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#include <math.h> |
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#include "MatVec3.h" |
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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#include "simError.h" |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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int i; |
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chi = 0.0; |
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for(i = 0; i < 9; i++) eta[i] = 0.0; |
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have_tau_thermostat = 0; |
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have_tau_barostat = 0; |
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have_target_temp = 0; |
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have_target_pressure = 0; |
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} |
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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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int i,j; |
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|
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void NPTf::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double rj[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double angle; |
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double press[9]; |
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const double p_convert = 1.63882576e8; |
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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eta[i][j] = 0.0; |
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oldEta[i][j] = 0.0; |
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} |
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} |
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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for (i=0; i < 9; i++) press[i] *= p_convert; |
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if( theInfo->useInitXSstate ){ |
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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|
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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|
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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eta[i][j] = etaArray[3*i+j]; |
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oldEta[i][j] = eta[i][j]; |
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} |
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} |
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} |
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} |
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} |
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instaVol = tStats->getVolume(); |
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// first evolve chi a half step |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
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eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
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eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
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eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
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eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
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eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
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eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
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eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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|
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vx = vel[atomIndex]; |
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vy = vel[atomIndex+1]; |
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vz = vel[atomIndex+2]; |
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|
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scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
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scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
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scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
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|
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vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
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vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
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vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
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} |
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vel[atomIndex] = vx; |
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vel[atomIndex+1] = vy; |
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vel[atomIndex+2] = vz; |
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template<typename T> NPTf<T>::~NPTf() { |
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// position whole step |
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// empty for now |
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} |
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rj[0] = pos[atomIndex]; |
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rj[1] = pos[atomIndex+1]; |
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rj[2] = pos[atomIndex+2]; |
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template<typename T> void NPTf<T>::resetIntegrator() { |
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info->wrapVector(rj); |
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int i, j; |
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scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
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scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
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scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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pos[atomIndex] += dt * (vel[atomIndex] + scx); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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|
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if( atoms[i]->isDirectional() ){ |
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T::resetIntegrator(); |
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} |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// get and convert the torque to body frame |
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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template<typename T> void NPTf<T>::evolveEtaA() { |
