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#include <math.h> |
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|
3 |
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#include "primitives/Atom.hpp" |
4 |
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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++) { |
108 |
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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]); |
111 |
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|
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} |
113 |
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|
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integrableObjects[i]->setVel( vel ); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
117 |
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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); |
129 |
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|
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this->rotationPropagation( integrableObjects[i], ji ); |
131 |
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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++) |
148 |
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oldPos[i*3 + j] = pos[j]; |
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} |
150 |
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|
151 |
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//the first estimation of r(t+dt) is equal to r(t) |
152 |
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|
153 |
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for(k = 0; k < 5; k ++){ |
154 |
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|
155 |
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for(i =0 ; i < integrableObjects.size(); i++){ |
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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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|
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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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|
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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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|
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// Scale the box after all the positions have been moved: |
174 |
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|
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this->scaleSimBox(); |
176 |
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} |
177 |
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|
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template<typename T> void NPT<T>::moveB( void ){ |
179 |
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|
180 |
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//new version of NPT |
181 |
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int i, j, k; |
182 |
< |
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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|
188 |
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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++) |
193 |
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oldVel[3*i + j] = vel[j]; |
194 |
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|
195 |
< |
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++) |
200 |
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oldJi[3*i + j] = ji[j]; |
201 |
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|
202 |
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} |
203 |
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} |
204 |
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|
205 |
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// do the iteration: |
206 |
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|
207 |
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instaVol = tStats->getVolume(); |
208 |
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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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|
216 |
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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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|
229 |
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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 |
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|
249 |
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if(nConstrained) |
250 |
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constrainB(); |
251 |
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|
252 |
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if ( this->chiConverged() && this->etaConverged() ) break; |
253 |
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} |
254 |
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|
255 |
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//calculate integral of chida |
256 |
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integralOfChidt += dt2*chi; |
257 |
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|
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 |
< |
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 |
> |
} |