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#include <cmath> |
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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 "simError.h" |
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// Basic isotropic thermostating and barostating via the Melchionna |
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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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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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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; |
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int i, j; |
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chi = 0.0; |
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for(i = 0; i < 9; i++) eta[i] = 0.0; |
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integralOfChidt = 0.0; |
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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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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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} |
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void NPTi::moveA() { |
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template<typename T> void NPTf<T>::moveA() { |
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int i,j,k; |
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int atomIndex, aMatIndex; |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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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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|
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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 angle; |
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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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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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tStats->getPressureTensor(press); |
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instaVol = tStats->getVolume(); |
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// first evolve chi a half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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for (i = 0; i < 9; i++) { |
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eta[i] += dt2 * ( instaVol * (sigma[i] - targetPressure*identMat[i])) |
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/ (NkBT*tb2)); |
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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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|
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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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|
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vScale[i][j] = eta[i][j] + chi; |
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|
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} else { |
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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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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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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atoms[i]->getVel( vel ); |
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atoms[i]->getPos( pos ); |
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atoms[i]->getFrc( frc ); |
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mass = atoms[i]->getMass(); |
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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|
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info->matVecMul3( vScale, vel, sc ); |
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for (j = 0; j < 3; j++) { |
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vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
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rj[j] = pos[j]; |
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} |
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atoms[i]->setVel( vel ); |
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|
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// position whole step |
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for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
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rj[0] = pos[j]; |
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rj[1] = pos[j+1]; |
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rj[2] = pos[j+2]; |
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info->wrapVector(rj); |
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info->wrapVector(rj); |
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info->matVecMul3( eta, rj, sc ); |
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pos[j] += dt * (vel[j] + eta*rj[0]); |
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pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
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pos[j+2] += dt * (vel[j+2] + eta*rj[2]); |
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} |
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for (j = 0; j < 3; j++ ) |
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pos[j] += dt * (vel[j] + sc[j]); |
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// Scale the box after all the positions have been moved: |
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info->scaleBox(exp(dt*eta)); |
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atoms[i]->setPos( pos ); |
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if( atoms[i]->isDirectional() ){ |