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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int i, j; |
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|
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) |
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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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else |
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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} |
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|
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} |
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|
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// Scale the box after all the positions have been moved: |
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+ |
for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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oldEta[i][j] = eta[i][j]; |
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} |
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template<typename T> void NPTf<T>::evolveEtaB() { |
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// Use a taylor expansion for eta products |
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|
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info->getBoxM(hm); |
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int i,j; |
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|
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+ |
for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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prevEta[i][j] = eta[i][j]; |
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|
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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} else { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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} |
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} |
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} |
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} |
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|
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template<typename T> void NPTf<T>::calcVelScale(void){ |
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int i,j; |
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|
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
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|
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< |
info->scaleBox(exp(dt*eta)); |
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> |
if (i == j) { |
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> |
vScale[i][j] += chi; |
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> |
} |
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> |
} |
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} |
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} |
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|
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|
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template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
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|
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matVecMul3( vScale, vel, sc ); |
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} |
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|
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void NPTi::moveB( void ){ |
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< |
int i,j,k; |
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int atomIndex; |
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DirectionalAtom* dAtom; |
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< |
double Tb[3]; |
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< |
double ji[3]; |
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< |
double instaTemp, instaPress, instaVol; |
| 187 |
< |
double tt2, tb2; |
| 188 |
< |
|
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< |
tt2 = tauThermostat * tauThermostat; |
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< |
tb2 = tauBarostat * tauBarostat; |
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> |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
| 141 |
> |
int j; |
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> |
double myVel[3]; |
| 143 |
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|
| 144 |
< |
instaTemp = tStats->getTemperature(); |
| 145 |
< |
instaPress = tStats->getPressure(); |
| 194 |
< |
instaVol = tStats->getVolume(); |
| 195 |
< |
|
| 196 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 197 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
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> |
for (j = 0; j < 3; j++) |
| 145 |
> |
myVel[j] = oldVel[3*index + j]; |
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|
| 147 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 148 |
< |
atomIndex = i * 3; |
| 149 |
< |
|
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< |
// velocity half step |
| 151 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 152 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 153 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 154 |
< |
- vel[j]*(chi+eta)); |
| 155 |
< |
|
| 156 |
< |
if( atoms[i]->isDirectional() ){ |
| 147 |
> |
matVecMul3( vScale, myVel, sc ); |
| 148 |
> |
} |
| 149 |
> |
|
| 150 |
> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
| 151 |
> |
int index, double sc[3]){ |
| 152 |
> |
int j; |
| 153 |
> |
double rj[3]; |
| 154 |
> |
|
| 155 |
> |
for(j=0; j<3; j++) |
| 156 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 157 |
> |
|
| 158 |
> |
matVecMul3( eta, rj, sc ); |
| 159 |
> |
} |
| 160 |
> |
|
| 161 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
| 162 |
> |
|
| 163 |
> |
int i,j,k; |
| 164 |
> |
double scaleMat[3][3]; |
| 165 |
> |
double eta2ij; |
| 166 |
> |
double bigScale, smallScale, offDiagMax; |
| 167 |
> |
double hm[3][3], hmnew[3][3]; |
| 168 |
> |
|
| 169 |
> |
|
| 170 |
> |
|
| 171 |
> |
// Scale the box after all the positions have been moved: |
| 172 |
> |
|
| 173 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 174 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 175 |
> |
|
| 176 |
> |
bigScale = 1.0; |
| 177 |
> |
smallScale = 1.0; |
| 178 |
> |
offDiagMax = 0.0; |
| 179 |
> |
|
| 180 |
> |
for(i=0; i<3; i++){ |
| 181 |
> |
for(j=0; j<3; j++){ |
| 182 |
> |
|
| 183 |
> |
// Calculate the matrix Product of the eta array (we only need |
| 184 |
> |
// the ij element right now): |
| 185 |
> |
|
| 186 |
> |
eta2ij = 0.0; |
| 187 |
> |
for(k=0; k<3; k++){ |
| 188 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
| 189 |
> |
} |
| 190 |
> |
|
| 191 |
> |
scaleMat[i][j] = 0.0; |
| 192 |
