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#include <math.h> |
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|
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#include "primitives/Atom.hpp" |
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#include "primitives/SRI.hpp" |
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#include "primitives/AbstractClasses.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "UseTheForce/ForceFields.hpp" |
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#include "brains/Thermo.hpp" |
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#include "io/ReadWrite.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "utils/simError.h" |
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|
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#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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#endif |
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|
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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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template<typename T> NPT<T>::NPT ( 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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DoubleData * chiValue; |
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DoubleData * integralOfChidtValue; |
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|
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chiValue = NULL; |
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integralOfChidtValue = NULL; |
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|
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chi = 0.0; |
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integralOfChidt = 0.0; |
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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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have_chi_tolerance = 0; |
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have_eta_tolerance = 0; |
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have_pos_iter_tolerance = 0; |
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|
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// retrieve chi and integralOfChidt from simInfo |
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data = info->getProperty(CHIVALUE_ID); |
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if(data){ |
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chiValue = dynamic_cast<DoubleData*>(data); |
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} |
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|
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
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} |
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|
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// chi and integralOfChidt should appear by pair |
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if(chiValue && integralOfChidtValue){ |
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chi = chiValue->getData(); |
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integralOfChidt = integralOfChidtValue->getData(); |
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} |
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|
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oldPos = new double[3*integrableObjects.size()]; |
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oldVel = new double[3*integrableObjects.size()]; |
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oldJi = new double[3*integrableObjects.size()]; |
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|
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} |
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|
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template<typename T> NPT<T>::~NPT() { |
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delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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|
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template<typename T> void NPT<T>::moveA() { |
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|
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//new version of NPT |
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int i, j, k; |
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double Tb[3], ji[3]; |
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double mass; |
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double vel[3], pos[3], frc[3]; |
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double sc[3]; |
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double COM[3]; |
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|
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor( press ); |
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instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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instaVol = tStats->getVolume(); |
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|
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tStats->getCOM(COM); |
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|
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//evolve velocity half step |
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|
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calcVelScale(); |
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|
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for( i=0; i<integrableObjects.size(); i++ ){ |
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|
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integrableObjects[i]->getVel( vel ); |
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integrableObjects[i]->getFrc( frc ); |
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|
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mass = integrableObjects[i]->getMass(); |
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|
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getVelScaleA( sc, vel ); |
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|
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for (j=0; j < 3; j++) { |
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|
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// velocity half step (use chi from previous step here): |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
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|
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} |
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|
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integrableObjects[i]->setVel( vel ); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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// get and convert the torque to body frame |
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|
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integrableObjects[i]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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integrableObjects[i]->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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this->rotationPropagation( integrableObjects[i], ji ); |
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|
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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|
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// evolve chi and eta half step |
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|
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evolveChiA(); |
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evolveEtaA(); |
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|
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//calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
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|
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//save the old positions |
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for(i = 0; i < integrableObjects.size(); i++){ |
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integrableObjects[i]->getPos(pos); |
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for(j = 0; j < 3; j++) |
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oldPos[i*3 + j] = pos[j]; |
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} |
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|
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//the first estimation of r(t+dt) is equal to r(t) |
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|
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for(k = 0; k < 5; k ++){ |
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|
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for(i =0 ; i < integrableObjects.size(); i++){ |
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|
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integrableObjects[i]->getVel(vel); |
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integrableObjects[i]->getPos(pos); |
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|
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this->getPosScale( pos, COM, i, sc ); |
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|
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
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|
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integrableObjects[i]->setPos( pos ); |
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} |
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|
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if(nConstrained) |
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constrainA(); |
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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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this->scaleSimBox(); |
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} |
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|
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template<typename T> void NPT<T>::moveB( void ){ |
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|
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//new version of NPT |
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int i, j, k; |
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double Tb[3], ji[3], sc[3]; |
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double vel[3], frc[3]; |
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double mass; |
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|
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// Set things up for the iteration: |
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|
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for( i=0; i<integrableObjects.size(); i++ ){ |
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|
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integrableObjects[i]->getVel( vel ); |
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|
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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integrableObjects[i]->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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oldJi[3*i + j] = ji[j]; |
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|
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} |
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} |
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|
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// do the iteration: |
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|
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instaVol = tStats->getVolume(); |
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|
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for (k=0; k < 4; k++) { |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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|
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// evolve chi another half step using the temperature at t + dt/2 |
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|
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this->evolveChiB(); |
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this->evolveEtaB(); |
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this->calcVelScale(); |
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|
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for( i=0; i<integrableObjects.size(); i++ ){ |
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|
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integrableObjects[i]->getFrc( frc ); |
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integrableObjects[i]->getVel(vel); |
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|
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mass = integrableObjects[i]->getMass(); |
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|
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getVelScaleB( sc, i ); |
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|
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// velocity half step |
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for (j=0; j < 3; j++) |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
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|
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integrableObjects[i]->setVel( vel ); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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// get and convert the torque to body frame |
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|
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integrableObjects[i]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
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|
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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|
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if(nConstrained) |
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constrainB(); |
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|
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if ( this->chiConverged() && this->etaConverged() ) break; |
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} |
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|
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//calculate integral of chida |
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integralOfChidt += dt2*chi; |
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|
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|
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} |
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|
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template<typename T> void NPT<T>::resetIntegrator() { |
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chi = 0.0; |
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T::resetIntegrator(); |
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} |
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|
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template<typename T> void NPT<T>::evolveChiA() { |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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oldChi = chi; |
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} |
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|
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template<typename T> void NPT<T>::evolveChiB() { |
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|
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prevChi = chi; |
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chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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} |
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|
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template<typename T> bool NPT<T>::chiConverged() { |
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|
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return ( fabs( prevChi - chi ) <= chiTolerance ); |
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} |
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|
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template<typename T> int NPT<T>::readyCheck() { |
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|
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//check parent's readyCheck() first |
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if (T::readyCheck() == -1) |
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return -1; |
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|
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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|
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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NPT error: You can't use the NPT integrator\n" |
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" without a targetTemp!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPT error: You can't use the NPT integrator\n" |
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" without a targetPressure!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauThermostat. |
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|
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NPT error: If you use the NPT\n" |
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" integrator, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauBarostat. |
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|
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if (!have_tau_barostat) { |
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sprintf( painCave.errMsg, |
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"If you use the NPT integrator, you must set tauBarostat.\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_chi_tolerance) { |
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sprintf( painCave.errMsg, |
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"Setting chi tolerance to 1e-6 in NPT integrator\n"); |
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chiTolerance = 1e-6; |
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have_chi_tolerance = 1; |
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painCave.severity = OOPSE_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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if (!have_eta_tolerance) { |
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sprintf( painCave.errMsg, |
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"Setting eta tolerance to 1e-6 in NPT integrator"); |
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etaTolerance = 1e-6; |
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have_eta_tolerance = 1; |
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painCave.severity = OOPSE_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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|
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NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). |
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|
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fkBT = (double)(info->getNDF()) * kB * targetTemp; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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return 1; |
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} |
