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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 "SimInfo.hpp" |
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#include "ForceFields.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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|
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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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// 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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// |
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// and |
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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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{ |
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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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|
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eta = 0.0; |
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oldEta = 0.0; |
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|
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// retrieve eta from simInfo if |
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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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eta = etaArray[0]; |
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oldEta = eta; |
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} |
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} |
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|
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} |
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|
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NPTi::~NPTi() { |
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//nothing for now |
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} |
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|
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void NPTi::resetIntegrator() { |
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eta = 0.0; |
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Integrator::resetIntegrator(); |
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} |
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|
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void NPTi::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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|
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void NPTi::evolveEtaB() { |
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|
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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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} |
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|
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void NPTi::getVelScaleA(double sc[3], double vel[3]) { |
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int i; |
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|
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for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta ); |
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} |
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|
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void NPTi::getVelScaleB(double sc[3], int index ){ |
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int i; |
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|
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for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta ); |
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} |
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|
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|
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void NPTi::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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|
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for(j=0; j<3; j++) |
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sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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|
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for(j=0; j<3; j++) |
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sc[j] *= eta; |
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} |
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|
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void NPTi::scaleSimBox( void ){ |
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|
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double scaleFactor; |
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|
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scaleFactor = exp(dt*eta); |
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|
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTi error: Attempting a Box scaling of more than 10 percent" |
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" check your tauBarostat, as it is probably too small!\n" |
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" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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info->scaleBox(scaleFactor); |
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} |
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|
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} |
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|
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bool NPTi::etaConverged() { |
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|
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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} |
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|
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double NPTi::getConservedQuantity(void){ |
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|
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double conservedQuantity; |
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double Energy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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|
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Energy = tStats->getTotalE(); |
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|
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thermostat_kinetic = fkBT* tt2 * chi * chi / |
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(2.0 * eConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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|
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|
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
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(2.0 * eConvert); |
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|
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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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eConvert; |
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|
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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// cout.width(8); |
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// cout.precision(8); |
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|
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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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|
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string NPTi::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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|
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sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt); |
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parameters += buffer; |
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|
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sprintf(buffer,"\t%lf\t0\t0;", eta); |
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parameters += buffer; |
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|
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sprintf(buffer,"\t0\t%lf\t0;", eta); |
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parameters += buffer; |
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|
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sprintf(buffer,"\t0\t0\t%lf;", eta); |
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parameters += buffer; |
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|
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return parameters; |
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|
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} |
