--- trunk/src/integrators/NPrT.cpp 2005/05/19 04:28:26 536 +++ trunk/src/integrators/NPrT.cpp 2006/05/17 21:51:42 963 @@ -50,33 +50,38 @@ namespace oopse { namespace oopse { NPrT::NPrT(SimInfo* info) : NPT(info) { Globals* simParams = info_->getSimParams(); - if (!simParams->haveTargetStress()) + if (!simParams->haveSurfaceTension()) { sprintf(painCave.errMsg, "If you use the NPT integrator, you must set tauBarostat.\n"); painCave.severity = OOPSE_ERROR; painCave.isFatal = 1; simError(); } else { - targetStress= simParams->getTargetStress(); + surfaceTension= simParams->getSurfaceTension()* OOPSEConstant::surfaceTensorConvert * OOPSEConstant::energyConvert; } } void NPrT::evolveEtaA() { - double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); - double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); - eta(0,0) -= Axy * (sx - targetStress) / (NkBT*tb2); - eta(1,1) -= Axy * (sy - targetStress) / (NkBT*tb2); + Mat3x3d hmat = currentSnapshot_->getHmat(); + RealType hz = hmat(2, 2); + RealType Axy = hmat(0,0) * hmat(1, 1); + RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); + RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); + eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2); + eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2); eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); oldEta = eta; } void NPrT::evolveEtaB() { - + Mat3x3d hmat = currentSnapshot_->getHmat(); + RealType hz = hmat(2, 2); + RealType Axy = hmat(0,0) * hmat(1, 1); prevEta = eta; - double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); - double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); - eta(0,0) -= Axy * (sx -targetStress) / (NkBT*tb2); - eta(1,1) -= Axy * (sy -targetStress) / (NkBT*tb2); + RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert); + RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert); + eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2); + eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2); eta(2,2) = oldEta(2, 2) + dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); } @@ -105,107 +110,25 @@ namespace oopse { void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { /**@todo */ - Vector3d rj = (oldPos[index] + pos)/2.0 -COM; + Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; sc = eta * rj; } void NPrT::scaleSimBox(){ - - int i; - int j; - int k; Mat3x3d scaleMat; - double eta2ij; - double bigScale, smallScale, offDiagMax; - Mat3x3d hm; - Mat3x3d hmnew; + scaleMat(0, 0) = exp(dt*eta(0, 0)); + scaleMat(1, 1) = exp(dt*eta(1, 1)); + scaleMat(2, 2) = exp(dt*eta(2, 2)); + Mat3x3d hmat = currentSnapshot_->getHmat(); + hmat = hmat *scaleMat; + currentSnapshot_->setHmat(hmat); - - // Scale the box after all the positions have been moved: - - // Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) - // Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) - - bigScale = 1.0; - smallScale = 1.0; - offDiagMax = 0.0; - - for(i=0; i<3; i++){ - for(j=0; j<3; j++){ - - // Calculate the matrix Product of the eta array (we only need - // the ij element right now): - - eta2ij = 0.0; - for(k=0; k<3; k++){ - eta2ij += eta(i, k) * eta(k, j); - } - - scaleMat(i, j) = 0.0; - // identity matrix (see above): - if (i == j) scaleMat(i, j) = 1.0; - // Taylor expansion for the exponential truncated at second order: - scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; - - - if (i != j) - if (fabs(scaleMat(i, j)) > offDiagMax) - offDiagMax = fabs(scaleMat(i, j)); - } - - if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); - if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); - } - - if ((bigScale > 1.01) || (smallScale < 0.99)) { - sprintf( painCave.errMsg, - "NPrT error: Attempting a Box scaling of more than 1 percent.\n" - " Check your tauBarostat, as it is probably too small!\n\n" - " scaleMat = [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " eta = [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n", - scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), - scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), - scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), - eta(0, 0),eta(0, 1),eta(0, 2), - eta(1, 0),eta(1, 1),eta(1, 2), - eta(2, 0),eta(2, 1),eta(2, 2)); - painCave.isFatal = 1; - simError(); - } else if (offDiagMax > 0.01) { - sprintf( painCave.errMsg, - "NPrT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" - " Check your tauBarostat, as it is probably too small!\n\n" - " scaleMat = [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " eta = [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n" - " [%lf\t%lf\t%lf]\n", - scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), - scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), - scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), - eta(0, 0),eta(0, 1),eta(0, 2), - eta(1, 0),eta(1, 1),eta(1, 2), - eta(2, 0),eta(2, 1),eta(2, 2)); - painCave.isFatal = 1; - simError(); - } else { - - Mat3x3d hmat = currentSnapshot_->getHmat(); - hmat = hmat *scaleMat; - currentSnapshot_->setHmat(hmat); - - } } bool NPrT::etaConverged() { int i; - double diffEta, sumEta; + RealType diffEta, sumEta; sumEta = 0; for(i = 0; i < 3; i++) { @@ -217,7 +140,7 @@ namespace oopse { return ( diffEta <= etaTolerance ); } - double NPrT::calcConservedQuantity(){ + RealType NPrT::calcConservedQuantity(){ chi= currentSnapshot_->getChi(); integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); @@ -233,30 +156,27 @@ namespace oopse { // of freedom). fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; - double conservedQuantity; - double totalEnergy; - double thermostat_kinetic; - double thermostat_potential; - double barostat_kinetic; - double barostat_potential; - double trEta; - totalEnergy = thermo.getTotalE(); + RealType totalEnergy = thermo.getTotalE(); - thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); + RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); - thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; + RealType thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; - SquareMatrix tmp = eta.transpose() * eta; - trEta = tmp.trace(); + SquareMatrix tmp = eta.transpose() * eta; + RealType trEta = tmp.trace(); - barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); + RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); - barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; + RealType barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; - conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + - barostat_kinetic + barostat_potential; + Mat3x3d hmat = currentSnapshot_->getHmat(); + RealType hz = hmat(2, 2); + RealType area = hmat(0,0) * hmat(1, 1); + RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + + barostat_kinetic + barostat_potential - surfaceTension * area/ OOPSEConstant::energyConvert; + return conservedQuantity; }