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#include <stdlib.h> |
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#include <math.h> |
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#include <string.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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// 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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NPT( 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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double *etaArray; |
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int i,j; |
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for(i = 0; i < 3; i++){ |
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} |
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} |
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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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} |
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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 != NULL){ |
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int test = data->getDarray(etaArray); |
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if( test == 9 ){ |
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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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delete[] etaArray; |
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} |
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else |
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std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test |
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<< ").\n" |
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<< " Simulation wil proceed with eta = 0;\n"; |
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} |
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} |
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NPTf::~NPTf() { |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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Integrator::resetIntegrator(); |
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NPT::resetIntegrator(); |
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} |
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void NPTf::evolveEtaA() { |
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double myVel[3]; |
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double vScale[3][3]; |
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// std::cerr << "velScaleB chi = " << chi << "\n"; |
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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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void NPTf::getPosScale(double pos[3], double COM[3], |
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int index, double sc[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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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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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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string NPTf::getAdditionalParameters(void){ |
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string parameters; |
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const int BUFFERSIZE = 2000; // size of the read buffer |
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char buffer[BUFFERSIZE]; |
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char* NPTf::getAdditionalParameters(void){ |
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sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt); |
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parameters += buffer; |
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sprintf(addParamBuffer, |
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"\t%G\t%G;" |
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"\t%G\t%G\t%G;" |
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"\t%G\t%G\t%G;" |
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"\t%G\t%G\t%G;", |
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chi, integralOfChidt, |
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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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); |
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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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parameters += buffer; |
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} |
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return parameters; |
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return addParamBuffer; |
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} |
