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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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DoubleGenericData * chiValue; |
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DoubleGenericData * 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->getPropertyByName(CHIVALUE_ID); |
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if(data){ |
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chiValue = dynamic_cast<DoubleGenericData*>(data); |
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} |
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|
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data = info->getPropertyByName(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleGenericData*>(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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Vector3d Tb, ji; |
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double mass; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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Vector3d sc; |
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Vector3d COM; |
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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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vel = integrableObjects[i]->getVel(); |
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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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Tb = integrableObjects[i]->getTrq(); |
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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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ji = integrableObjects[i]->getJ(); |
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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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pos = integrableObjects[i]->getPos(); |
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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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vel = integrableObjects[i]->getVel(); |
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pos = integrableObjects[i]->getPos(); |
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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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Vector3d Tb; |
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Vector3d ji; |
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Vector3d sc; |
187 |
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Vector3d vel; |
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Vector3d frc; |
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double mass; |
190 |
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|
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// Set things up for the iteration: |
192 |
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|
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for( i=0; i<integrableObjects.size(); i++ ){ |
194 |
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|
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vel = integrableObjects[i]->getVel(); |
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|
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
199 |
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|
200 |
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if( integrableObjects[i]->isDirectional() ){ |
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|
202 |
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ji = integrableObjects[i]->getJ(); |
203 |
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|
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for (j=0; j < 3; j++) |
205 |
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oldJi[3*i + j] = ji[j]; |
206 |
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|
207 |
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} |
208 |
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} |
209 |
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|
210 |
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// do the iteration: |
211 |
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|
212 |
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instaVol = tStats->getVolume(); |
213 |
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|
214 |
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for (k=0; k < 4; k++) { |
