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#include <math.h> |
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|
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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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// 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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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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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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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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|
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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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|
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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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|
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} |
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|
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template<typename T> NPTf<T>::~NPTf() { |
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|
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// empty for now |
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} |
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|
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template<typename T> void NPTf<T>::resetIntegrator() { |
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|
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int i, j; |
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chi = 0.0; |
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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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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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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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T::resetIntegrator(); |
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} |
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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 ri[3], vi[3], sc[3]; |
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double instaTemp, instaVol; |
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double tt2, tb2, eta2ij; |
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double angle; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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template<typename T> void NPTf<T>::evolveEtaA() { |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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int i, j; |
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|
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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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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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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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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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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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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template<typename T> void NPTf<T>::evolveEtaB() { |
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|
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vScale[i][j] = eta[i][j] + chi; |
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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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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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|
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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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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vScale[i][j] = eta[i][j]; |
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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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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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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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vi[0] = vel[atomIndex]; |
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vi[1] = vel[atomIndex+1]; |
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vi[2] = vel[atomIndex+2]; |
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|
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info->matVecMul3( vScale, vi, sc ); |
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|
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vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
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vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
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vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
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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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info->matVecMul3( vScale, vel, sc ); |
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} |
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|
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vel[atomIndex] = vi[0] |
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vel[atomIndex+1] = vi[1]; |
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vel[atomIndex+2] = vi[2]; |
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template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
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int j; |
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double myVel[3]; |
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double vScale[3][3]; |
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|
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// position whole step |
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for (j = 0; j < 3; j++) |
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myVel[j] = oldVel[3*index + j]; |
