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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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} |
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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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if(etaValue){ |
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etaArray = etaValue->getData(); |
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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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etaArray = etaValue->getData(); |
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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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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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oldEta[i][j] = eta[i][j]; |
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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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template<typename T> void NPTf<T>::calcVelScale(void){ |
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int i,j; |
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double vScale[3][3]; |
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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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} |
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} |
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} |
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info->matVecMul3( vScale, vel, sc ); |
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template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
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matVecMul3( vScale, vel, sc ); |
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} |
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template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
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int i,j; |
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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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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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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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for (j = 0; j < 3; j++) |
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myVel[j] = oldVel[3*index + j]; |
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info->matVecMul3( vScale, myVel, sc ); |
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matVecMul3( vScale, myVel, sc ); |
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} |
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template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
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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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info->matVecMul3( eta, rj, sc ); |
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matVecMul3( eta, rj, sc ); |
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} |
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template<typename T> void NPTf<T>::scaleSimBox( void ){ |
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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; |
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if (i != j) |
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if (fabs(scaleMat[i][j]) > offDiagMax) |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" eta = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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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], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
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eta[0][0],eta[0][1],eta[0][2], |
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eta[1][0],eta[1][1],eta[1][2], |
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eta[2][0],eta[2][1],eta[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.01) { |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" eta = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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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], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
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eta[0][0],eta[0][1],eta[0][2], |
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eta[1][0],eta[1][1],eta[1][2], |
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eta[2][0],eta[2][1],eta[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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info->getBoxM(hm); |
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info->matMul3(hm, scaleMat, hmnew); |
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matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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} |
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} |
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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info->transposeMat3(eta, a); |
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info->matMul3(a, eta, b); |
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trEta = info->matTrace3(b); |
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transposeMat3(eta, a); |
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matMul3(a, eta, b); |
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trEta = matTrace3(b); |
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barostat_kinetic = NkBT * tb2 * trEta / |
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(2.0 * eConvert); |
