--- trunk/src/integrators/NPTxyz.cpp 2005/01/12 22:41:40 246 +++ trunk/src/integrators/NPTxyz.cpp 2012/08/31 17:29:35 1792 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -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, 24107 (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" @@ -44,7 +45,7 @@ #include "integrators/IntegratorCreator.hpp" #include "integrators/NPTxyz.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/simError.h" // Basic non-isotropic thermostating and barostating via the Melchionna @@ -57,119 +58,120 @@ // // Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. -namespace oopse { +namespace OpenMD { -double NPTxyz::calcConservedQuantity(){ + RealType NPTxyz::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; + RealType conservedQuantity; + RealType totalEnergy; + RealType thermostat_kinetic; + RealType thermostat_potential; + RealType barostat_kinetic; + RealType barostat_potential; + RealType trEta; - totalEnergy = thermo.getTotalE(); + totalEnergy = thermo.getTotalEnergy(); - thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); + thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first + / (2.0 * PhysicalConstants::energyConvert); - thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; + thermostat_potential = fkBT* thermostat.second + / 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; + barostat_kinetic + barostat_potential; return conservedQuantity; -} + } -void NPTxyz::scaleSimBox(){ + void NPTxyz::scaleSimBox(){ - int i,j,k; + int i, j; Mat3x3d scaleMat; - double eta2ij, scaleFactor; - double bigScale, smallScale, offDiagMax; + RealType scaleFactor; + RealType bigScale, smallScale; 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) - // 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++){ - scaleMat(i, j) = 0.0; - if(i==j) { - scaleMat(i, j) = 1.0; - } - } + for(j=0; j<3; j++){ + scaleMat(i, j) = 0.0; + if(i==j) { + scaleMat(i, j) = 1.0; + } + } } for(i=0;i<3;i++){ - // calculate the scaleFactors + // calculate the scaleFactors - scaleFactor = exp(dt*eta(i, i)); + scaleFactor = exp(dt*eta(i, i)); - scaleMat(i, i) = scaleFactor; + scaleMat(i, i) = scaleFactor; - if (scaleMat(i, i) > bigScale) { - bigScale = scaleMat(i, i); - } + if (scaleMat(i, i) > bigScale) { + bigScale = scaleMat(i, i); + } - if (scaleMat(i, i) < smallScale) { - smallScale = scaleMat(i, i); - } + if (scaleMat(i, i) < smallScale) { + smallScale = scaleMat(i, i); + } } if ((bigScale > 1.1) || (smallScale < 0.9)) { - sprintf( painCave.errMsg, - "NPTxyz error: Attempting a Box scaling of more than 10 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", - 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)); - painCave.isFatal = 1; - simError(); + sprintf( painCave.errMsg, + "NPTxyz error: Attempting a Box scaling of more than 10 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", + 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)); + painCave.isFatal = 1; + simError(); } else { - Mat3x3d hmat = currentSnapshot_->getHmat(); - hmat = hmat *scaleMat; - currentSnapshot_->setHmat(hmat); + Mat3x3d hmat = snap->getHmat(); + hmat = hmat *scaleMat; + snap->setHmat(hmat); } -} + } -void NPTxyz::loadEta() { - eta= currentSnapshot_->getEta(); -} + void NPTxyz::loadEta() { + eta= snap->getBarostat(); + } }