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#include <math.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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|
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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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|
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NPTi::NPTi ( 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 NPTi::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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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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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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|
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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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|
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for (i = 0; i < 9; i++) { |
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eta[i] += dt2 * ( instaVol * (sigma[i] - targetPressure*identMat[i])) |
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/ (NkBT*tb2)); |
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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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|
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} |
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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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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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template<typename T> NPTf<T>::~NPTf() { |
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|
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// position whole step |
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// empty for now |
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} |
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|
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for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
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rj[0] = pos[j]; |
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rj[1] = pos[j+1]; |
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rj[2] = pos[j+2]; |
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template<typename T> void NPTf<T>::resetIntegrator() { |
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|
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info->wrapVector(rj); |
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int i, j; |
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|
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pos[j] += dt * (vel[j] + eta*rj[0]); |
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pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
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pos[j+2] += dt * (vel[j+2] + eta*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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|
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T::resetIntegrator(); |
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} |
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|
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template<typename T> void NPTf<T>::evolveEtaA() { |
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|
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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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// 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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|
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info->scaleBox(exp(dt*eta)); |
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|
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if( atoms[i]->isDirectional() ){ |
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template<typename T> void NPTf<T>::evolveEtaB() { |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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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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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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int i,j; |
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|
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
103 |
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ji[2] = dAtom->getJz(); |
104 |
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|
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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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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
111 |
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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] ); |
117 |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
120 |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
121 |
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|
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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] ); |
125 |
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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] ); |
129 |
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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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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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|
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void NPTi::moveB( void ){ |