215 |
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|
216 |
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instaTemp = tStats->getTemperature(); |
217 |
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instaPress = tStats->getPressure(); |
218 |
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|
219 |
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// evolve chi another half step using the temperature at t + dt/2 |
220 |
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|
221 |
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this->evolveChiB(); |
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this->evolveEtaB(); |
223 |
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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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|
227 |
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integrableObjects[i]->getFrc( frc ); |
228 |
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vel = integrableObjects[i]->getVel(); |
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|
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mass = integrableObjects[i]->getMass(); |
231 |
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|
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getVelScaleB( sc, i ); |
233 |
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|
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// velocity half step |
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for (j=0; j < 3; j++) |
236 |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
237 |
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|
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integrableObjects[i]->setVel( vel ); |
239 |
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|
240 |
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if( integrableObjects[i]->isDirectional() ){ |
241 |
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|
242 |
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// get and convert the torque to body frame |
243 |
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|
244 |
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Tb = integrableObjects[i]->getTrq(); |
245 |
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integrableObjects[i]->lab2Body( Tb ); |
246 |
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|
247 |
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for (j=0; j < 3; j++) |
248 |
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ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
249 |
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|
250 |
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integrableObjects[i]->setJ( ji ); |
251 |
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} |
252 |
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} |
253 |
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|
254 |
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if(nConstrained) |
255 |
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constrainB(); |
256 |
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|
257 |
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if ( this->chiConverged() && this->etaConverged() ) break; |
258 |
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} |
259 |
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|
260 |
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//calculate integral of chida |
261 |
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integralOfChidt += dt2*chi; |
262 |
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|
263 |
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|
264 |
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} |
265 |
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|
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template<typename T> void NPT<T>::resetIntegrator() { |
267 |
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chi = 0.0; |
268 |
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T::resetIntegrator(); |
269 |
< |
} |
270 |
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|
271 |
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template<typename T> void NPT<T>::evolveChiA() { |
272 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
273 |
< |
oldChi = chi; |
274 |
< |
} |
275 |
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|
276 |
< |
template<typename T> void NPT<T>::evolveChiB() { |
277 |
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|
