--- trunk/src/integrators/NPTf.cpp 2005/01/12 22:41:40 246 +++ trunk/src/integrators/NPTf.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 "brains/SimInfo.hpp" @@ -44,250 +45,250 @@ #include "integrators/IntegratorCreator.hpp" #include "integrators/NPTf.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { -// Basic non-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 non-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. -void NPTf::evolveEtaA() { + void NPTf::evolveEtaA() { - int i, j; + int i, j; for(i = 0; i < 3; i ++){ - for(j = 0; j < 3; j++){ - if( i == j) { - eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); - } else { - eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); - } - } + for(j = 0; j < 3; j++){ + if( i == j) { + eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); + } else { + eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); + } + } } for(i = 0; i < 3; i++) { - for (j = 0; j < 3; j++) { + for (j = 0; j < 3; j++) { oldEta(i, j) = eta(i, j); - } + } } -} + } -void NPTf::evolveEtaB() { + void NPTf::evolveEtaB() { int i; int j; for(i = 0; i < 3; i++) { - for (j = 0; j < 3; j++) { - prevEta(i, j) = eta(i, j); - } + for (j = 0; j < 3; j++) { + prevEta(i, j) = eta(i, j); + } } for(i = 0; i < 3; i ++){ - for(j = 0; j < 3; j++){ - if( i == j) { - eta(i, j) = oldEta(i, j) + dt2 * instaVol * - (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); - } else { - eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); - } - } + for(j = 0; j < 3; j++){ + if( i == j) { + eta(i, j) = oldEta(i, j) + dt2 * instaVol * + (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); + } else { + eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); + } + } } -} + } -void NPTf::calcVelScale(){ + void NPTf::calcVelScale(){ - for (int i = 0; i < 3; i++ ) { - for (int j = 0; j < 3; j++ ) { - vScale(i, j) = eta(i, j); + for (int i = 0; i < 3; i++ ) { + for (int j = 0; j < 3; j++ ) { + vScale(i, j) = eta(i, j); - if (i == j) { - vScale(i, j) += chi; + if (i == j) { + vScale(i, j) += thermostat.first; + } } } } -} -void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ + void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ sc = vScale * vel; -} + } -void NPTf::getVelScaleB(Vector3d& sc, int index ) { - sc = vScale * oldVel[index]; -} + void NPTf::getVelScaleB(Vector3d& sc, int index ) { + sc = vScale * oldVel[index]; + } -void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { + void NPTf::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 NPTf::scaleSimBox(){ + void NPTf::scaleSimBox(){ - int i; - int j; - int k; - Mat3x3d scaleMat; - double eta2ij; - double bigScale, smallScale, offDiagMax; - Mat3x3d hm; - Mat3x3d hmnew; + int i; + int j; + int k; + Mat3x3d scaleMat; + RealType eta2ij; + RealType bigScale, smallScale, offDiagMax; + Mat3x3d hm; + Mat3x3d hmnew; - // Scale the box after all the positions have been moved: + // 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) + // 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; + bigScale = 1.0; + smallScale = 1.0; + offDiagMax = 0.0; - for(i=0; i<3; i++){ - for(j=0; j<3; j++){ + 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): + // 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); - } + 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; + 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 (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 (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, + "NPTf 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, + "NPTf 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 { - if ((bigScale > 1.01) || (smallScale < 0.99)) { - sprintf( painCave.errMsg, - "NPTf 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, - "NPTf 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); + Mat3x3d hmat = snap->getHmat(); + hmat = hmat *scaleMat; + snap->setHmat(hmat); + } } -} -bool NPTf::etaConverged() { + bool NPTf::etaConverged() { int i; - double diffEta, sumEta; + RealType diffEta, sumEta; sumEta = 0; for(i = 0; i < 3; i++) { - sumEta += pow(prevEta(i, i) - eta(i, i), 2); + sumEta += pow(prevEta(i, i) - eta(i, i), 2); } diffEta = sqrt( sumEta / 3.0 ); return ( diffEta <= etaTolerance ); -} + } -double NPTf::calcConservedQuantity(){ - - chi= currentSnapshot_->getChi(); - integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); + RealType NPTf::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 * thermostat.first * + thermostat.first /(2.0 * PhysicalConstants::energyConvert); - thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); + thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; - thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::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 NPTf::loadEta() { - eta= currentSnapshot_->getEta(); + void NPTf::loadEta() { + eta= snap->getBarostat(); //if (!eta.isDiagonal()) { // sprintf( painCave.errMsg, @@ -295,10 +296,10 @@ void NPTf::loadEta() { // painCave.isFatal = 1; // simError(); //} -} + } -void NPTf::saveEta() { - currentSnapshot_->setEta(eta); -} + void NPTf::saveEta() { + snap->setBarostat(eta); + } }