--- trunk/OOPSE/libmdtools/NPTf.cpp 2003/09/19 16:01:07 772 +++ trunk/OOPSE/libmdtools/NPTf.cpp 2003/11/06 22:01:37 855 @@ -1,4 +1,4 @@ -#include +#include #include "Atom.hpp" #include "SRI.hpp" #include "AbstractClasses.hpp" @@ -7,7 +7,7 @@ #include "Thermo.hpp" #include "ReadWrite.hpp" #include "Integrator.hpp" -#include "simError.h" +#include "simError.h" #ifdef IS_MPI #include "mpiSimulation.hpp" @@ -17,223 +17,184 @@ // modification of the Hoover algorithm: // // Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, -// Molec. Phys., 78, 533. +// 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 ) { - int i, j; - chi = 0.0; - integralOfChidt = 0.0; + GenericData* data; + DoubleArrayData * etaValue; + vector etaArray; + int i,j; - for(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) + for(i = 0; i < 3; i++){ + for (j = 0; j < 3; j++){ + eta[i][j] = 0.0; + oldEta[i][j] = 0.0; + } + } - have_tau_thermostat = 0; - have_tau_barostat = 0; - have_target_temp = 0; - have_target_pressure = 0; - have_chi_tolerance = 0; - have_eta_tolerance = 0; - have_pos_iter_tolerance = 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]; + } + } + } + } + } - oldPos = new double[3*nAtoms]; - oldVel = new double[3*nAtoms]; - oldJi = new double[3*nAtoms]; -#ifdef IS_MPI - Nparticles = mpiSim->getTotAtoms(); -#else - Nparticles = theInfo->n_atoms; -#endif - } template NPTf::~NPTf() { - delete[] oldPos; - delete[] oldVel; - delete[] oldJi; + + // empty for now } -template void NPTf::moveA() { +template void NPTf::resetIntegrator() { - // new version of NPTf - int i, j, k; - DirectionalAtom* dAtom; - double Tb[3], ji[3]; - double A[3][3], I[3][3]; - double angle, mass; - double vel[3], pos[3], frc[3]; + int i, j; - double rj[3]; - double instaTemp, instaPress, instaVol; - double tt2, tb2; - double sc[3]; - double eta2ij; - double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; - double bigScale, smallScale, offDiagMax; - double COM[3]; + for(i = 0; i < 3; i++) + for (j = 0; j < 3; j++) + eta[i][j] = 0.0; - tt2 = tauThermostat * tauThermostat; - tb2 = tauBarostat * tauBarostat; + T::resetIntegrator(); +} - instaTemp = tStats->getTemperature(); - tStats->getPressureTensor(press); - instaVol = tStats->getVolume(); - - tStats->getCOM(COM); +template void NPTf::evolveEtaA() { - //calculate scale factor of veloity - 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; - } + 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); } } - - //evolve velocity half step - for( i=0; igetVel( vel ); - atoms[i]->getFrc( frc ); + for(i = 0; i < 3; i++) + for (j = 0; j < 3; j++) + oldEta[i][j] = eta[i][j]; +} - mass = atoms[i]->getMass(); - - info->matVecMul3( vScale, vel, sc ); +template void NPTf::evolveEtaB() { - for (j=0; j < 3; j++) { - // velocity half step - vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); - } + int i,j; - atoms[i]->setVel( vel ); - - if( atoms[i]->isDirectional() ){ + for(i = 0; i < 3; i++) + for (j = 0; j < 3; j++) + prevEta[i][j] = eta[i][j]; - dAtom = (DirectionalAtom *)atoms[i]; + 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); + } + } + } +} - // get and convert the torque to body frame - - dAtom->getTrq( Tb ); - dAtom->lab2Body( Tb ); - - // get the angular momentum, and propagate a half step +template void NPTf::getVelScaleA(double sc[3], double vel[3]) { + int i,j; + double vScale[3][3]; - dAtom->getJ( ji ); + for (i = 0; i < 3; i++ ) { + for (j = 0; j < 3; j++ ) { + vScale[i][j] = eta[i][j]; - for (j=0; j < 3; j++) - ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); - - // use the angular velocities to propagate the rotation matrix a - // full time step - - dAtom->getA(A); - dAtom->getI(I); - - // rotate about the x-axis - angle = dt2 * ji[0] / I[0][0]; - this->rotate( 1, 2, angle, ji, A ); - - // rotate about the y-axis - angle = dt2 * ji[1] / I[1][1]; - this->rotate( 2, 0, angle, ji, A ); - - // rotate about the z-axis - angle = dt * ji[2] / I[2][2]; - this->rotate( 0, 1, angle, ji, A); - - // rotate about the y-axis - angle = dt2 * ji[1] / I[1][1]; - this->rotate( 2, 0, angle, ji, A ); - - // rotate about