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int i,j,k; |
119 |
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int atomIndex; |
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DirectionalAtom* dAtom; |
146 |
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double Tb[3]; |
147 |
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double ji[3]; |
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double instaTemp, instaPress, instaVol; |
149 |
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double tt2, tb2; |
150 |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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> |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
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int i,j; |
119 |
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double vScale[3][3]; |
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|
|
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instaTemp = tStats->getTemperature(); |
122 |
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instaPress = tStats->getPressure(); |
123 |
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instaVol = tStats->getVolume(); |
121 |
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for (i = 0; i < 3; i++ ) { |
122 |
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for (j = 0; j < 3; j++ ) { |
123 |
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vScale[i][j] = eta[i][j]; |
124 |
|
|
125 |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
126 |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
127 |
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|
161 |
< |
for( i=0; i<nAtoms; i++ ){ |
162 |
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atomIndex = i * 3; |
163 |
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|
164 |
< |
// velocity half step |
165 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
166 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
167 |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
168 |
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- vel[j]*(chi+eta)); |
169 |
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|
170 |
< |
if( atoms[i]->isDirectional() ){ |
171 |
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|
172 |
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dAtom = (DirectionalAtom *)atoms[i]; |
173 |
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|
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// get and convert the torque to body frame |
175 |
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|
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Tb[0] = dAtom->getTx(); |
177 |
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Tb[1] = dAtom->getTy(); |
178 |
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Tb[2] = dAtom->getTz(); |
179 |
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|
180 |
< |
dAtom->lab2Body( Tb ); |
181 |
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|
182 |
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// get the angular momentum, and complete the angular momentum |
183 |
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// half step |
184 |
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|
185 |
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ji[0] = dAtom->getJx(); |
186 |
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ji[1] = dAtom->getJy(); |
187 |
< |
ji[2] = dAtom->getJz(); |
188 |
< |
|
189 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
190 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
191 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
192 |
< |
|
193 |
< |
dAtom->setJx( ji[0] ); |
194 |
< |
dAtom->setJy( ji[1] ); |
195 |
< |
dAtom->setJz( ji[2] ); |
125 |
> |
if (i == j) { |
126 |
> |
vScale[i][j] += chi; |
127 |
> |
} |
128 |
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} |
129 |
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} |
130 |
+ |
|
131 |
+ |
info->matVecMul3( vScale, vel, sc ); |
132 |
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} |
133 |
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|
134 |
< |
int NPTi::readyCheck() { |
135 |
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|
136 |
< |
// First check to see if we have a target temperature. |
137 |
< |
// Not having one is fatal. |
138 |
< |
|
139 |
< |
if (!have_target_temp) { |
140 |
< |
sprintf( painCave.errMsg, |
141 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
142 |
< |
" without a targetTemp!\n" |
143 |
< |
); |
144 |
< |
painCave.isFatal = 1; |
145 |
< |
simError(); |
146 |
< |
return -1; |
134 |
> |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
135 |
> |
int i,j; |
136 |
> |
double myVel[3]; |
137 |
> |
double vScale[3][3]; |
138 |
> |
|
139 |
> |
for (i = 0; i < 3; i++ ) { |
140 |
> |
for (j = 0; j < 3; j++ ) { |
141 |
> |
vScale[i][j] = eta[i][j]; |
142 |
> |
|
143 |
> |
if (i == j) { |
144 |
> |
vScale[i][j] += chi; |
145 |
> |
} |
146 |
> |
} |
147 |
|
} |
148 |
|
|
149 |
< |
if (!have_target_pressure) { |
150 |
< |
sprintf( painCave.errMsg, |
151 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
152 |
< |
" without a targetPressure!\n" |
153 |
< |
); |
154 |
< |
painCave.isFatal = 1; |
155 |
< |
simError(); |
156 |
< |
return -1; |
149 |
> |
for (j = 0; j < 3; j++) |
150 |
> |
myVel[j] = oldVel[3*index + j]; |
151 |
> |
|
152 |
> |
info->matVecMul3( vScale, myVel, sc ); |
153 |
> |
} |
154 |
> |
|
155 |
> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
156 |
> |
int index, double sc[3]){ |
157 |
> |
int j; |
158 |
> |
double rj[3]; |
159 |
> |
|
160 |
> |
for(j=0; j<3; j++) |
161 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
162 |
> |
|
163 |
> |
info->matVecMul3( eta, rj, sc ); |
164 |
> |
} |
165 |
