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