> |
// identity matrix (see above): |
| 193 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
| 194 |
> |
// Taylor expansion for the exponential truncated at second order: |
| 195 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 196 |
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|
| 197 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 198 |
< |
|
| 199 |
< |
// get and convert the torque to body frame |
| 200 |
< |
|
| 214 |
< |
Tb[0] = dAtom->getTx(); |
| 215 |
< |
Tb[1] = dAtom->getTy(); |
| 216 |
< |
Tb[2] = dAtom->getTz(); |
| 217 |
< |
|
| 218 |
< |
dAtom->lab2Body( Tb ); |
| 219 |
< |
|
| 220 |
< |
// get the angular momentum, and complete the angular momentum |
| 221 |
< |
// half step |
| 222 |
< |
|
| 223 |
< |
ji[0] = dAtom->getJx(); |
| 224 |
< |
ji[1] = dAtom->getJy(); |
| 225 |
< |
ji[2] = dAtom->getJz(); |
| 226 |
< |
|
| 227 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 228 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 229 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 230 |
< |
|
| 231 |
< |
dAtom->setJx( ji[0] ); |
| 232 |
< |
dAtom->setJy( ji[1] ); |
| 233 |
< |
dAtom->setJz( ji[2] ); |
| 197 |
> |
|
| 198 |
> |
if (i != j) |
| 199 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 200 |
> |
offDiagMax = fabs(scaleMat[i][j]); |
| 201 |
|
} |
| 235 |
– |
} |
| 236 |
– |
} |
| 202 |
|
|
| 203 |
< |
int NPTi::readyCheck() { |
| 204 |
< |
|
| 240 |
< |
// First check to see if we have a target temperature. |
| 241 |
< |
// Not having one is fatal. |
| 242 |
< |
|
| 243 |
< |
if (!have_target_temp) { |
| 244 |
< |
sprintf( painCave.errMsg, |
| 245 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 246 |
< |
" without a targetTemp!\n" |
| 247 |
< |
); |
| 248 |
< |
painCave.isFatal = 1; |
| 249 |
< |
simError(); |
| 250 |
< |
return -1; |
| 203 |
> |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 204 |
> |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 205 |
|
} |
| 206 |
|
|
| 207 |
< |
if (!have_target_pressure) { |
| 207 |
> |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 208 |
|
sprintf( painCave.errMsg, |
| 209 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 210 |
< |
" without a targetPressure!\n" |
| 211 |
< |
); |
| 209 |
> |
"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
| 210 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 211 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 212 |
> |
" [%lf\t%lf\t%lf]\n" |
| 213 |
> |
" [%lf\t%lf\t%lf]\n" |
| 214 |
> |
" eta = [%lf\t%lf\t%lf]\n" |
| 215 |
> |
" [%lf\t%lf\t%lf]\n" |
| 216 |
> |
" [%lf\t%lf\t%lf]\n", |
| 217 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 218 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 219 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
| 220 |
> |
eta[0][0],eta[0][1],eta[0][2], |
| 221 |
> |
eta[1][0],eta[1][1],eta[1][2], |
| 222 |
> |
eta[2][0],eta[2][1],eta[2][2]); |
| 223 |
|
painCave.isFatal = 1; |
| 224 |
|
simError(); |
| 225 |
< |
return -1; |
| 261 |
< |
} |
| 262 |
< |
|
| 263 |
< |
// We must set tauThermostat. |
| 264 |
< |
|
| 265 |
< |
if (!have_tau_thermostat) { |
| 225 |
> |
} else if (offDiagMax > 0.01) { |
| 226 |
|
sprintf( painCave.errMsg, |
| 227 |
< |
"NPTi error: If you use the NPTi\n" |
| 228 |
< |
" integrator, you must set tauThermostat.\n"); |
| 227 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
| 228 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 229 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 230 |
> |
" [%lf\t%lf\t%lf]\n" |
| 231 |
> |
" [%lf\t%lf\t%lf]\n" |
| 232 |
> |
" eta = [%lf\t%lf\t%lf]\n" |
| 233 |
> |
" [%lf\t%lf\t%lf]\n" |
| 234 |
> |
" [%lf\t%lf\t%lf]\n", |
| 235 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 236 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 237 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
| 238 |
> |
eta[0][0],eta[0][1],eta[0][2], |
| 239 |
> |
eta[1][0],eta[1][1],eta[1][2], |
| 240 |
> |
eta[2][0],eta[2][1],eta[2][2]); |
| 241 |
|
painCave.isFatal = 1; |
| 242 |
|
simError(); |
| 243 |
< |
return -1; |
| 244 |
< |
} |
| 243 |
> |
} else { |
| 244 |
> |
info->getBoxM(hm); |
| 245 |
> |
matMul3(hm, scaleMat, hmnew); |
| 246 |
> |
info->setBoxM(hmnew); |
| 247 |
> |
} |
| 248 |
> |
} |
| 249 |
|
|
| 250 |
< |
// We must set tauBarostat. |
| 251 |
< |
|
| 252 |
< |
if (!have_tau_barostat) { |
| 277 |
< |
sprintf( painCave.errMsg, |
| 278 |
< |
"NPTi error: If you use the NPTi\n" |
| 279 |
< |
" integrator, you must set tauBarostat.\n"); |
| 280 |
< |
painCave.isFatal = 1; |
| 281 |
< |
simError(); |
| 282 |
< |
return -1; |
| 283 |
< |
} |
| 250 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
| 251 |
> |
int i; |
| 252 |
> |
double diffEta, sumEta; |
| 253 |
|
|
| 254 |
< |
// We need NkBT a lot, so just set it here: |
| 254 |
> |
sumEta = 0; |
| 255 |
> |
for(i = 0; i < 3; i++) |
| 256 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 257 |
|
|
| 258 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
| 258 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
| 259 |
|
|
| 260 |
< |
return 1; |
| 260 |
> |
return ( diffEta <= etaTolerance ); |
| 261 |
|
} |
| 262 |
+ |
|
| 263 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 264 |
+ |
|
| 265 |
+ |
double conservedQuantity; |
| 266 |
+ |
double totalEnergy; |
| 267 |
+ |
double thermostat_kinetic; |
| 268 |
+ |
double thermostat_potential; |
| 269 |
+ |
double barostat_kinetic; |
| 270 |
+ |
double barostat_potential; |
| 271 |
+ |
double trEta; |
| 272 |
+ |
double a[3][3], b[3][3]; |
| 273 |
+ |
|
| 274 |
+ |
totalEnergy = tStats->getTotalE(); |
| 275 |
+ |
|
| 276 |
+ |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 277 |
+ |
(2.0 * eConvert); |
| 278 |
+ |
|
| 279 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 280 |
+ |
|
| 281 |
+ |
transposeMat3(eta, a); |
| 282 |
+ |
matMul3(a, eta, b); |
| 283 |
+ |
trEta = matTrace3(b); |
| 284 |
+ |
|
| 285 |
+ |
barostat_kinetic = NkBT * tb2 * trEta / |
| 286 |
+ |
(2.0 * eConvert); |
| 287 |
+ |
|
| 288 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 289 |
+ |
eConvert; |
| 290 |
+ |
|
| 291 |
+ |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 292 |
+ |
barostat_kinetic + barostat_potential; |
| 293 |
+ |
|
| 294 |
+ |
return conservedQuantity; |
| 295 |
+ |
|
| 296 |
+ |
} |
| 297 |
+ |
|
| 298 |
+ |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
| 299 |
+ |
string parameters; |
| 300 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 301 |
+ |
char buffer[BUFFERSIZE]; |
| 302 |
+ |
|
| 303 |
+ |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 304 |
+ |
parameters += buffer; |
| 305 |
+ |
|
| 306 |
+ |
for(int i = 0; i < 3; i++){ |
| 307 |
+ |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 308 |
+ |
parameters += buffer; |
| 309 |
+ |
} |
| 310 |
+ |
|
| 311 |
+ |
return parameters; |
| 312 |
+ |
|
| 313 |
+ |
} |