the x-axis - angle = dt2 * ji[0] / I[0][0]; - this->rotate( 1, 2, angle, ji, A ); - - dAtom->setJ( ji ); - dAtom->setA( A ); - } + if (i == j) { + vScale[i][j] += chi; + } + } } - // advance chi half step - chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; + info->matVecMul3( vScale, vel, sc ); +} - // calculate the integral of chidt - integralOfChidt += dt2*chi; +template void NPTf::getVelScaleB(double sc[3], int index ){ + int i,j; + double myVel[3]; + double vScale[3][3]; - // advance eta half step + for (i = 0; i < 3; i++ ) { + for (j = 0; j < 3; j++ ) { + vScale[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/p_convert) / (NkBT*tb2); - else - eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); + if (i == j) { + vScale[i][j] += chi; + } } - - //save the old positions - for(i = 0; i < nAtoms; i++){ - atoms[i]->getPos(pos); - for(j = 0; j < 3; j++) - oldPos[i*3 + j] = pos[j]; } - - //the first estimation of r(t+dt) is equal to r(t) - - for(k = 0; k < 4; k ++){ - for(i =0 ; i < nAtoms; i++){ + for (j = 0; j < 3; j++) + myVel[j] = oldVel[3*index + j]; - atoms[i]->getVel(vel); - atoms[i]->getPos(pos); + info->matVecMul3( vScale, myVel, sc ); +} - for(j = 0; j < 3; j++) - rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; - - info->matVecMul3( eta, rj, sc ); - - for(j = 0; j < 3; j++) - pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); +template void NPTf::getPosScale(double pos[3], double COM[3], + int index, double sc[3]){ + int j; + double rj[3]; - atoms[i]->setPos( pos ); + for(j=0; j<3; j++) + rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; - } + info->matVecMul3( eta, rj, sc ); +} - if (nConstrained) { - constrainA(); - } - } +template void NPTf::scaleSimBox( void ){ - + int i,j,k; + double scaleMat[3][3]; + double eta2ij; + 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; - + 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]; } - + scaleMat[i][j] = 0.0; // identity matrix (see above): if (i == j) scaleMat[i][j] = 1.0; @@ -241,17 +202,17 @@ template void NPTf::moveA() { scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; if (i != j) - if (fabs(scaleMat[i][j]) > offDiagMax) + 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)) { + + if ((bigScale > 1.01) || (smallScale < 0.99)) { sprintf( painCave.errMsg, - "NPTf error: Attempting a Box scaling of more than 10 percent.\n" + "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" @@ -261,9 +222,9 @@ template void NPTf::moveA() { scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); painCave.isFatal = 1; simError(); - } else if (offDiagMax > 0.1) { + } else if (offDiagMax > 0.01) { sprintf( painCave.errMsg, - "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" + "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" @@ -278,222 +239,25 @@ template void NPTf::moveA() { info->matMul3(hm, scaleMat, hmnew); info->setBoxM(hmnew); } - } -template void NPTf::moveB( void ){ +template bool NPTf::etaConverged() { + int i; + double diffEta, sumEta; - //new version of NPTf - int i, j, k; - DirectionalAtom* dAtom; - double Tb[3], ji[3]; - double vel[3], myVel[3], frc[3]; - double mass; - - double instaTemp, instaPress, instaVol; - double tt2, tb2; - double sc[3]; - double press[3][3], vScale[3][3]; - double oldChi, prevChi; - double oldEta[3][3], prevEta[3][3], diffEta; - - tt2 = tauThermostat * tauThermostat; - tb2 = tauBarostat * tauBarostat; - - // Set things up for the iteration: - - oldChi = chi; - + sumEta = 0; for(i = 0; i < 3; i++) - for(j = 0; j < 3; j++) - oldEta[i][j] = eta[i][j]; + sumEta += pow(prevEta[i][i] - eta[i][i], 2); - for( i=0; igetVel( vel ); - - for (j=0; j < 3; j++) - oldVel[3*i + j] = vel[j]; - - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - - dAtom->getJ( ji ); - - for (j=0; j < 3; j++) - oldJi[3*i + j] = ji[j]; - - } - } - - // do the iteration: - - instaVol = tStats->getVolume(); - - for (k=0; k < 4; k++) { - - instaTemp = tStats->getTemperature(); - tStats->getPressureTensor(press); - - // evolve chi another half step using the temperature at t + dt/2 - - prevChi = chi; - chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; - - for(i = 0; i < 3; i++) - for(j = 0; j < 3; j++) - prevEta[i][j] = eta[i][j]; - - //advance eta half step and calculate scale factor for velocity - - 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); - vScale[i][j] = eta[i][j] + chi; - } else { - eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); - vScale[i][j] = eta[i][j]; - } - } - - for( i=0; igetFrc( frc ); - atoms[i]->getVel(vel); - - mass = atoms[i]->getMass(); - - for (j = 0; j < 3; j++) - myVel[j] = oldVel[3*i + j]; - - info->matVecMul3( vScale, myVel, sc ); - - // velocity half step - for (j=0; j < 3; j++) { - // velocity half step (use chi from previous step here): - vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); - } - - atoms[i]->setVel( vel ); - - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - - // get and convert the torque to body frame - - dAtom->getTrq( Tb ); - dAtom->lab2Body( Tb ); - - for (j=0; j < 3; j++) - ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); - - dAtom->setJ( ji ); - } - } - - if (nConstrained) { - constrainB(); - } - - diffEta = 0; - for(i = 0; i < 3; i++) - diffEta += pow(prevEta[i][i] - eta[i][i], 2); - - if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) - break; - } - - //calculate integral of chidt - integralOfChidt += dt2*chi; - + return ( diffEta <= etaTolerance ); } -template void NPTf::resetIntegrator() { - int i,j; - - chi = 0.0; - - for(i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - eta[i][j] = 0.0; - -} - -template int NPTf::readyCheck() { - - //check parent's readyCheck() first - if (T::readyCheck() == -1) - return -1; - - // First check to see if we have a target temperature. - // Not having one is fatal. - - if (!have_target_temp) { - sprintf( painCave.errMsg, - "NPTf error: You can't use the NPTf integrator\n" - " without a targetTemp!\n" - ); - painCave.isFatal = 1; - simError(); - return -1; - } - - if (!have_target_pressure) { - sprintf( painCave.errMsg, - "NPTf error: You can't use the NPTf integrator\n" - " without a targetPressure!\n" - ); - painCave.isFatal = 1; - simError(); - return -1; - } - - // We must set tauThermostat. - - if (!have_tau_thermostat) { - sprintf( painCave.errMsg, - "NPTf error: If you use the NPTf\n" - " integrator, you must set tauThermostat.\n"); - painCave.isFatal = 1; - simError(); - return -1; - } - - // We must set tauBarostat. - - if (!have_tau_barostat) { - sprintf( painCave.errMsg, - "NPTf error: If you use the NPTf\n" - " integrator, you must set tauBarostat.\n"); - painCave.isFatal = 1; - simError(); - return -1; - } - - - // We need NkBT a lot, so just set it here: This is the RAW number - // of particles, so no subtraction or addition of constraints or - // orientational degrees of freedom: - - NkBT = (double)Nparticles * 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). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons - - fkBT = (double)info->ndf * kB * targetTemp; - - return 1; -} - template double NPTf::getConservedQuantity(void){ double conservedQuantity; - double Energy; + double totalEnergy; double thermostat_kinetic; double thermostat_potential; double barostat_kinetic; @@ -501,9 +265,9 @@ template double NPTf::getConservedQuant double trEta; double a[3][3], b[3][3]; - Energy = tStats->getTotalE(); + totalEnergy = tStats->getTotalE(); - thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / + thermostat_kinetic = fkBT * tt2 * chi * chi / (2.0 * eConvert); thermostat_potential = fkBT* integralOfChidt / eConvert; @@ -512,21 +276,32 @@ template double NPTf::getConservedQuant info->matMul3(a, eta, b); trEta = info->matTrace3(b); - barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / + barostat_kinetic = NkBT * tb2 * trEta / (2.0 * eConvert); - - barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / + + barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / eConvert; - conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + + 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; - return conservedQuantity; } + +template string NPTf::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; + +}