278 |
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prevChi = chi; |
279 |
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chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
280 |
< |
} |
281 |
< |
|
282 |
< |
template<typename T> bool NPT<T>::chiConverged() { |
283 |
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|
284 |
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return ( fabs( prevChi - chi ) <= chiTolerance ); |
285 |
< |
} |
286 |
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|
287 |
< |
template<typename T> int NPT<T>::readyCheck() { |
288 |
< |
|
289 |
< |
//check parent's readyCheck() first |
290 |
< |
if (T::readyCheck() == -1) |
291 |
< |
return -1; |
292 |
< |
|
293 |
< |
// First check to see if we have a target temperature. |
294 |
< |
// Not having one is fatal. |
295 |
< |
|
296 |
< |
if (!have_target_temp) { |
297 |
< |
sprintf( painCave.errMsg, |
298 |
< |
"NPT error: You can't use the NPT integrator\n" |
299 |
< |
" without a targetTemp!\n" |
300 |
< |
); |
301 |
< |
painCave.isFatal = 1; |
302 |
< |
simError(); |
303 |
< |
return -1; |
304 |
< |
} |
305 |
< |
|
306 |
< |
if (!have_target_pressure) { |
307 |
< |
sprintf( painCave.errMsg, |
308 |
< |
"NPT error: You can't use the NPT integrator\n" |
309 |
< |
" without a targetPressure!\n" |
310 |
< |
); |
311 |
< |
painCave.isFatal = 1; |
312 |
< |
simError(); |
313 |
< |
return -1; |
314 |
< |
} |
315 |
< |
|
316 |
< |
// We must set tauThermostat. |
317 |
< |
|
318 |
< |
if (!have_tau_thermostat) { |
319 |
< |
sprintf( painCave.errMsg, |
320 |
< |
"NPT error: If you use the NPT\n" |
321 |
< |
" integrator, you must set tauThermostat.\n"); |
322 |
< |
painCave.isFatal = 1; |
323 |
< |
simError(); |
324 |
< |
return -1; |
325 |
< |
} |
326 |
< |
|
327 |
< |
// We must set tauBarostat. |
328 |
< |
|
329 |
< |
if (!have_tau_barostat) { |
330 |
< |
sprintf( painCave.errMsg, |
331 |
< |
"If you use the NPT integrator, you must set tauBarostat.\n"); |
332 |
< |
painCave.severity = OOPSE_ERROR; |
333 |
< |
painCave.isFatal = 1; |
334 |
< |
simError(); |
335 |
< |
return -1; |
336 |
< |
} |
337 |
< |
|
338 |
< |
if (!have_chi_tolerance) { |
339 |
< |
sprintf( painCave.errMsg, |
340 |
< |
"Setting chi tolerance to 1e-6 in NPT integrator\n"); |
341 |
< |
chiTolerance = 1e-6; |
342 |
< |
have_chi_tolerance = 1; |
343 |
< |
painCave.severity = OOPSE_INFO; |
344 |
< |
painCave.isFatal = 0; |
345 |
< |
simError(); |
346 |
< |
} |
347 |
< |
|
348 |
< |
if (!have_eta_tolerance) { |
349 |
< |
sprintf( painCave.errMsg, |
350 |
< |
"Setting eta tolerance to 1e-6 in NPT integrator"); |
351 |
< |
etaTolerance = 1e-6; |
352 |
< |
have_eta_tolerance = 1; |
353 |
< |
painCave.severity = OOPSE_INFO; |
354 |
< |
painCave.isFatal = 0; |
355 |
< |
simError(); |
356 |
< |
} |
357 |
< |
|
358 |
< |
// We need NkBT a lot, so just set it here: This is the RAW number |
359 |
< |
// of integrableObjects, so no subtraction or addition of constraints or |
360 |
< |
// orientational degrees of freedom: |
361 |
< |
|
362 |
< |
NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp; |
363 |
< |
|
364 |
< |
// fkBT is used because the thermostat operates on more degrees of freedom |
365 |
< |
// than the barostat (when there are particles with orientational degrees |
366 |
< |
// of freedom). |
367 |
< |
|
368 |
< |
fkBT = (double)(info->getNDF()) * kB * targetTemp; |
369 |
< |
|
370 |
< |
tt2 = tauThermostat * tauThermostat; |
371 |
< |
tb2 = tauBarostat * tauBarostat; |
372 |
< |
|
373 |
< |
return 1; |
374 |
< |
} |
1 |
> |
#include <math.h> |
2 |
> |
|
3 |
> |
#include "brains/SimInfo.hpp" |
4 |
> |
#include "brains/Thermo.hpp" |
5 |
> |
#include "integrators/NPT.hpp" |
6 |
> |
#include "utils/simError.h" |
7 |
> |
|
8 |
> |
|
9 |
> |
// Basic isotropic thermostating and barostating via the Melchionna |
10 |
> |
// modification of the Hoover algorithm: |
11 |
> |
// |
12 |
> |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
13 |
> |
// Molec. Phys., 78, 533. |
14 |
> |
// |
15 |
> |
// and |
16 |
> |
// |
17 |
> |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
18 |
> |
|
19 |
> |
namespace oopse { |
20 |
> |
|
21 |
> |
NPT::NPT(SimInfo* info) : |
22 |
> |
VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6) { |
23 |
> |
|
24 |
> |
Globals* globals = info_->getGlobals(); |
25 |
> |
|
26 |
> |
if (globals->getUseInitXSstate()) { |
27 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
28 |
> |
currSnapshot->setChi(0.0); |
29 |
