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#include <cmath> |
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#include <math.h> |
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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 "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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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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int i, j; |
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chi = 0.0; |
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integralOfChidt = 0.0; |
32 |
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|
33 |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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|
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int i,j; |
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|
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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|
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eta[i][j] = 0.0; |
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oldEta[i][j] = 0.0; |
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} |
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} |
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} |
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|
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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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template<typename T> NPTf<T>::~NPTf() { |
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|
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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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// empty for now |
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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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template<typename T> void NPTf<T>::resetIntegrator() { |
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|
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int i, j; |
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|
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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|
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T::resetIntegrator(); |
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} |
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|
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template<typename T> NPTf<T>::~NPTf() { |
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delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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template<typename T> void NPTf<T>::evolveEtaA() { |
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|
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int i, j; |
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|
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) |
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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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else |
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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} |
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} |
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|
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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oldEta[i][j] = eta[i][j]; |
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} |
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|
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template<typename T> void NPTf<T>::moveA() { |
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template<typename T> void NPTf<T>::evolveEtaB() { |
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|
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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 A[3][3], I[3][3]; |
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double angle, mass; |
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double vel[3], pos[3], frc[3]; |
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int i,j; |
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|
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double rj[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double sc[3]; |
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double eta2ij; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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double bigScale, smallScale, offDiagMax; |
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double COM[3]; |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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prevEta[i][j] = eta[i][j]; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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} else { |
90 |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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} |
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} |
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} |
