--- trunk/src/integrators/NPrT.cpp 2005/05/19 15:49:53 537 +++ trunk/src/integrators/NPrT.cpp 2013/06/16 15:15:42 1879 @@ -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 +28,16 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "brains/SimInfo.hpp" @@ -44,46 +45,46 @@ #include "integrators/IntegratorCreator.hpp" #include "integrators/NPrT.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { 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.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } else { - targetStress= simParams->getTargetStress(); + surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert; } } void NPrT::evolveEtaA() { - Mat3x3d hmat = currentSnapshot_->getHmat(); - double hz = hmat(2, 2); - double Axy = hmat(0,0) * hmat(1, 1); - 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); - eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); + Mat3x3d hmat = snap->getHmat(); + RealType hz = hmat(2, 2); + RealType Axy = hmat(0,0) * hmat(1, 1); + RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); + RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::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/PhysicalConstants::pressureConvert) / (NkBT*tb2); oldEta = eta; } void NPrT::evolveEtaB() { - Mat3x3d hmat = currentSnapshot_->getHmat(); - double hz = hmat(2, 2); - double Axy = hmat(0,0) * hmat(1, 1); + Mat3x3d hmat = snap->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/PhysicalConstants::pressureConvert); + RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::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); + (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); } void NPrT::calcVelScale(){ @@ -93,7 +94,7 @@ namespace oopse { vScale(i, j) = eta(i, j); if (i == j) { - vScale(i, j) += chi; + vScale(i, j) += thermostat.first; } } } @@ -110,107 +111,25 @@ 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 = snap->getHmat(); + hmat = hmat *scaleMat; + snap->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++) { @@ -222,52 +141,47 @@ namespace oopse { return ( diffEta <= etaTolerance ); } - double NPrT::calcConservedQuantity(){ - - chi= currentSnapshot_->getChi(); - integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); + RealType NPrT::calcConservedQuantity(){ + thermostat = snap->getThermostat(); loadEta(); // 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; - totalEnergy = thermo.getTotalE(); + RealType totalEnergy = thermo.getTotalEnergy(); - thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); + RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert); - thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; + RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::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 * PhysicalConstants::energyConvert); - barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; + RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; - conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + - barostat_kinetic + barostat_potential; + Mat3x3d hmat = snap->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/ PhysicalConstants::energyConvert; + return conservedQuantity; } void NPrT::loadEta() { - eta= currentSnapshot_->getEta(); + eta= snap->getBarostat(); //if (!eta.isDiagonal()) { // sprintf( painCave.errMsg, @@ -278,7 +192,7 @@ namespace oopse { } void NPrT::saveEta() { - currentSnapshot_->setEta(eta); + snap->setBarostat(eta); } }