, k; + double determinant; + + 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]); + } + + return determinant; +} + +void SimInfo::invertMat3(double a[3][3], double b[3][3]) { + + int i, j, k, l, m, n; + double determinant; + + 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::matMul3(double a[3][3], double b[3][3], double c[3][3]) { + double r00, r01, r02, r10, r11, r12, r20, r21, r22; + + 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; +} + +void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { + double a0, a1, a2; + + 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; +} + +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::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 ); // 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 ); // 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 ); @@ -241,17 +334,37 @@ void SimInfo::wrapVector( double thePos[3] ){ int i, j, k; double scaled[3]; - // calc the scaled coordinates. + if( !orthoRhombic ){ + // calc the scaled coordinates. - for(i=0; i<3; i++) - scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; - // wrap the scaled coordinates + matVecMul3(HmatInv, thePos, scaled); + + for(i=0; i<3; i++) + scaled[i] -= roundMe(scaled[i]); + + // calc the wrapped real coordinates from the wrapped scaled coordinates + + matVecMul3(Hmat, scaled, thePos); - for(i=0; i<3; i++) - scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); - - + } + else{ + // calc the scaled coordinates. + + for(i=0; i<3; i++) + scaled[i] = thePos[i]*HmatInv[i][i]; + + // 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[i]*Hmat[i][i]; + } + } @@ -297,10 +410,6 @@ void SimInfo::refreshSim(){ fInfo.rt = 0.0; fInfo.dielect = 0.0; - fInfo.box[0] = box_x; - fInfo.box[1] = box_y; - fInfo.box[2] = box_z; - fInfo.rlist = rList; fInfo.rcut = rCut;