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} |
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|
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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instaVol = tStats->getVolume(); |
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|
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tStats->getCOM(COM); |
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template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
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int i,j; |
98 |
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double vScale[3][3]; |
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|
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//calculate scale factor of veloity |
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
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} |
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} |
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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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info->matVecMul3( vScale, vel, sc ); |
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} |
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|
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atoms[i]->getVel( vel ); |
114 |
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atoms[i]->getFrc( frc ); |
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template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
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int i,j; |
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double myVel[3]; |
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double vScale[3][3]; |
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|
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mass = atoms[i]->getMass(); |
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|
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info->matVecMul3( vScale, vel, sc ); |
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|
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for (j=0; j < 3; j++) { |
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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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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
121 |
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|
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if (i == j) { |
123 |
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vScale[i][j] += chi; |
124 |
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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]; |
118 |
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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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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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|
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dAtom->getA(A); |
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dAtom->getI(I); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / I[2][2]; |
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this->rotate( 0, 1, angle, ji, A); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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|
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dAtom->setJ( ji ); |
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dAtom->setA( A ); |
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} |
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} |
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|
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// advance chi half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
164 |
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|
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//calculate the integral of chidt |
166 |
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integralOfChidt += dt2*chi; |
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|
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//advance eta half step |
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for(i = 0; i < 3; i ++) |
170 |
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for(j = 0; j < 3; j++){ |
171 |
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if( i == j) |
172 |
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eta[i][j] += dt2 * instaVol * |
173 |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
174 |
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else |
175 |
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eta[i][j] += dt2 * instaVol * press[i][j] / ( NkBT*tb2); |
176 |
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} |
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|
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//save the old positions |
179 |
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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++) |
182 |
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oldPos[i*3 + j] = pos[j]; |
183 |
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} |