> |
currSnapshot->setIntegralOfChiDt(0.0); |
30 |
> |
} |
31 |
> |
|
32 |
> |
if (!globals->haveTargetTemp()) { |
33 |
> |
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n"); |
34 |
> |
painCave.isFatal = 1; |
35 |
> |
painCave.severity = OOPSE_ERROR; |
36 |
> |
simError(); |
37 |
> |
} else { |
38 |
> |
targetTemp = globals->getTargetTemp(); |
39 |
> |
} |
40 |
> |
|
41 |
> |
// We must set tauThermostat |
42 |
> |
if (!globals->haveTauThermostat()) { |
43 |
> |
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
44 |
> |
"\tintegrator, you must set tauThermostat_.\n"); |
45 |
> |
|
46 |
> |
painCave.severity = OOPSE_ERROR; |
47 |
> |
painCave.isFatal = 1; |
48 |
> |
simError(); |
49 |
> |
} else { |
50 |
> |
tauThermostat = globals->getTauThermostat(); |
51 |
> |
} |
52 |
> |
|
53 |
> |
if (!globals->haveTargetPressure()) { |
54 |
> |
sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n" |
55 |
> |
" without a targetPressure!\n"); |
56 |
> |
|
57 |
> |
painCave.isFatal = 1; |
58 |
> |
simError(); |
59 |
> |
} else { |
60 |
> |
targetPressure = globals->getTargetPressure(); |
61 |
> |
} |
62 |
> |
|
63 |
> |
if (!globals->haveTauBarostat()) { |
64 |
> |
sprintf(painCave.errMsg, |
65 |
> |
"If you use the NPT integrator, you must set tauBarostat.\n"); |
66 |
> |
painCave.severity = OOPSE_ERROR; |
67 |
> |
painCave.isFatal = 1; |
68 |
> |
simError(); |
69 |
> |
} else { |
70 |
> |
tauBarostat = globals->getTauBarostat(); |
71 |
> |
} |
72 |
> |
|
73 |
> |
tt2 = tauThermostat * tauThermostat; |
74 |
> |
tb2 = tauBarostat * tauBarostat; |
75 |
> |
|
76 |
> |
update(); |
77 |
> |
} |
78 |
> |
|
79 |
> |
NPT::~NPT() { |
80 |
> |
} |
81 |
> |
|
82 |
> |
void NPT::update() { |
83 |
> |
oldPos.resize(info_->getNIntegrableObjects()); |
84 |
> |
oldVel.resize(info_->getNIntegrableObjects()); |
85 |
> |
oldJi.resize(info_->getNIntegrableObjects()); |
86 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
87 |
> |
// of integrableObjects, so no subtraction or addition of constraints or |
88 |
> |
// orientational degrees of freedom: |
89 |
> |
NkBT = info_->getNGlobalIntegrableObjects()*kB *targetTemp; |
90 |
> |
|
91 |
> |
// fkBT is used because the thermostat operates on more degrees of freedom |
92 |
> |
// than the barostat (when there are particles with orientational degrees |
93 |
> |
// of freedom). |
94 |
> |
fkBT = info_->getNdf()*kB *targetTemp; |
95 |
> |
} |
96 |
> |
|
97 |
> |
void NPT::moveA() { |
98 |
> |
typename SimInfo::MoleculeIterator i; |
99 |
> |
typename Molecule::IntegrableObjectIterator j; |
100 |
> |
Molecule* mol; |
101 |
> |
StuntDouble* integrableObject; |
102 |
> |
Vector3d Tb, ji; |
103 |
> |
double mass; |
104 |
> |
Vector3d vel; |
105 |
> |
Vector3d pos; |
106 |
> |
Vector3d frc; |
107 |
> |
Vector3d sc; |
108 |
> |
Vector3d COM; |
109 |
> |
int index; |
110 |
> |
|
111 |
> |
instaTemp = tStats->getTemperature(); |
112 |
> |
tStats->getPressureTensor(press); |
113 |
> |
instaPress = p_convert * (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
114 |
> |
instaVol = tStats->getVolume(); |
115 |
> |
|
116 |
> |
tStats->getCOM(COM); |
117 |
> |
|
118 |
> |
//evolve velocity half step |
119 |
> |
|
120 |
> |
calcVelScale(); |
121 |
> |
|
122 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
123 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
124 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
125 |
> |
|
126 |
> |
vel = integrableObject->getVel(); |
127 |
> |
frc = integrableObject->getFrc(); |
128 |
> |
|
129 |
> |
mass = integrableObject->getMass(); |
130 |
> |
|
131 |
> |
getVelScaleA(sc, vel); |
132 |
> |
|
133 |
> |
// velocity half step (use chi from previous step here): |
134 |
> |
//vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
135 |
> |
vel += dt2*eConvert/mass* frc - dt2*sc; |
136 |
> |
integrableObject->setVel(vel); |
137 |
> |
|
138 |
> |
if (integrableObject->isDirectional()) { |
139 |
> |
|
140 |
> |
// get and convert the torque to body frame |
141 |
> |
|
142 |
> |
Tb = integrableObject->getTrq(); |
143 |
> |
integrableObject->lab2Body(Tb); |
144 |
> |
|
145 |
> |
// get the angular momentum, and propagate a half step |
146 |
> |
|
147 |
> |
ji = integrableObject->getJ(); |
148 |
> |
|
149 |
> |
//ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
150 |
> |
ji += dt2*eConvert * Tb - dt2*chi* ji; |
151 |
> |
|
152 |
> |
this->rotationPropagation(integrableObject, ji); |
153 |
> |
|
154 |
> |
integrableObject->setJ(ji); |
155 |
> |
} |
156 |
> |
|
157 |
> |
} |
158 |
