--- trunk/OOPSE/libmdtools/SimInfo.cpp 2003/07/15 19:56:08 617 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2003/10/28 16:03:37 829 @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include using namespace std; @@ -26,15 +26,31 @@ 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; + haveOrigRcut = 0; + haveOrigEcr = 0; + boxIsInit = 0; + + resetTime = 1e99; + + usePBC = 0; useLJ = 0; useSticky = 0; @@ -43,9 +59,23 @@ SimInfo::SimInfo(){ 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, j; @@ -64,8 +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 ] @@ -73,16 +102,12 @@ void SimInfo::setBoxM( double theBox[3][3] ){ // [ 2 5 8 ] double FortranHmatInv[9]; // the inverted Hmat (for Fortran); + + if( !boxIsInit ) boxIsInit = 1; 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(); @@ -95,49 +120,6 @@ void SimInfo::setBoxM( double theBox[3][3] ){ 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 (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(); - } - } } @@ -299,10 +281,26 @@ void SimInfo::printMat9(double A[9] ){ << "[ " << 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 @@ -312,26 +310,67 @@ void SimInfo::calcBoxL( void ){ 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[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[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 ){ @@ -369,7 +408,7 @@ int SimInfo::getNDF(){ int SimInfo::getNDF(){ - int ndf_local, ndf; + int ndf_local; ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; @@ -379,13 +418,13 @@ 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; @@ -398,24 +437,33 @@ 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( useReactionField )fInfo.dielect = dielectric; } @@ -461,6 +509,172 @@ void SimInfo::refreshSim(){ this->ndf = this->getNDF(); this->ndfRaw = this->getNDFraw(); + this->ndfTrans = this->getNDFtranslational(); +} + +void SimInfo::setRcut( double theRcut ){ + + if( !haveOrigRcut ){ + haveOrigRcut = 1; + origRcut = theRcut; + } + + rCut = theRcut; + checkCutOffs(); } +void SimInfo::setEcr( double theEcr ){ + + if( !haveOrigEcr ){ + haveOrigEcr = 1; + origEcr = theEcr; + } + + ecr = theEcr; + checkCutOffs(); +} + +void SimInfo::setEcr( double theEcr, double theEst ){ + + est = theEst; + setEcr( theEcr ); +} + + +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 at time %lf\n", + rCut, currentTime ); + painCave.isFatal = 0; + simError(); + } + } + else if ((rCut > maxCutoff)&&(usePBC)) { + sprintf( painCave.errMsg, + "New Box size is setting the long range cutoff radius " + "to %lf at time %lf\n", + maxCutoff, currentTime ); + painCave.isFatal = 0; + simError(); + rCut = 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 at time %lf\n", + maxCutoff, currentTime ); + painCave.isFatal = 0; + simError(); + ecr = maxCutoff; + } + + 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 ){ + + 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(); + } + +} + +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; +}