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|
|
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< |
//the first estimation of r(t+dt) is equal to r(t) |
129 |
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|
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< |
for(k = 0; k < 4; k ++){ |
128 |
> |
for (j = 0; j < 3; j++) |
129 |
> |
myVel[j] = oldVel[3*index + j]; |
130 |
|
|
131 |
< |
for(i =0 ; i < nAtoms; i++){ |
131 |
> |
info->matVecMul3( vScale, myVel, sc ); |
132 |
> |
} |
133 |
|
|
134 |
< |
atoms[i]->getVel(vel); |
135 |
< |
atoms[i]->getPos(pos); |
134 |
> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
135 |
> |
int index, double sc[3]){ |
136 |
> |
int j; |
137 |
> |
double rj[3]; |
138 |
|
|
139 |
< |
for(j = 0; j < 3; j++) |
140 |
< |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
196 |
< |
|
197 |
< |
info->matVecMul3( eta, rj, sc ); |
198 |
< |
|
199 |
< |
for(j = 0; j < 3; j++) |
200 |
< |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
139 |
> |
for(j=0; j<3; j++) |
140 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
141 |
|
|
142 |
< |
atoms[i]->setPos( pos ); |
142 |
> |
info->matVecMul3( eta, rj, sc ); |
143 |
> |
} |
144 |
|
|
145 |
< |
} |
145 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
146 |
|
|
147 |
< |
} |
147 |
> |
int i,j,k; |
148 |
> |
double scaleMat[3][3]; |
149 |
> |
double eta2ij; |
150 |
> |
double bigScale, smallScale, offDiagMax; |
151 |
> |
double hm[3][3], hmnew[3][3]; |
152 |
> |
|
153 |
|
|
154 |
< |
|
154 |
> |
|
155 |
|
// Scale the box after all the positions have been moved: |
156 |
|
|
157 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
216 |
|
info->matMul3(hm, scaleMat, hmnew); |
217 |
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info->setBoxM(hmnew); |
218 |
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} |
273 |
– |
|
219 |
|
} |
220 |
|
|
221 |
< |
template<typename T> void NPTf<T>::moveB( void ){ |
221 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
222 |
> |
int i; |
223 |
> |
double diffEta, sumEta; |
224 |
|
|
225 |
< |
int i, j, k; |
279 |
< |
DirectionalAtom* dAtom; |
280 |
< |
double Tb[3], ji[3]; |
281 |
< |
double vel[3], frc[3]; |
282 |
< |
double mass; |
283 |
< |
|
284 |
< |
double instaTemp, instaPress, instaVol; |
285 |
< |
double tt2, tb2; |
286 |
< |
double sc[3]; |
287 |
< |
double press[3][3], vScale[3][3]; |
288 |
< |
double oldChi, prevChi; |
289 |
< |
double oldEta[3][3], preEta[3][3], diffEta; |
290 |
< |
|
291 |
< |
tt2 = tauThermostat * tauThermostat; |
292 |
< |
tb2 = tauBarostat * tauBarostat; |
293 |
< |
|
294 |
< |
|
295 |
< |
// Set things up for the iteration: |
296 |
< |
|
297 |
< |
oldChi = chi; |
298 |
< |
|
225 |
> |
sumEta = 0; |
226 |
|
for(i = 0; i < 3; i++) |
227 |
< |
for(j = 0; j < 3; j++) |
301 |
< |
oldEta[i][j] = eta[i][j]; |
302 |
< |
|
303 |
< |
for( i=0; i<nAtoms; i++ ){ |
304 |
< |
|
305 |
< |
atoms[i]->getVel( vel ); |
306 |
< |
|
307 |
< |
for (j=0; j < 3; j++) |
308 |
< |
oldVel[3*i + j] = vel[j]; |
309 |
< |
|
310 |
< |
if( atoms[i]->isDirectional() ){ |
311 |
< |
|
312 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
313 |
< |
|
314 |
< |
dAtom->getJ( ji ); |
315 |
< |
|
316 |
< |
for (j=0; j < 3; j++) |
317 |
< |
oldJi[3*i + j] = ji[j]; |
318 |
< |
|
319 |
< |
} |
320 |
< |
} |
321 |
< |
|
322 |
< |
// do the iteration: |
323 |
< |
|
324 |
< |
instaVol = tStats->getVolume(); |
227 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
228 |
|
|
229 |
< |
for (k=0; k < 4; k++) { |
327 |
< |
|
328 |
< |
instaTemp = tStats->getTemperature(); |
329 |
< |
tStats->getPressureTensor(press); |
330 |
< |
|
331 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
332 |
< |
|
333 |
< |
prevChi = chi; |
334 |
< |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
335 |
< |
|
336 |
< |
for(i = 0; i < 3; i++) |
337 |
< |
for(j = 0; j < 3; j++) |
338 |
< |
preEta[i][j] = eta[i][j]; |
339 |
< |
|
340 |
< |
//advance eta half step and calculate scale factor for velocity |
341 |
< |
for(i = 0; i < 3; i ++) |
342 |
< |
for(j = 0; j < 3; j++){ |
343 |
< |
if( i == j){ |
344 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
345 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
346 |
< |
vScale[i][j] = eta[i][j] + chi; |
347 |
< |
} |
348 |
< |
else |
349 |
< |
{ |
350 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
351 |
< |
vScale[i][j] = eta[i][j]; |
352 |
< |
} |
353 |
< |
} |
354 |
< |
|
355 |
< |
//advance velocity half step |
356 |
< |
for( i=0; i<nAtoms; i++ ){ |
357 |
< |
|
358 |
< |
atoms[i]->getFrc( frc ); |
359 |
< |
atoms[i]->getVel(vel); |
360 |
< |
|
361 |
< |
mass = atoms[i]->getMass(); |
362 |
< |
|
363 |
< |
info->matVecMul3( vScale, vel, sc ); |
364 |
< |
|
365 |
< |
for (j=0; j < 3; j++) { |
366 |
< |
// velocity half step (use chi from previous step here): |
367 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
368 |
< |
} |
369 |
< |
|
370 |
< |
atoms[i]->setVel( vel ); |
371 |
< |
|
372 |
< |
if( atoms[i]->isDirectional() ){ |
373 |
< |
|
374 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
229 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
230 |
|
|
231 |
< |
// get and convert the torque to body frame |
377 |
< |