> |
|
166 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
167 |
> |
|
168 |
> |
int i,j,k; |
169 |
> |
double scaleMat[3][3]; |
170 |
> |
double eta2ij; |
171 |
> |
double bigScale, smallScale, offDiagMax; |
172 |
> |
double hm[3][3], hmnew[3][3]; |
173 |
> |
|
174 |
> |
|
175 |
> |
|
176 |
> |
// Scale the box after all the positions have been moved: |
177 |
> |
|
178 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
179 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
180 |
> |
|
181 |
> |
bigScale = 1.0; |
182 |
> |
smallScale = 1.0; |
183 |
> |
offDiagMax = 0.0; |
184 |
> |
|
185 |
> |
for(i=0; i<3; i++){ |
186 |
> |
for(j=0; j<3; j++){ |
187 |
> |
|
188 |
> |
// Calculate the matrix Product of the eta array (we only need |
189 |
> |
// the ij element right now): |
190 |
> |
|
191 |
> |
eta2ij = 0.0; |
192 |
> |
for(k=0; k<3; k++){ |
193 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
194 |
> |
} |
195 |
> |
|
196 |
> |
scaleMat[i][j] = 0.0; |
197 |
> |
// identity matrix (see above): |
198 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
199 |
> |
// Taylor expansion for the exponential truncated at second order: |
200 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
201 |
> |
|
202 |
> |
if (i != j) |
203 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
204 |
> |
offDiagMax = fabs(scaleMat[i][j]); |
205 |
> |
} |
206 |
> |
|
207 |
> |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
208 |
> |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
209 |
|
} |
210 |
< |
|
211 |
< |
// We must set tauThermostat. |
226 |
< |
|
227 |
< |
if (!have_tau_thermostat) { |
210 |
> |
|
211 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
212 |
|
sprintf( painCave.errMsg, |
213 |
< |
"NPTi error: If you use the NPTi\n" |
214 |
< |
" integrator, you must set tauThermostat.\n"); |
213 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
214 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
215 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
216 |
> |
" [%lf\t%lf\t%lf]\n" |
217 |
> |
" [%lf\t%lf\t%lf]\n", |
218 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
219 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
220 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
221 |
|
painCave.isFatal = 1; |
222 |
|
simError(); |
223 |
< |
return -1; |
234 |
< |
} |
235 |
< |
|
236 |
< |
// We must set tauBarostat. |
237 |
< |
|
238 |
< |
if (!have_tau_barostat) { |
223 |
> |
} else if (offDiagMax > 0.1) { |
224 |
|
sprintf( painCave.errMsg, |
225 |
< |
"NPTi error: If you use the NPTi\n" |
226 |
< |
" integrator, you must set tauBarostat.\n"); |
225 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
226 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
227 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
228 |
> |
" [%lf\t%lf\t%lf]\n" |
229 |
> |
" [%lf\t%lf\t%lf]\n", |
230 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
231 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
232 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
233 |
|
painCave.isFatal = 1; |
234 |
|
simError(); |
235 |
< |
return -1; |
236 |
< |
} |
235 |
> |
} else { |
236 |
> |
info->getBoxM(hm); |
237 |
> |
info->matMul3(hm, scaleMat, hmnew); |
238 |
> |
info->setBoxM(hmnew); |
239 |
> |
} |
240 |
> |
} |
241 |
|
|
242 |
< |
// We need NkBT a lot, so just set it here: |
242 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
243 |
> |
int i; |
244 |
> |
double diffEta, sumEta; |
245 |
|
|
246 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
246 |
> |
sumEta = 0; |
247 |
> |
for(i = 0; i < 3; i++) |
248 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
249 |
|
|
250 |
< |
return 1; |
250 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
251 |
> |
|
252 |
> |
return ( diffEta <= etaTolerance ); |
253 |
|
} |
254 |
+ |
|
255 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
256 |
+ |
|
257 |
+ |
double conservedQuantity; |
258 |
+ |
double totalEnergy; |
259 |
+ |
double thermostat_kinetic; |
260 |
+ |
double thermostat_potential; |
261 |
+ |
double barostat_kinetic; |
262 |
+ |
double barostat_potential; |
263 |
+ |
double trEta; |
264 |
+ |
double a[3][3], b[3][3]; |
265 |
+ |
|
266 |
+ |
totalEnergy = tStats->getTotalE(); |
267 |
+ |
|
268 |
+ |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
269 |
+ |
(2.0 * eConvert); |
270 |
+ |
|
271 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
272 |
+ |
|
273 |
+ |
info->transposeMat3(eta, a); |
274 |
+ |
info->matMul3(a, eta, b); |
275 |
+ |
trEta = info->matTrace3(b); |
276 |
+ |
|
277 |
+ |
barostat_kinetic = NkBT * tb2 * trEta / |
278 |
+ |
(2.0 * eConvert); |
279 |
+ |
|
280 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
281 |
+ |
eConvert; |
282 |
+ |
|
283 |
+ |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
284 |
+ |
barostat_kinetic + barostat_potential; |
285 |
+ |
|
286 |
+ |
// cout.width(8); |
287 |
+ |
// cout.precision(8); |
288 |
+ |
|
289 |
+ |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
290 |
+ |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
291 |
+ |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
292 |
+ |
|
293 |
+ |
return conservedQuantity; |
294 |
+ |
|
295 |
+ |
} |
296 |
+ |
|
297 |
+ |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
298 |
+ |
string parameters; |
299 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
300 |
+ |
char buffer[BUFFERSIZE]; |
301 |
+ |
|
302 |
+ |
sprintf(buffer,"\t%f\t%f;", chi, integralOfChidt); |
303 |
+ |
parameters += buffer; |
304 |
+ |
|
305 |
+ |
for(int i = 0; i < 3; i++){ |
306 |
+ |
sprintf(buffer,"\t%g\t%g\t%g;", eta[3*i], eta[3*i+1], eta[3*i+2]); |
307 |
+ |
parameters += buffer; |
308 |
+ |
} |
309 |
+ |
|
310 |
+ |
return parameters; |
311 |
+ |
|
312 |
+ |
} |