--- trunk/src/integrators/NPTf.cpp 2004/09/24 16:27:58 3 +++ trunk/src/integrators/NPTf.cpp 2006/05/17 21:51:42 963 @@ -1,313 +1,304 @@ -#include - -#include "math/MatVec3.h" -#include "primitives/Atom.hpp" -#include "primitives/SRI.hpp" -#include "primitives/AbstractClasses.hpp" +/* + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * 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 + * notice, this list of conditions and the following disclaimer. + * + * 3. 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. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * 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. + */ + #include "brains/SimInfo.hpp" -#include "UseTheForce/ForceFields.hpp" #include "brains/Thermo.hpp" -#include "io/ReadWrite.hpp" -#include "integrators/Integrator.hpp" +#include "integrators/IntegratorCreator.hpp" +#include "integrators/NPTf.hpp" +#include "primitives/Molecule.hpp" +#include "utils/OOPSEConstant.hpp" #include "utils/simError.h" -#ifdef IS_MPI -#include "brains/mpiSimulation.hpp" -#endif +namespace oopse { -// 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. -template NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): - T( theInfo, the_ff ) -{ - GenericData* data; - DoubleArrayData * etaValue; - vector etaArray; - int i,j; + void NPTf::evolveEtaA() { - for(i = 0; i < 3; i++){ - for (j = 0; j < 3; j++){ + int i, j; - eta[i][j] = 0.0; - oldEta[i][j] = 0.0; - } - } - - - if( theInfo->useInitXSstate ){ - // retrieve eta array from simInfo if it exists - data = info->getProperty(ETAVALUE_ID); - if(data){ - etaValue = dynamic_cast(data); - - if(etaValue){ - etaArray = etaValue->getData(); - - for(i = 0; i < 3; i++){ - for (j = 0; j < 3; j++){ - eta[i][j] = etaArray[3*i+j]; - oldEta[i][j] = eta[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(i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + oldEta(i, j) = eta(i, j); + } + } + } -} + void NPTf::evolveEtaB() { -template NPTf::~NPTf() { + int i; + int j; - // empty for now -} + for(i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + prevEta(i, j) = eta(i, j); + } + } -template void NPTf::resetIntegrator() { - - int i, j; - - for(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - eta[i][j] = 0.0; - - T::resetIntegrator(); -} - -template void NPTf::evolveEtaA() { - - 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/p_convert) / (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++){ + 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(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - oldEta[i][j] = eta[i][j]; -} + } -template void NPTf::evolveEtaB() { + void NPTf::calcVelScale(){ - int i,j; + for (int i = 0; i < 3; i++ ) { + for (int j = 0; j < 3; j++ ) { + vScale(i, j) = eta(i, j); - for(i = 0; i < 3; i++) - 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/p_convert) / (NkBT*tb2); - } else { - eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); + if (i == j) { + vScale(i, j) += chi; + } } } } -} -template void NPTf::calcVelScale(void){ - int i,j; + void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ + sc = vScale * vel; + } - for (i = 0; i < 3; i++ ) { - for (j = 0; j < 3; j++ ) { - vScale[i][j] = eta[i][j]; - - if (i == j) { - vScale[i][j] += chi; - } - } + void NPTf::getVelScaleB(Vector3d& sc, int index ) { + sc = vScale * oldVel[index]; } -} -template void NPTf::getVelScaleA(double sc[3], double vel[3]) { - - matVecMul3( vScale, vel, sc ); -} + void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { -template void NPTf::getVelScaleB(double sc[3], int index ){ - int j; - double myVel[3]; + /**@todo */ + Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; + sc = eta * rj; + } - for (j = 0; j < 3; j++) - myVel[j] = oldVel[3*index + j]; - - matVecMul3( vScale, myVel, sc ); -} + void NPTf::scaleSimBox(){ -template void NPTf::getPosScale(double pos[3], double COM[3], - int index, double sc[3]){ - int j; - double rj[3]; + int i; + int j; + int k; + Mat3x3d scaleMat; + RealType eta2ij; + RealType bigScale, smallScale, offDiagMax; + Mat3x3d hm; + Mat3x3d