--- trunk/OOPSE-3.0/src/integrators/NPTxyz.cpp 2004/10/21 16:22:01 1625 +++ trunk/OOPSE-3.0/src/integrators/NPTxyz.cpp 2005/01/12 22:41:40 1930 @@ -1,19 +1,52 @@ -#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/NPTxyz.hpp" +#include "primitives/Molecule.hpp" +#include "utils/OOPSEConstant.hpp" #include "utils/simError.h" -#ifdef IS_MPI -#include "brains/mpiSimulation.hpp" -#endif - // Basic non-isotropic thermostating and barostating via the Melchionna // modification of the Hoover algorithm: // @@ -24,287 +57,119 @@ template NPTxyz::NPTxyz ( SimInfo *theI // // Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. -template NPTxyz::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff): - T( theInfo, the_ff ) -{ - GenericData* data; - DoubleVectorGenericData * etaValue; - int i,j; +namespace oopse { - for(i = 0; i < 3; i++){ - for (j = 0; j < 3; j++){ + +double NPTxyz::calcConservedQuantity(){ - eta[i][j] = 0.0; - oldEta[i][j] = 0.0; - } - } + // 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; + // 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; - if( theInfo->useInitXSstate ){ + double conservedQuantity; + double totalEnergy; + double thermostat_kinetic; + double thermostat_potential; + double barostat_kinetic; + double barostat_potential; + double trEta; - // retrieve eta array from simInfo if it exists - data = info->getProperty(ETAVALUE_ID); - if(data){ - etaValue = dynamic_cast(data); - - if(etaValue){ - - for(i = 0; i < 3; i++){ - for (j = 0; j < 3; j++){ - eta[i][j] = (*etaValue)[3*i+j]; - oldEta[i][j] = eta[i][j]; - } - } - } - } - } -} + totalEnergy = thermo.getTotalE(); -template NPTxyz::~NPTxyz() { + thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); - // empty for now -} + thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; -template void NPTxyz::resetIntegrator() { + SquareMatrix tmp = eta.transpose() * eta; + trEta = tmp.trace(); - int i, j; + barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); - for(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - eta[i][j] = 0.0; + barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; - T::resetIntegrator(); -} + conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + + barostat_kinetic + barostat_potential; -template void NPTxyz::evolveEtaA() { - int i, j; + return conservedQuantity; - 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] = 0.0; - } - } - - for(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - oldEta[i][j] = eta[i][j]; } -template void NPTxyz::evolveEtaB() { + +void NPTxyz::scaleSimBox(){ - int i,j; + int i,j,k; + Mat3x3d scaleMat; + double eta2ij, scaleFactor; + double bigScale, smallScale, offDiagMax; + Mat3x3d hm; + Mat3x3d hmnew; - 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] = 0.0; - } - } - } -} -template void NPTxyz::calcVelScale(void) { - int i,j; - - 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; - } - } - } -} - -template void NPTxyz::getVelScaleA(double sc[3], double vel[3]) { - matVecMul3( vScale, vel, sc ); -} - -template void NPTxyz::getVelScaleB(double sc[3], int index ){ - int j; - double myVel[3]; - - for (j = 0; j < 3; j++) - myVel[j] = oldVel[3*index + j]; - - matVecMul3( vScale, myVel, sc ); -} - -template void NPTxyz::getPosScale(double pos[3], double COM[3], - int index, double sc[3]){ - int j; - double rj[3]; - - for(j=0; j<3; j++) - rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; - - matVecMul3( eta, rj, sc ); -} - -template void NPTxyz::scaleSimBox( void ){ - - int i,j,k; - double scaleMat[3][3]; - double eta2ij, scaleFactor; - double bigScale, smallScale, offDiagMax; - double hm[3][3], hmnew[3][3]; - - - // 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; + 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(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(i=0;i<3;i++){ + for(i=0;i<3;i++){ // 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] < smallScale) smallScale = scaleMat[i][i]; - } + if (scaleMat(i, i) > bigScale) { + bigScale = scaleMat(i, i); + } + + if (scaleMat(i, i) < smallScale) { + smallScale = scaleMat(i, i); + } + } -// for(i=0; i<3; i++){ -// for(j=0; j<3; j++){ + 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(); + } else { -// // 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 > 1.1) || (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(); - } else { - info->getBoxM(hm); - matMul3(hm, scaleMat, hmnew); - info->setBoxM(hmnew); - } + Mat3x3d hmat = currentSnapshot_->getHmat(); + hmat = hmat *scaleMat; + currentSnapshot_->setHmat(hmat); + } } -template bool NPTxyz::etaConverged() { - int i; - double diffEta, sumEta; - - sumEta = 0; - for(i = 0; i < 3; i++) - sumEta += pow(prevEta[i][i] - eta[i][i], 2); - - diffEta = sqrt( sumEta / 3.0 ); - - return ( diffEta <= etaTolerance ); +void NPTxyz::loadEta() { + eta= currentSnapshot_->getEta(); } -template double NPTxyz::getConservedQuantity(void){ - - 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]; - - totalEnergy = tStats->getTotalE(); - - thermostat_kinetic = fkBT * tt2 * chi * chi / - (2.0 * eConvert); - - thermostat_potential = fkBT* integralOfChidt / eConvert; - - transposeMat3(eta, a); - matMul3(a, eta, b); - trEta = matTrace3(b); - - barostat_kinetic = NkBT * tb2 * trEta / - (2.0 * eConvert); - - barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / - eConvert; - - conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + - barostat_kinetic + barostat_potential; - -// cout.width(8); -// cout.precision(8); - -// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << -// "\t" << thermostat_potential << "\t" << barostat_kinetic << -// "\t" << barostat_potential << "\t" << conservedQuantity << endl; - - return conservedQuantity; - } - -template string NPTxyz::getAdditionalParameters(void){ - string parameters; - const int BUFFERSIZE = 2000; // size of the read buffer - char buffer[BUFFERSIZE]; - - 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; - } - - return parameters; - -}