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#include <stdlib.h> |
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#include <math.h> |
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|
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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|
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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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NPT::NPT ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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|
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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 != NULL ){ |
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chi = data->getDval(); |
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} |
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|
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data != NULL ){ |
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integralOfChidt = data->getDval(); |
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} |
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|
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oldPos = new double[3*nAtoms]; |
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oldVel = new double[3*nAtoms]; |
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oldJi = new double[3*nAtoms]; |
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#ifdef IS_MPI |
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Nparticles = mpiSim->getTotAtoms(); |
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#else |
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Nparticles = theInfo->n_atoms; |
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#endif |
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|
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} |
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|
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NPT::~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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void NPT::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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DirectionalAtom* dAtom; |
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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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for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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|
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mass = atoms[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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atoms[i]->setVel( vel ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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dAtom->getTrq( Tb ); |
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dAtom->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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dAtom->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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this->rotationPropagation( dAtom, ji ); |
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|
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dAtom->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 < nAtoms; i++){ |
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atoms[i]->getPos(pos); |
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for(j = 0; j < 3; j++) |
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oldPos[i*3 + j] = pos[j]; |
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} |
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|
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//the first estimation of r(t+dt) is equal to r(t) |
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|
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for(k = 0; k < 5; k ++){ |
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|
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for(i =0 ; i < nAtoms; i++){ |
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|
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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|
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this->getPosScale( pos, COM, i, sc ); |
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|
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
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|
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atoms[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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|
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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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void NPT::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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DirectionalAtom* dAtom; |
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double Tb[3], ji[3], sc[3]; |
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double vel[3], frc[3], qVel[3]; |
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double mass; |
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|
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// Set things up for the iteration: |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getVel( vel ); |
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|
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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dAtom->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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oldJi[3*i + j] = ji[j]; |
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|
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} |
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} |
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|
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// do the iteration: |
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|
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instaVol = tStats->getVolume(); |
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|
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for (k=0; k < 4; k++) { |
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|
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atoms[0]->getVel(vel); |
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|
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// std::cerr << "vel atom0 = " |
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// << vel[0] << ", " << vel[1] << ", " << vel[2] << "\n"; |
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|
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instaTemp = tStats->getTemperature(); |
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|
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std::cerr << "instaTemp MoveB = " << instaTemp << "\n"; |
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|
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instaPress = tStats->getPressure(); |
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|
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// evolve chi another half step using the temperature at t + dt/2 |
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|
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this->evolveChiB(); |
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this->evolveEtaB(); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getFrc( frc ); |
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atoms[i]->getVel(vel); |
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|
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mass = atoms[i]->getMass(); |
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|
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getVelScaleB( sc, i ); |
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|
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for(j=0;j<3;j++) |
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qVel[j] = vel[j]; |
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|
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// velocity half step |
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for (j=0; j < 3; j++) |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
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|
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// std::cerr << " vel of " << i << " => " |
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// << vel[0] << ", " << vel[1] << ", " << vel[2] << "\n"; |
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|
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double delVel = 0.0; |
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for(j=0;j<3;j++) |
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delVel += pow( (qVel[j] - vel[j]), 2 ); |
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|
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delVel = sqrt(delVel); |
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|
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std::cerr << "delVel[" << i << "] = " << delVel << "\n"; |
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|
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atoms[i]->setVel( vel ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
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|
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dAtom->setJ( ji ); |
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} |
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} |
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|
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if (nConstrained){ |
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constrainB(); |
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} |
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|
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if ( this->chiConverged() && this->etaConverged() ) break; |
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} |
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|
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//calculate integral of chida |
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integralOfChidt += dt2*chi; |
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|
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|
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} |
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|
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void NPT::resetIntegrator() { |
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chi = 0.0; |
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Integrator::resetIntegrator(); |
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} |
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|
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void NPT::evolveChiA() { |
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|
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std::cerr << "\n" |
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<< "evolveChiA before:\n" |
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<< "chi = " << chi << "\n" |
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<< "oldChi = " << oldChi << "\n" |
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<< "\n" |
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<< "instaTemp = " << instaTemp << "\n" |
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<< "targetTemp = " << targetTemp << "\n" |
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<< "dt2 = " << dt2 << "\n" |
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<< "tt2 = " << tt2 << "\n"; |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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oldChi = chi; |
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|
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std::cerr << "\n" |
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<< "evolveChiA after:\n" |
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<< "chi = " << chi << "\n" |
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<< "oldChi = " << oldChi << "\n" |
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<< "\n" |
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<< "instaTemp = " << instaTemp << "\n" |
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<< "targetTemp = " << targetTemp << "\n" |
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<< "dt2 = " << dt2 << "\n" |
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<< "tt2 = " << tt2 << "\n"; |
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|
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} |
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|
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void NPT::evolveChiB() { |
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|
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std::cerr << "\n" |
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<< "evolveChiB before:\n" |
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<< "chi = " << chi << "\n" |
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<< "oldChi = " << oldChi << "\n" |
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<< "\n" |
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<< "instaTemp = " << instaTemp << "\n" |
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<< "targetTemp = " << targetTemp << "\n" |
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<< "dt2 = " << dt2 << "\n" |
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<< "tt2 = " << tt2 << "\n"; |
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|
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prevChi = chi; |
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chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
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std::cerr << "\n" |
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<< "evolveChiB after:\n" |
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<< "chi = " << chi << "\n" |
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<< "oldChi = " << oldChi << "\n" |
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<< "\n" |
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<< "instaTemp = " << instaTemp << "\n" |
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<< "targetTemp = " << targetTemp << "\n" |
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<< "dt2 = " << dt2 << "\n" |
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<< "tt2 = " << tt2 << "\n"; |
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} |
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|
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bool NPT::chiConverged() { |
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|
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return ( fabs( prevChi - chi ) <= chiTolerance ); |
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} |
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|
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int NPT::readyCheck() { |
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|
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//check parent's readyCheck() first |
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if (Integrator::readyCheck() == -1) |
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return -1; |
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|
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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|
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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NPT error: You can't use the NPT integrator\n" |
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" without a targetTemp!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPT error: You can't use the NPT integrator\n" |
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" without a targetPressure!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauThermostat. |
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|
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NPT error: If you use the NPT\n" |
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" integrator, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauBarostat. |
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|
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if (!have_tau_barostat) { |
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sprintf( painCave.errMsg, |
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"NPT error: If you use the NPT\n" |
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" integrator, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_chi_tolerance) { |
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sprintf( painCave.errMsg, |
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"NPT warning: setting chi tolerance to 1e-6\n"); |
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chiTolerance = 1e-6; |
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have_chi_tolerance = 1; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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if (!have_eta_tolerance) { |
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sprintf( painCave.errMsg, |
| 409 |
"NPT warning: setting eta tolerance to 1e-6\n"); |
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etaTolerance = 1e-6; |
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have_eta_tolerance = 1; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of particles, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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|
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NkBT = (double)Nparticles * kB * targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
| 423 |
// than the barostat (when there are particles with orientational degrees |
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// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
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|
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fkBT = (double)info->ndf * kB * targetTemp; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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return 1; |
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} |