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// get and convert the torque to body frame |
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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dAtom->getJ( ji ); |
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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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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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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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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] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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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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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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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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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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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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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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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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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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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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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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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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> |
// Scale the box after all the positions have been moved: |
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|
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> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
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|
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bigScale = 1.0; |
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> |
smallScale = 1.0; |
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> |
offDiagMax = 0.0; |
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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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// Calculate the matrix Product of the eta array (we only need |
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> |
// the ij element right now): |
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> |
|
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> |
eta2ij = 0.0; |
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> |
for(k=0; k<3; k++){ |
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> |
eta2ij += eta[i][k] * eta[k][j]; |
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> |
} |
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> |
|
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> |
scaleMat[i][j] = 0.0; |
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> |
// identity matrix (see above): |
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> |
if (i == j) scaleMat[i][j] = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
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> |
|
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> |
if (i != j) |
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> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
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> |
offDiagMax = fabs(scaleMat[i][j]); |
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} |
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< |
|
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> |
|
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> |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
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> |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
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+ |
|
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.1) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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+ |
simError(); |
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} else { |
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info->getBoxM(hm); |
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info->matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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} |
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|
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} |
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|
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< |
void NPTi::moveB( void ){ |
| 232 |
< |
int i,j,k; |
| 233 |
< |
int atomIndex; |
| 231 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
| 232 |
> |
|
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> |
int i, j; |
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DirectionalAtom* dAtom; |
| 235 |
< |
double Tb[3]; |
| 236 |
< |
double ji[3]; |
| 235 |
> |
double Tb[3], ji[3]; |
| 236 |
> |
double vel[3], frc[3]; |
| 237 |
> |
double mass; |
| 238 |
> |
|
| 239 |
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double instaTemp, instaPress, instaVol; |
| 240 |
|
double tt2, tb2; |
| 241 |
+ |
double sc[3]; |
| 242 |
+ |
double press[3][3], vScale[3][3]; |
| 243 |
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|
| 244 |
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tt2 = tauThermostat * tauThermostat; |
| 245 |
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tb2 = tauBarostat * tauBarostat; |
