--- trunk/src/integrators/NPAT.cpp 2005/05/19 04:28:26 536 +++ trunk/src/integrators/NPAT.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ #include "brains/SimInfo.hpp" @@ -44,14 +44,14 @@ #include "integrators/IntegratorCreator.hpp" #include "integrators/NPAT.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { void NPAT::evolveEtaA() { - eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); + eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); oldEta = eta; } @@ -59,7 +59,7 @@ namespace oopse { prevEta = eta; eta(2,2) = oldEta(2, 2) + dt2 * instaVol * - (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); + (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); } void NPAT::calcVelScale(){ @@ -86,107 +86,31 @@ namespace oopse { void NPAT::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 NPAT::scaleSimBox(){ - - int i; - int j; - int k; Mat3x3d scaleMat; - double eta2ij; - double bigScale, smallScale, offDiagMax; - Mat3x3d hm; - Mat3x3d hmnew; - - - // 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)); + for(int i=0; i<3; i++){ + for(int j=0; j<3; j++){ + scaleMat(i, j) = 0.0; + if(i==j) { + scaleMat(i, j) = 1.0; + } } - - 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, - "NPAT 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, - "NPAT 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); - - } + + scaleMat(2, 2) = exp(dt*eta(2, 2)); + Mat3x3d hmat = currentSnapshot_->getHmat(); + hmat = hmat *scaleMat; + currentSnapshot_->setHmat(hmat); } bool NPAT::etaConverged() { int i; - double diffEta, sumEta; + RealType diffEta, sumEta; sumEta = 0; for(i = 0; i < 3; i++) { @@ -198,7 +122,7 @@ namespace oopse { return ( diffEta <= etaTolerance ); } - double NPAT::calcConservedQuantity(){ + RealType NPAT::calcConservedQuantity(){ chi= currentSnapshot_->getChi(); integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); @@ -207,33 +131,33 @@ namespace oopse { // We need NkBT a lot, so just set it here: This is the RAW number // of integrableObjects, so no subtraction or addition of constraints or // orientational degrees of freedom: - NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; + NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; // fkBT is used because the thermostat operates on more degrees of freedom // than the barostat (when there are particles with orientational degrees // of freedom). - fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; + fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; - double conservedQuantity; - double totalEnergy; - double thermostat_kinetic; - double thermostat_potential; - double barostat_kinetic; - double barostat_potential; - double trEta; + RealType conservedQuantity; + RealType totalEnergy; + RealType thermostat_kinetic; + RealType thermostat_potential; + RealType barostat_kinetic; + RealType barostat_potential; + RealType trEta; totalEnergy = thermo.getTotalE(); - thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); + thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); - thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; + thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; - SquareMatrix tmp = eta.transpose() * eta; + SquareMatrix tmp = eta.transpose() * eta; trEta = tmp.trace(); - barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); + barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); - barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; + barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + barostat_kinetic + barostat_potential;