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|
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ri[0] = pos[atomIndex]; |
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ri[1] = pos[atomIndex+1]; |
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ri[2] = pos[atomIndex+2]; |
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info->matVecMul3( vScale, myVel, sc ); |
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} |
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|
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info->wrapVector(ri); |
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template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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double rj[3]; |
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|
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info->matVecMul3( eta, ri, sc ); |
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for(j=0; j<3; j++) |
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rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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|
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pos[atomIndex] += dt * (vel[atomIndex] + sc[0]); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]); |
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|
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if( atoms[i]->isDirectional() ){ |
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info->matVecMul3( eta, rj, sc ); |
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} |
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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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template<typename T> void NPTf<T>::scaleSimBox( void ){ |
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|
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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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|
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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 |
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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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// 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 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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} |
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|
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} |
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int i,j,k; |
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double scaleMat[3][3]; |
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double eta2ij; |
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double bigScale, smallScale, offDiagMax; |
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double hm[3][3], hmnew[3][3]; |
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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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|
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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
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|
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bigScale = 1.0; |
177 |
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smallScale = 1.0; |
178 |
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offDiagMax = 0.0; |
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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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for(k=0; k<3; k++){ |
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eta2ij += eta[i][k] * eta[k][j]; |
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} |
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|
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|
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scaleMat[i][j] = 0.0; |
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// identity matrix (see above): |
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if (i == j) scaleMat[i][j] = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
196 |
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|
197 |
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if (i != j) |
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if (fabs(scaleMat[i][j]) > offDiagMax) |
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offDiagMax = fabs(scaleMat[i][j]); |
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} |
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|
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if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
203 |
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if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
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|
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info->getBoxM(hm); |
207 |
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info->matMul3(hm, scaleMat, hmnew); |
208 |
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info->setBoxM(hmnew); |
209 |
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|
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|
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> |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
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sprintf( painCave.errMsg, |
208 |
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"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
209 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
210 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
211 |
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" [%lf\t%lf\t%lf]\n" |
212 |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
215 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
217 |
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simError(); |
218 |
> |
} else if (offDiagMax > 0.01) { |
219 |
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sprintf( painCave.errMsg, |
220 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
221 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
222 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
223 |
> |
" [%lf\t%lf\t%lf]\n" |
224 |
> |
" [%lf\t%lf\t%lf]\n", |
225 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
226 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
