--- trunk/src/integrators/NPTi.cpp 2005/01/12 22:41:40 246 +++ trunk/src/integrators/NPTi.cpp 2013/06/16 15:15:42 1879 @@ -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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "NPTi.hpp" @@ -44,142 +45,141 @@ #include "brains/Thermo.hpp" #include "integrators/NPT.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { -// Basic isotropic thermostating and barostating via the Melchionna -// modification of the Hoover algorithm: -// -// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, -// Molec. Phys., 78, 533. -// -// and -// -// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. + // Basic isotropic thermostating and barostating via the Melchionna + // modification of the Hoover algorithm: + // + // Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, + // Molec. Phys., 78, 533. + // + // and + // + // Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. -NPTi::NPTi ( SimInfo *info) : NPT(info){ + NPTi::NPTi ( SimInfo *info) : NPT(info){ -} + } -void NPTi::evolveEtaA() { + void NPTi::evolveEtaA() { eta += dt2 * ( instaVol * (instaPress - targetPressure) / - (OOPSEConstant::pressureConvert*NkBT*tb2)); + (PhysicalConstants::pressureConvert*NkBT*tb2)); oldEta = eta; -} + } -void NPTi::evolveEtaB() { + void NPTi::evolveEtaB() { prevEta = eta; eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / - (OOPSEConstant::pressureConvert*NkBT*tb2)); -} + (PhysicalConstants::pressureConvert*NkBT*tb2)); + } -void NPTi::calcVelScale() { - vScale = chi + eta; -} + void NPTi::calcVelScale() { + vScale = thermostat.first + eta; + } -void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { + void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { sc = vel * vScale; -} + } -void NPTi::getVelScaleB(Vector3d& sc, int index ){ + void NPTi::getVelScaleB(Vector3d& sc, int index ){ sc = oldVel[index] * vScale; -} + } -void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, - int index, Vector3d& sc){ + void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, + int index, Vector3d& sc){ /**@todo*/ - sc = (oldPos[index] + pos)/2.0 -COM; + sc = (oldPos[index] + pos)/(RealType)2.0 -COM; sc *= eta; -} + } -void NPTi::scaleSimBox(){ + void NPTi::scaleSimBox(){ - double scaleFactor; + RealType scaleFactor; scaleFactor = exp(dt*eta); if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { - sprintf( painCave.errMsg, - "NPTi error: Attempting a Box scaling of more than 10 percent" - " check your tauBarostat, as it is probably too small!\n" - " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor - ); - painCave.isFatal = 1; - simError(); + sprintf( painCave.errMsg, + "NPTi error: Attempting a Box scaling of more than 10 percent" + " check your tauBarostat, as it is probably too small!\n" + " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor + ); + painCave.isFatal = 1; + simError(); } else { - Mat3x3d hmat = currentSnapshot_->getHmat(); - hmat *= scaleFactor; - currentSnapshot_->setHmat(hmat); + Mat3x3d hmat = snap->getHmat(); + hmat *= scaleFactor; + snap->setHmat(hmat); } -} + } -bool NPTi::etaConverged() { + bool NPTi::etaConverged() { return ( fabs(prevEta - eta) <= etaTolerance ); -} + } -double NPTi::calcConservedQuantity(){ + RealType NPTi::calcConservedQuantity(){ - chi= currentSnapshot_->getChi(); - integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); + 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 Energy; - double thermostat_kinetic; - double thermostat_potential; - double barostat_kinetic; - double barostat_potential; + RealType conservedQuantity; + RealType Energy; + RealType thermostat_kinetic; + RealType thermostat_potential; + RealType barostat_kinetic; + RealType barostat_potential; - Energy =thermo.getTotalE(); + Energy =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; - barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert); + barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert); - barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) / - OOPSEConstant::energyConvert; + barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) / + PhysicalConstants::energyConvert; conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + - barostat_kinetic + barostat_potential; + barostat_kinetic + barostat_potential; return conservedQuantity; -} + } -void NPTi::loadEta() { - Mat3x3d etaMat = currentSnapshot_->getEta(); + void NPTi::loadEta() { + Mat3x3d etaMat = snap->getBarostat(); eta = etaMat(0,0); - //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) { + //if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) { // sprintf( painCave.errMsg, // "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); // painCave.isFatal = 1; // simError(); //} -} + } -void NPTi::saveEta() { + void NPTi::saveEta() { Mat3x3d etaMat(0.0); etaMat(0, 0) = eta; etaMat(1, 1) = eta; etaMat(2, 2) = eta; - currentSnapshot_->setEta(etaMat); + snap->setBarostat(etaMat); + } } - -}