|
378 |
< |
dAtom->getTrq( Tb ); |
379 |
< |
dAtom->lab2Body( Tb ); |
380 |
< |
|
381 |
< |
for (j=0; j < 3; j++) |
382 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
383 |
< |
|
384 |
< |
dAtom->setJ( ji ); |
385 |
< |
} |
386 |
< |
} |
387 |
< |
|
388 |
< |
|
389 |
< |
diffEta = 0; |
390 |
< |
for(i = 0; i < 3; i++) |
391 |
< |
diffEta += pow(preEta[i][i] - eta[i][i], 2); |
392 |
< |
|
393 |
< |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
394 |
< |
break; |
395 |
< |
} |
396 |
< |
|
397 |
< |
//calculate integral of chida |
398 |
< |
integralOfChidt += dt2*chi; |
399 |
< |
|
400 |
< |
|
231 |
> |
return ( diffEta <= etaTolerance ); |
232 |
|
} |
233 |
|
|
234 |
< |
template<typename T> void NPTf<T>::resetIntegrator() { |
404 |
< |
int i,j; |
234 |
> |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
235 |
|
|
236 |
< |
chi = 0.0; |
236 |
> |
double conservedQuantity; |
237 |
> |
double totalEnergy; |
238 |
> |
double thermostat_kinetic; |
239 |
> |
double thermostat_potential; |
240 |
> |
double barostat_kinetic; |
241 |
> |
double barostat_potential; |
242 |
> |
double trEta; |
243 |
> |
double a[3][3], b[3][3]; |
244 |
|
|
245 |
< |
for(i = 0; i < 3; i++) |
409 |
< |
for (j = 0; j < 3; j++) |
410 |
< |
eta[i][j] = 0.0; |
245 |
> |
totalEnergy = tStats->getTotalE(); |
246 |
|
|
247 |
< |
} |
247 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
248 |
> |
(2.0 * eConvert); |
249 |
|
|
250 |
< |
template<typename T> int NPTf<T>::readyCheck() { |
250 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
251 |
|
|
252 |
< |
//check parent's readyCheck() first |
253 |
< |
if (T::readyCheck() == -1) |
254 |
< |
return -1; |
255 |
< |
|
256 |
< |
// First check to see if we have a target temperature. |
257 |
< |
// Not having one is fatal. |
252 |
> |
info->transposeMat3(eta, a); |
253 |
> |
info->matMul3(a, eta, b); |
254 |
> |
trEta = info->matTrace3(b); |
255 |
> |
|
256 |
> |
barostat_kinetic = NkBT * tb2 * trEta / |
257 |
> |
(2.0 * eConvert); |
258 |
|
|
259 |
< |
if (!have_target_temp) { |
260 |
< |
sprintf( painCave.errMsg, |
425 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
426 |
< |
" without a targetTemp!\n" |
427 |
< |
); |
428 |
< |
painCave.isFatal = 1; |
429 |
< |
simError(); |
430 |
< |
return -1; |
431 |
< |
} |
259 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
260 |
> |
eConvert; |
261 |
|
|
262 |
< |
if (!have_target_pressure) { |
263 |
< |
sprintf( painCave.errMsg, |
435 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
436 |
< |
" without a targetPressure!\n" |
437 |
< |
); |
438 |
< |
painCave.isFatal = 1; |
439 |
< |
simError(); |
440 |
< |
return -1; |
441 |
< |
} |
262 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
263 |
> |
barostat_kinetic + barostat_potential; |
264 |
|
|
265 |
< |
// We must set tauThermostat. |
266 |
< |
|
445 |
< |
if (!have_tau_thermostat) { |
446 |
< |
sprintf( painCave.errMsg, |
447 |
< |
"NPTf error: If you use the NPTf\n" |
448 |
< |
" integrator, you must set tauThermostat.\n"); |
449 |
< |
painCave.isFatal = 1; |
450 |
< |
simError(); |
451 |
< |
return -1; |
452 |
< |
} |
265 |
> |
// cout.width(8); |
266 |
> |
// cout.precision(8); |
267 |
|
|
268 |
< |
// We must set tauBarostat. |
269 |
< |
|
270 |
< |
if (!have_tau_barostat) { |
457 |
< |
sprintf( painCave.errMsg, |
458 |
< |
"NPTf error: If you use the NPTf\n" |
459 |
< |
" integrator, you must set tauBarostat.\n"); |
460 |
< |
painCave.isFatal = 1; |
461 |
< |
simError(); |
462 |
< |
return -1; |
463 |
< |
} |
268 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
269 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
270 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
271 |
|
|
272 |
< |
// We need NkBT a lot, so just set it here: |
466 |
< |
|
467 |
< |
NkBT = (double)Nparticles * kB * targetTemp; |
468 |
< |
fkBT = (double)info->ndf * kB * targetTemp; |
469 |
< |
|
470 |
< |
return 1; |
471 |
< |
} |
472 |
< |
|
473 |
< |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
474 |
< |
|
475 |
< |
double conservedQuantity; |
476 |
< |
double tb2; |
477 |
< |
double trEta; |
478 |
< |
double U; |
479 |
< |
double thermo; |
480 |
< |
double integral; |
481 |
< |
double baro; |
482 |
< |
double PV; |
483 |
< |
|
484 |
< |
U = tStats->getTotalE(); |
485 |
< |
thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
486 |
< |
|
487 |
< |
tb2 = tauBarostat * tauBarostat; |
488 |
< |
trEta = info->matTrace3(eta); |
489 |
< |
baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert; |
490 |
< |
|
491 |
< |
integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert; |
492 |
< |
|
493 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
494 |
< |
|
495 |
< |
|
496 |
< |
cout.width(8); |
497 |
< |
cout.precision(8); |
272 |
> |
return conservedQuantity; |
273 |
|
|
499 |
– |
cout << info->getTime() << "\t" |
500 |
– |
<< chi << "\t" |
501 |
– |
<< trEta << "\t" |
502 |
– |
<< U << "\t" |
503 |
– |
<< thermo << "\t" |
504 |
– |
<< baro << "\t" |
505 |
– |
<< integral << "\t" |
506 |
– |
<< PV << "\t" |
507 |
– |
<< U+thermo+integral+PV+baro << endl; |
508 |
– |
|
509 |
– |
conservedQuantity = U+thermo+integral+PV+baro; |
510 |
– |
return conservedQuantity; |
511 |
– |
|
274 |
|
} |