> |
} |
159 |
> |
// evolve chi and eta half step |
160 |
> |
|
161 |
> |
evolveChiA(); |
162 |
> |
evolveEtaA(); |
163 |
> |
|
164 |
> |
//calculate the integral of chidt |
165 |
> |
integralOfChidt += dt2 * chi; |
166 |
> |
|
167 |
> |
index = 0; |
168 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
169 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
170 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
171 |
> |
oldPos[index++] = integrableObject->getPos(); |
172 |
> |
} |
173 |
> |
} |
174 |
> |
|
175 |
> |
//the first estimation of r(t+dt) is equal to r(t) |
176 |
> |
|
177 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
178 |
> |
index = 0; |
179 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
180 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
181 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
182 |
> |
|
183 |
> |
vel = integrableObject->getVel(); |
184 |
> |
pos = integrableObject->getPos(); |
185 |
> |
|
186 |
> |
this->getPosScale(pos, COM, index, sc); |
187 |
> |
|
188 |
> |
pos = oldPos[index] + dt * (vel + sc); |
189 |
> |
integrableObject->setPos(pos); |
190 |
> |
|
191 |
> |
++index; |
192 |
> |
} |
193 |
> |
} |
194 |
> |
|
195 |
> |
//constraintAlgorithm->doConstrainA(); |
196 |
> |
} |
197 |
> |
|
198 |
> |
// Scale the box after all the positions have been moved: |
199 |
> |
|
200 |
> |
this->scaleSimBox(); |
201 |
> |
} |
202 |
> |
|
203 |
> |
void NPT::moveB(void) { |
204 |
> |
typename SimInfo::MoleculeIterator i; |
205 |
> |
typename Molecule::IntegrableObjectIterator j; |
206 |
> |
Molecule* mol; |
207 |
> |
StuntDouble* integrableObject; |
208 |
> |
int index; |
209 |
> |
Vector3d Tb; |
210 |
> |
Vector3d ji; |
211 |
> |
Vector3d sc; |
212 |
> |
Vector3d vel; |
213 |
> |
Vector3d frc; |
214 |
> |
double mass; |
215 |
> |
|
216 |
> |
//save velocity and angular momentum |
217 |
> |
index = 0; |
218 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
219 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
220 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
221 |
> |
|
222 |
> |
oldVel[index] = integrableObject->getVel(); |
223 |
> |
oldJi[3 * i + j] = integrableObject->getJ(); |
224 |
> |
++index; |
225 |
> |
} |
226 |
> |
} |
227 |
> |
|
228 |
> |
// do the iteration: |
229 |
> |
instaVol = tStats->getVolume(); |
230 |
> |
|
231 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
232 |
> |
instaTemp = tStats->getTemperature(); |
233 |
> |
instaPress = tStats->getPressure(); |
234 |
> |
|
235 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
236 |
> |
this->evolveChiB(); |
237 |
> |
this->evolveEtaB(); |
238 |
> |
this->calcVelScale(); |
239 |
> |
|
240 |
> |
index = 0; |
241 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
242 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
243 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
244 |
> |
integrableObject->getFrc(frc); |
245 |
> |
vel = integrableObject->getVel(); |
246 |
> |
|
247 |
> |
mass = integrableObject->getMass(); |
248 |
> |
|
249 |
> |
getVelScaleB(sc, i); |
250 |
> |
|
251 |
> |
// velocity half step |
252 |
> |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * eConvert - sc[j]); |
253 |
> |
vel = oldVel[index] + dt2*eConvert/mass* frc - dt2*sc; |
254 |
> |
integrableObject->setVel(vel); |
255 |
> |
|
256 |
> |
if (integrableObject->isDirectional()) { |
257 |
> |
// get and convert the torque to body frame |
258 |
> |
Tb = integrableObject->getTrq(); |
259 |
> |
integrableObject->lab2Body(Tb); |
260 |
> |
|
261 |
> |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
262 |
> |
ji = oldJi[index] + dt2*eConvert*Tb - dt2*chi*oldJi[index]; |
263 |
> |
integrableObject->setJ(ji); |
264 |
> |
} |
265 |
> |
|
266 |
> |
++index; |
267 |
> |
} |
268 |
> |
} |
269 |
> |
|
270 |
> |
//constraintAlgorithm->doConstrainB(); |
271 |
> |
|
272 |
> |
if (this->chiConverged() && this->etaConverged()) |
273 |
> |
break; |
274 |
> |
} |
275 |
> |
|
276 |
> |
//calculate integral of chidt |
277 |
> |
integralOfChidt += dt2 * chi; |
278 |
> |
} |
279 |
> |
|
280 |
> |
void NPT::evolveChiA() { |
281 |
> |
chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
282 |
> |
oldChi = chi; |
283 |
> |
} |
284 |
> |
|
285 |
> |
void NPT::evolveChiB() { |
286 |
> |
prevChi = chi; |
287 |
> |
chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
288 |
> |
} |
289 |
> |
|
290 |
> |
bool NPT::chiConverged() { |
291 |
> |
return (fabs(prevChi - chi) <= chiTolerance); |
292 |
> |
} |
293 |
> |
|
294 |
> |
} |