227 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
228 |
> |
painCave.isFatal = 1; |
229 |
> |
simError(); |
230 |
> |
} else { |
231 |
> |
info->getBoxM(hm); |
232 |
> |
info->matMul3(hm, scaleMat, hmnew); |
233 |
> |
info->setBoxM(hmnew); |
234 |
> |
} |
235 |
|
} |
236 |
|
|
237 |
< |
void NPTf::moveB( void ){ |
238 |
< |
int i,j, k; |
239 |
< |
int atomIndex; |
202 |
< |
DirectionalAtom* dAtom; |
203 |
< |
double Tb[3]; |
204 |
< |
double ji[3]; |
205 |
< |
double vi[3], sc[3]; |
206 |
< |
double instaTemp, instaVol; |
207 |
< |
double tt2, tb2; |
208 |
< |
double press[3][3], vScale[3][3]; |
209 |
< |
|
210 |
< |
tt2 = tauThermostat * tauThermostat; |
211 |
< |
tb2 = tauBarostat * tauBarostat; |
237 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
238 |
> |
int i; |
239 |
> |
double diffEta, sumEta; |
240 |
|
|
241 |
< |
instaTemp = tStats->getTemperature(); |
242 |
< |
tStats->getPressureTensor(press); |
243 |
< |
instaVol = tStats->getVolume(); |
216 |
< |
|
217 |
< |
// first evolve chi a half step |
218 |
< |
|
219 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
220 |
< |
|
221 |
< |
for (i = 0; i < 3; i++ ) { |
222 |
< |
for (j = 0; j < 3; j++ ) { |
223 |
< |
if (i == j) { |
241 |
> |
sumEta = 0; |
242 |
> |
for(i = 0; i < 3; i++) |
243 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
244 |
|
|
245 |
< |
eta[i][j] += dt2 * instaVol * |
226 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
245 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
246 |
|
|
247 |
< |
vScale[i][j] = eta[i][j] + chi; |
248 |
< |
|
230 |
< |
} else { |
231 |
< |
|
232 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
247 |
> |
return ( diffEta <= etaTolerance ); |
248 |
> |
} |
249 |
|
|
250 |
< |
vScale[i][j] = eta[i][j]; |
235 |
< |
|
236 |
< |
} |
237 |
< |
} |
238 |
< |
} |
250 |
> |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
251 |
|
|
252 |
< |
for( i=0; i<nAtoms; i++ ){ |
253 |
< |
atomIndex = i * 3; |
252 |
> |
double conservedQuantity; |
253 |
> |
double totalEnergy; |
254 |
> |
double thermostat_kinetic; |
255 |
> |
double thermostat_potential; |
256 |
> |
double barostat_kinetic; |
257 |
> |
double barostat_potential; |
258 |
> |
double trEta; |
259 |
> |
double a[3][3], b[3][3]; |
260 |
|
|
261 |
< |
// velocity half step |
244 |
< |
|
245 |
< |
vi[0] = vel[atomIndex]; |
246 |
< |
vi[1] = vel[atomIndex+1]; |
247 |
< |
vi[2] = vel[atomIndex+2]; |
248 |
< |
|
249 |
< |
info->matVecMul3( vScale, vi, sc ); |
250 |
< |
|
251 |
< |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
252 |
< |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
253 |
< |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
261 |
> |
totalEnergy = tStats->getTotalE(); |
262 |
|
|
263 |
< |
vel[atomIndex] = vi[0] |
264 |
< |
vel[atomIndex+1] = vi[1]; |
257 |
< |
vel[atomIndex+2] = vi[2]; |
258 |
< |
|
259 |
< |
if( atoms[i]->isDirectional() ){ |
260 |
< |
|
261 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
262 |
< |
|
263 |
< |
// get and convert the torque to body frame |
264 |
< |
|
265 |
< |
Tb[0] = dAtom->getTx(); |
266 |
< |
Tb[1] = dAtom->getTy(); |
267 |
< |
Tb[2] = dAtom->getTz(); |
268 |
< |
|
269 |
< |
dAtom->lab2Body( Tb ); |
270 |
< |
|
271 |
< |
// get the angular momentum, and complete the angular momentum |
272 |
< |
// half step |
273 |
< |
|
274 |
< |
ji[0] = dAtom->getJx(); |
275 |
< |
ji[1] = dAtom->getJy(); |
276 |
< |
ji[2] = dAtom->getJz(); |
277 |
< |
|
278 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
279 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
280 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
281 |
< |
|
282 |
< |
dAtom->setJx( ji[0] ); |
283 |
< |
dAtom->setJy( ji[1] ); |
284 |
< |
dAtom->setJz( ji[2] ); |
285 |
< |
} |
286 |
< |
} |
287 |
< |
} |
263 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
264 |
> |
(2.0 * eConvert); |
265 |
|
|
266 |
< |
int NPTf::readyCheck() { |
290 |
< |
|
291 |
< |
// First check to see if we have a target temperature. |
292 |
< |
// Not having one is fatal. |
293 |
< |
|
294 |
< |
if (!have_target_temp) { |
295 |
< |
sprintf( painCave.errMsg, |
296 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
297 |
< |
" without a targetTemp!\n" |
298 |
< |
); |
299 |
< |
painCave.isFatal = 1; |
300 |
< |
simError(); |
301 |
< |
return -1; |
302 |
< |
} |
266 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
267 |
|
|
268 |
< |
if (!have_target_pressure) { |
269 |
< |
sprintf( painCave.errMsg, |
270 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
307 |
< |
" without a targetPressure!\n" |
308 |
< |
); |
309 |
< |
painCave.isFatal = 1; |
310 |
< |
simError(); |
311 |
< |
return -1; |
312 |
< |
} |
313 |
< |
|
314 |
< |
// We must set tauThermostat. |
315 |
< |
|
316 |
< |
if (!have_tau_thermostat) { |
317 |
< |
sprintf( painCave.errMsg, |
318 |
< |
"NPTf error: If you use the NPTf\n" |
319 |
< |
" integrator, you must set tauThermostat.\n"); |
320 |
< |
painCave.isFatal = 1; |
321 |
< |
simError(); |
322 |
< |
return -1; |
323 |
< |
} |
268 |
> |
info->transposeMat3(eta, a); |
269 |
> |
info->matMul3(a, eta, b); |
270 |
> |
trEta = info->matTrace3(b); |
271 |
|
|
272 |
< |
// We must set tauBarostat. |
273 |
< |
|
327 |
< |
if (!have_tau_barostat) { |
328 |
< |
sprintf( painCave.errMsg, |
329 |
< |
"NPTf error: If you use the NPTf\n" |
330 |
< |
" integrator, you must set tauBarostat.\n"); |
331 |
< |
painCave.isFatal = 1; |
332 |
< |
simError(); |
333 |
< |
return -1; |
334 |
< |
} |
272 |
> |
barostat_kinetic = NkBT * tb2 * trEta / |
273 |
> |
(2.0 * eConvert); |
274 |
|
|
275 |
< |
// We need NkBT a lot, so just set it here: |
275 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
276 |
> |
eConvert; |
277 |
|
|
278 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
278 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
279 |
> |
barostat_kinetic + barostat_potential; |
280 |
|
|
281 |
< |
return 1; |
281 |
> |
return conservedQuantity; |
282 |
> |
|
283 |
|
} |
284 |
+ |
|
285 |
+ |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
286 |
+ |
string parameters; |
287 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
288 |
+ |
char buffer[BUFFERSIZE]; |
289 |
+ |
|
290 |
+ |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
291 |
+ |
parameters += buffer; |
292 |
+ |
|
293 |
+ |
for(int i = 0; i < 3; i++){ |
294 |
+ |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
295 |
+ |
parameters += buffer; |
296 |
+ |
} |
297 |
+ |
|
298 |
+ |
return parameters; |
299 |
+ |
|
300 |
+ |
} |