hmnew; - for(j=0; j<3; j++) - rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; - matVecMul3( eta, rj, sc ); -} -template void NPTf::scaleSimBox( void ){ + // Scale the box after all the positions have been moved: - int i,j,k; - double scaleMat[3][3]; - double eta2ij; - double bigScale, smallScale, offDiagMax; - double hm[3][3], hmnew[3][3]; + // 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++){ - // Scale the box after all the positions have been moved: + // Calculate the matrix Product of the eta array (we only need + // the ij element right now): - // Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) - // Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) + eta2ij = 0.0; + for(k=0; k<3; k++){ + eta2ij += eta(i, k) * eta(k, j); + } - bigScale = 1.0; - smallScale = 1.0; - offDiagMax = 0.0; + 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; + - 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]; + if (i != j) + if (fabs(scaleMat(i, j)) > offDiagMax) + offDiagMax = fabs(scaleMat(i, 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 (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 { - info->getBoxM(hm); - matMul3(hm, scaleMat, hmnew); - info->setBoxM(hmnew); + Mat3x3d hmat = currentSnapshot_->getHmat(); + hmat = hmat *scaleMat; + currentSnapshot_->setHmat(hmat); + + } } -} -template bool NPTf::etaConverged() { - int i; - double diffEta, sumEta; + bool NPTf::etaConverged() { + int i; + RealType diffEta, sumEta; - sumEta = 0; - for(i = 0; i < 3; i++) - sumEta += pow(prevEta[i][i] - eta[i][i], 2); + sumEta = 0; + for(i = 0; i < 3; i++) { + sumEta += pow(prevEta(i, i) - eta(i, i), 2); + } + + diffEta = sqrt( sumEta / 3.0 ); - diffEta = sqrt( sumEta / 3.0 ); + return ( diffEta <= etaTolerance ); + } - return ( diffEta <= etaTolerance ); -} + RealType NPTf::calcConservedQuantity(){ -template double NPTf::getConservedQuantity(void){ + chi= currentSnapshot_->getChi(); + integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); + 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; - double conservedQuantity; - double totalEnergy; - double thermostat_kinetic; - double thermostat_potential; - double barostat_kinetic; - double barostat_potential; - double trEta; - double a[3][3], b[3][3]; + // 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; + + RealType conservedQuantity; + RealType totalEnergy; + RealType thermostat_kinetic; + RealType thermostat_potential; + RealType barostat_kinetic; + RealType barostat_potential; + RealType trEta; - totalEnergy = tStats->getTotalE(); + totalEnergy = thermo.getTotalE(); - thermostat_kinetic = fkBT * tt2 * chi * chi / - (2.0 * eConvert); + thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); - thermostat_potential = fkBT* integralOfChidt / eConvert; + thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; - transposeMat3(eta, a); - matMul3(a, eta, b); - trEta = matTrace3(b); + SquareMatrix tmp = eta.transpose() * eta; + trEta = tmp.trace(); + + barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); - barostat_kinetic = NkBT * tb2 * trEta / - (2.0 * eConvert); + barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; - barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / - eConvert; + conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + + barostat_kinetic + barostat_potential; - conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + - barostat_kinetic + barostat_potential; + return conservedQuantity; - return conservedQuantity; + } -} + void NPTf::loadEta() { + eta= currentSnapshot_->getEta(); -template string NPTf::getAdditionalParameters(void){ - string parameters; - const int BUFFERSIZE = 2000; // size of the read buffer - char buffer[BUFFERSIZE]; + //if (!eta.isDiagonal()) { + // sprintf( painCave.errMsg, + // "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); + // painCave.isFatal = 1; + // simError(); + //} + } - sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); - parameters += buffer; - - for(int i = 0; i < 3; i++){ - sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); - parameters += buffer; + void NPTf::saveEta() { + currentSnapshot_->setEta(eta); } - return parameters; - }