--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/08/07 21:47:18 670 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2003/09/25 19:27:15 787 @@ -26,16 +26,20 @@ SimInfo::SimInfo(){ 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; + origRcut = -1.0; ecr = 0.0; + origEcr = -1.0; est = 0.0; oldEcr = 0.0; oldRcut = 0.0; @@ -44,6 +48,7 @@ SimInfo::SimInfo(){ haveOrigEcr = 0; boxIsInit = 0; + resetTime = 1e99; usePBC = 0; @@ -89,8 +94,7 @@ void SimInfo::setBoxM( double theBox[3][3] ){ void SimInfo::setBoxM( double theBox[3][3] ){ - int i, j, 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 ] @@ -275,12 +279,28 @@ void SimInfo::printMat9(double A[9] ){ << "[ " << 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; - int i; // boxVol = Determinant of Hmat @@ -291,30 +311,66 @@ void SimInfo::calcBoxL( void ){ dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; dsq = dx*dx + dy*dy + dz*dz; boxL[0] = sqrt( dsq ); - maxCutoff = 0.5 * boxL[0]; + //maxCutoff = 0.5 * boxL[0]; // boxLy dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; dsq = dx*dx + dy*dy + dz*dz; boxL[1] = sqrt( dsq ); - if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; + //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; + // boxLz dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; dsq = dx*dx + dy*dy + dz*dz; boxL[2] = sqrt( dsq ); - if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; + //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 ){ @@ -362,7 +418,7 @@ int SimInfo::getNDF(){ ndf = ndf_local; #endif - ndf = ndf - 3; + ndf = ndf - 3 - nZconstraints; return ndf; } @@ -381,7 +437,23 @@ int SimInfo::getNDFraw() { return ndfRaw; } - + +int SimInfo::getNDFtranslational() { + int ndfTrans_local, ndfTrans; + + 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; @@ -437,7 +509,7 @@ void SimInfo::refreshSim(){ this->ndf = this->getNDF(); this->ndfRaw = this->getNDFraw(); - + this->ndfTrans = this->getNDFtranslational(); } @@ -473,79 +545,84 @@ void SimInfo::checkCutOffs( void ){ void SimInfo::checkCutOffs( void ){ int cutChanged = 0; - - - + if( boxIsInit ){ //we need to check cutOffs against the box - + + //detect the change of rCut if(( maxCutoff > rCut )&&(usePBC)){ if( rCut < origRcut ){ - rCut = origRcut; - if (rCut > maxCutoff) rCut = maxCutoff; - - sprintf( painCave.errMsg, - "New Box size is setting the long range cutoff radius " - "to %lf\n", - rCut ); - painCave.isFatal = 0; - simError(); + rCut = origRcut; + + if (rCut > maxCutoff) + rCut = maxCutoff; + + sprintf( painCave.errMsg, + "New Box size is setting the long range cutoff radius " + "to %lf at time %lf\n", + rCut, currentTime ); + painCave.isFatal = 0; + simError(); } } - - if( maxCutoff > ecr ){ - if( ecr < origEcr ){ - rCut = origEcr; - if (ecr > maxCutoff) ecr = maxCutoff; - - sprintf( painCave.errMsg, - "New Box size is setting the electrostaticCutoffRadius " - "to %lf\n", - ecr ); - painCave.isFatal = 0; - simError(); - } - } - - - if ((rCut > maxCutoff)&&(usePBC)) { + else if ((rCut > maxCutoff)&&(usePBC)) { sprintf( painCave.errMsg, "New Box size is setting the long range cutoff radius " - "to %lf\n", - maxCutoff ); + "to %lf at time %lf\n", + maxCutoff, currentTime ); painCave.isFatal = 0; simError(); rCut = maxCutoff; } - if( ecr > maxCutoff){ + + //detect the change of ecr + if( maxCutoff > ecr ){ + if( ecr < origEcr ){ + ecr = origEcr; + if (ecr > maxCutoff) ecr = maxCutoff; + + sprintf( painCave.errMsg, + "New Box size is setting the electrostaticCutoffRadius " + "to %lf at time %lf\n", + ecr, currentTime ); + painCave.isFatal = 0; + simError(); + } + } + else if( ecr > maxCutoff){ sprintf( painCave.errMsg, "New Box size is setting the electrostaticCutoffRadius " - "to %lf\n", - maxCutoff ); + "to %lf at time %lf\n", + maxCutoff, currentTime ); painCave.isFatal = 0; simError(); ecr = maxCutoff; } + if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; - } - - - if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; - - // rlist is the 1.0 plus max( rcut, ecr ) - - ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; - - if( cutChanged ){ + // rlist is the 1.0 plus max( rcut, ecr ) - notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); + ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; + + if( cutChanged ){ + + notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); + } + + oldEcr = ecr; + oldRcut = rCut; + + } 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(); } - - oldEcr = ecr; - oldRcut = rCut; + } void SimInfo::addProperty(GenericData* prop){ @@ -595,4 +672,9 @@ vector SimInfo::getProperties(){ return result; } +double SimInfo::matTrace3(double m[3][3]){ + double trace; + trace = m[0][0] + m[1][1] + m[2][2]; + return trace; +}