--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/04/01 16:50:14 441 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2003/07/15 21:34:56 618 @@ -1,6 +1,9 @@ #include #include +#include +#include +using namespace std; #include "SimInfo.hpp" #define __C @@ -9,6 +12,15 @@ #include "fortranWrappers.hpp" +#ifdef IS_MPI +#include "mpiSimulation.hpp" +#endif + +inline double roundMe( double x ){ + return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); +} + + SimInfo* currentInfo; SimInfo::SimInfo(){ @@ -16,10 +28,13 @@ SimInfo::SimInfo(){ n_constraints = 0; n_oriented = 0; n_dipoles = 0; + ndf = 0; + ndfRaw = 0; the_integrator = NULL; setTemp = 0; thermalTime = 0.0; rCut = 0.0; + ecr = 0.0; usePBC = 0; useLJ = 0; @@ -29,54 +44,407 @@ SimInfo::SimInfo(){ useGB = 0; useEAM = 0; + wrapMeSimInfo( this ); +} +void SimInfo::setBox(double newBox[3]) { + + int i, j; + double tempMat[3][3]; - wrapMeSimInfo( this ); + for(i=0; i<3; i++) + for (j=0; j<3; j++) tempMat[i][j] = 0.0;; + + tempMat[0][0] = newBox[0]; + tempMat[1][1] = newBox[1]; + tempMat[2][2] = newBox[2]; + + setBoxM( tempMat ); + +} + +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); + + + 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"; + + calcBoxL(); + calcHmatInv(); + + 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); + + 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( ecr > maxCutoff ){ + + sprintf( painCave.errMsg, + "New Box size is forcing electrostatic cutoff radius " + "down to %lf\n", + maxCutoff ); + painCave.isFatal = 0; + simError(); + + ecr = maxCutoff; + est = 0.05 * ecr; + + refreshSim(); + } + +} + + +void SimInfo::getBoxM (double theBox[3][3]) { + + 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[3][3]; + int i, j; + + // cerr << "Scaling box by " << scale << "\n"; + + for(i=0; i<3; i++) + for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; + + setBoxM(theBox); + +} + +void SimInfo::calcHmatInv( void ) { + + 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 + + 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; + + for (i = 0; i < 3; i++ ) { + for (j = 0 ; j < 3; j++) { + if (i != j) { + if (orthoRhombic) { + if (Hmat[i][j] >= tol) orthoRhombic = 0; + } + } + } + } +} + +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 = 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 ); + + // boxLy + + 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[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; + dsq = dx*dx + dy*dy + dz*dz; + boxLz = sqrt( dsq ); + +} + + +void SimInfo::wrapVector( double thePos[3] ){ + + int i, j, k; + double scaled[3]; + + if( !orthoRhombic ){ + // calc 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); + + } + 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]; + } + +} + + +int SimInfo::getNDF(){ + int ndf_local, ndf; + + ndf_local = 3 * n_atoms + 3 * n_oriented - 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; + + return ndf; +} + +int SimInfo::getNDFraw() { + int ndfRaw_local, ndfRaw; + + // Raw degrees of freedom that we have to set + ndfRaw_local = 3 * n_atoms + 3 * n_oriented; + +#ifdef IS_MPI + MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); +#else + ndfRaw = ndfRaw_local; +#endif + + return ndfRaw; +} + 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.box[0] = box_x; - fInfo.box[1] = box_y; - fInfo.box[2] = box_z; - fInfo.rlist = rList; fInfo.rcut = rCut; - fInfo.rrf = ecr; - fInfo.rt = ecr - est; - fInfo.dielect = dielectric; + if( useDipole ){ + fInfo.rrf = ecr; + fInfo.rt = ecr - est; + if( useReactionField )fInfo.dielect = dielectric; + } + fInfo.SIM_uses_PBC = usePBC; + //fInfo.SIM_uses_LJ = 0; fInfo.SIM_uses_LJ = useLJ; - - //fInfo.SIM_uses_sticky = useSticky; - fInfo.SIM_uses_sticky = 0; + fInfo.SIM_uses_sticky = useSticky; + //fInfo.SIM_uses_sticky = 0; fInfo.SIM_uses_dipoles = useDipole; //fInfo.SIM_uses_dipoles = 0; - fInfo.SIM_uses_RF = useReactionField; + //fInfo.SIM_uses_RF = useReactionField; + fInfo.SIM_uses_RF = 0; fInfo.SIM_uses_GB = useGB; fInfo.SIM_uses_EAM = useEAM; excl = Exclude::getArray(); +#ifdef IS_MPI + n_global = mpiSim->getTotAtoms(); +#else + n_global = n_atoms; +#endif + isError = 0; -// fInfo; -// n_atoms; -// identArray; -// n_exclude; -// excludes; -// nGlobalExcludes; -// globalExcludes; -// isError; + setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, + &nGlobalExcludes, globalExcludes, molMembershipArray, + &isError ); - setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, - &nGlobalExcludes, globalExcludes, &isError ); - if( isError ){ sprintf( painCave.errMsg, @@ -90,5 +458,9 @@ void SimInfo::refreshSim(){ "succesfully sent the simulation information to fortran.\n"); MPIcheckPoint(); #endif // is_mpi + + this->ndf = this->getNDF(); + this->ndfRaw = this->getNDFraw(); + }