| 246 |
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|
| 247 |
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instaTemp = tStats->getTemperature(); |
| 248 |
< |
instaPress = tStats->getPressure(); |
| 248 |
> |
tStats->getPressureTensor(press); |
| 249 |
|
instaVol = tStats->getVolume(); |
| 250 |
< |
|
| 250 |
> |
|
| 251 |
> |
// first evolve chi a half step |
| 252 |
> |
|
| 253 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 159 |
– |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 254 |
|
|
| 255 |
+ |
for (i = 0; i < 3; i++ ) { |
| 256 |
+ |
for (j = 0; j < 3; j++ ) { |
| 257 |
+ |
if (i == j) { |
| 258 |
+ |
|
| 259 |
+ |
eta[i][j] += dt2 * instaVol * |
| 260 |
+ |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 261 |
+ |
|
| 262 |
+ |
vScale[i][j] = eta[i][j] + chi; |
| 263 |
+ |
|
| 264 |
+ |
} else { |
| 265 |
+ |
|
| 266 |
+ |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 267 |
+ |
|
| 268 |
+ |
vScale[i][j] = eta[i][j]; |
| 269 |
+ |
|
| 270 |
+ |
} |
| 271 |
+ |
} |
| 272 |
+ |
} |
| 273 |
+ |
|
| 274 |
|
for( i=0; i<nAtoms; i++ ){ |
| 275 |
< |
atomIndex = i * 3; |
| 275 |
> |
|
| 276 |
> |
atoms[i]->getVel( vel ); |
| 277 |
> |
atoms[i]->getFrc( frc ); |
| 278 |
> |
|
| 279 |
> |
mass = atoms[i]->getMass(); |
| 280 |
|
|
| 281 |
|
// velocity half step |
| 282 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 283 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 167 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 168 |
< |
- vel[j]*(chi+eta)); |
| 282 |
> |
|
| 283 |
> |
info->matVecMul3( vScale, vel, sc ); |
| 284 |
|
|
| 285 |
+ |
for (j = 0; j < 3; j++) { |
| 286 |
+ |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 287 |
+ |
} |
| 288 |
+ |
|
| 289 |
+ |
atoms[i]->setVel( vel ); |
| 290 |
+ |
|
| 291 |
|
if( atoms[i]->isDirectional() ){ |
| 292 |
< |
|
| 292 |
> |
|
| 293 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 294 |
< |
|
| 294 |
> |
|
| 295 |
|
// get and convert the torque to body frame |
| 296 |
|
|
| 297 |
< |
Tb[0] = dAtom->getTx(); |
| 177 |
< |
Tb[1] = dAtom->getTy(); |
| 178 |
< |
Tb[2] = dAtom->getTz(); |
| 179 |
< |
|
| 297 |
> |
dAtom->getTrq( Tb ); |
| 298 |
|
dAtom->lab2Body( Tb ); |
| 299 |
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|
| 300 |
< |
// get the angular momentum, and complete the angular momentum |
| 183 |
< |
// half step |
| 300 |
> |
// get the angular momentum, and propagate a half step |
| 301 |
|
|
| 302 |
< |
ji[0] = dAtom->getJx(); |
| 186 |
< |
ji[1] = dAtom->getJy(); |
| 187 |
< |
ji[2] = dAtom->getJz(); |
| 302 |
> |
dAtom->getJ( ji ); |
| 303 |
|
|
| 304 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 305 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 191 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 304 |
> |
for (j=0; j < 3; j++) |
| 305 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 306 |
|
|
| 307 |
< |
dAtom->setJx( ji[0] ); |
| 308 |
< |
dAtom->setJy( ji[1] ); |
| 309 |
< |
dAtom->setJz( ji[2] ); |
| 196 |
< |
} |
| 307 |
> |
dAtom->setJ( ji ); |
| 308 |
> |
|
| 309 |
> |
} |
| 310 |
|
} |
| 311 |
|
} |
| 312 |
|
|
| 313 |
< |
int NPTi::readyCheck() { |
| 313 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 314 |
> |
int i,j; |
| 315 |
> |
|
| 316 |
> |
chi = 0.0; |
| 317 |
> |
|
| 318 |
> |
for(i = 0; i < 3; i++) |
| 319 |
> |
for (j = 0; j < 3; j++) |
| 320 |
> |
eta[i][j] = 0.0; |
| 321 |
> |
|
| 322 |
> |
} |
| 323 |
> |
|
| 324 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
| 325 |
> |
|
| 326 |
> |
//check parent's readyCheck() first |
| 327 |
> |
if (T::readyCheck() == -1) |
| 328 |
> |
return -1; |
| 329 |
|
|
| 330 |
|
// First check to see if we have a target temperature. |
| 331 |
|
// Not having one is fatal. |
| 332 |
|
|
| 333 |
|
if (!have_target_temp) { |
| 334 |
|
sprintf( painCave.errMsg, |
| 335 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 335 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
| 336 |
|
" without a targetTemp!\n" |
| 337 |
|
); |
| 338 |
|
painCave.isFatal = 1; |
| 342 |
|
|
| 343 |
|
if (!have_target_pressure) { |
| 344 |
|
sprintf( painCave.errMsg, |
| 345 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 345 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
| 346 |
|
" without a targetPressure!\n" |
| 347 |
|
); |
| 348 |
|
painCave.isFatal = 1; |
| 354 |
|
|
| 355 |
|
if (!have_tau_thermostat) { |
| 356 |
|
sprintf( painCave.errMsg, |
| 357 |
< |
"NPTi error: If you use the NPTi\n" |
| 357 |
> |
"NPTf error: If you use the NPTf\n" |
| 358 |
|
" integrator, you must set tauThermostat.\n"); |
| 359 |
|
painCave.isFatal = 1; |
| 360 |
|
simError(); |
| 365 |
|
|
| 366 |
|
if (!have_tau_barostat) { |
| 367 |
|
sprintf( painCave.errMsg, |
| 368 |
< |
"NPTi error: If you use the NPTi\n" |
| 368 |
> |
"NPTf error: If you use the NPTf\n" |
| 369 |
|
" integrator, you must set tauBarostat.\n"); |
| 370 |
|
painCave.isFatal = 1; |
| 371 |
|
simError(); |
| 378 |
|
|
| 379 |
|
return 1; |
| 380 |
|
} |
| 381 |
+ |
|
| 382 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 383 |
+ |
|
| 384 |
+ |
double conservedQuantity; |
| 385 |
+ |
double tb2; |
| 386 |
+ |
double eta2[3][3]; |
| 387 |
+ |
double trEta; |
| 388 |
+ |
|
| 389 |
+ |
//HNVE |
| 390 |
+ |
conservedQuantity = tStats->getTotalE(); |
| 391 |
+ |
|
| 392 |
+ |
//HNVT |
| 393 |
+ |
conservedQuantity += (info->getNDF() * kB * targetTemp * |
| 394 |
+ |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi /2)) / eConvert; |
| 395 |
+ |
|
| 396 |
+ |
//HNPT |
| 397 |
+ |
tb2 = tauBarostat *tauBarostat; |
| 398 |
+ |
|
| 399 |
+ |
trEta = info->matTrace3(eta); |
| 400 |
+ |
|
| 401 |
+ |
conservedQuantity += (targetPressure * tStats->getVolume() / p_convert + |
| 402 |
+ |
3*NkBT/2 * tb2 * trEta * trEta) / eConvert; |
| 403 |
+ |
|
| 404 |
+ |
return conservedQuantity; |
| 405 |
+ |
} |
