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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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} |
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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 (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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if ((bigScale > 1.01) || (smallScale < 0.99)) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
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"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
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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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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.1) { |
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} else if (offDiagMax > 0.01) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
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"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
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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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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); |
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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// cout.width(8); |
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// cout.precision(8); |
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
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// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
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return conservedQuantity; |
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} |
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const int BUFFERSIZE = 2000; // size of the read buffer |
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char buffer[BUFFERSIZE]; |
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sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt); |
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sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
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parameters += buffer; |
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for(int i = 0; i < 3; i++){ |
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sprintf(buffer,"\t%lf\t%lf\t%lf;", eta[3*i], eta[3*i+1], eta[3*i+2]); |
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sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
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parameters += buffer; |
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} |
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