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#include <cmath> |
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#include "Atom.hpp" |
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#include "SRI.hpp" |
4 |
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#include "AbstractClasses.hpp" |
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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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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
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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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|
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< |
void NPTf::moveA() { |
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template<typename T> void NPTf<T>::moveA() { |
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|
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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]; |
42 |
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double ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3]; |
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double hm[9]; |
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double vx, vy, vz; |
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double scx, scy, scz; |
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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 press[9]; |
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const double p_convert = 1.63882576e8; |
52 |
> |
double sc[3]; |
53 |
> |
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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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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|
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for (i=0; i < 9; i++) press[i] *= p_convert; |
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|
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instaVol = tStats->getVolume(); |
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|
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// first evolve chi a half step |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
68 |
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eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
69 |
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eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
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eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
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eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
72 |
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eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
74 |
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eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
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eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
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eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
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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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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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|
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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|
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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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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
88 |
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|
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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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|
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mass = atoms[i]->getMass(); |
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|
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// velocity half step |
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|
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info->matVecMul3( vScale, vel, sc ); |
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|
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vx = vel[atomIndex]; |
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vy = vel[atomIndex+1]; |
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vz = vel[atomIndex+2]; |
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|
86 |
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scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
87 |
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scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
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scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
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|
90 |
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vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
91 |
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vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
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vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
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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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|
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vel[atomIndex] = vx; |
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vel[atomIndex+1] = vy; |
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vel[atomIndex+2] = vz; |
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atoms[i]->setVel( vel ); |
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|
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// position whole step |
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|
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rj[0] = pos[atomIndex]; |
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rj[1] = pos[atomIndex+1]; |
102 |
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rj[2] = pos[atomIndex+2]; |
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|
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info->wrapVector(rj); |
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|
110 |
< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
107 |
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scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
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scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
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> |
info->matVecMul3( eta, rj, sc ); |
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|
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pos[atomIndex] += dt * (vel[atomIndex] + scx); |
113 |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
114 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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> |
for (j = 0; j < 3; j++ ) |
113 |
> |
pos[j] += dt * (vel[j] + sc[j]); |
114 |
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|
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> |
atoms[i]->setPos( pos ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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|
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// get and convert the torque to body frame |
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|
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Tb[0] = dAtom->getTx(); |
121 |
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Tb[1] = dAtom->getTy(); |
122 |
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Tb[2] = dAtom->getTz(); |
123 |
< |
|
123 |
> |
dAtom->getTrq( Tb ); |
124 |
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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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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
130 |
< |
ji[2] = dAtom->getJz(); |
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> |
dAtom->getJ( ji ); |
129 |
> |
|
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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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|
132 |
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
133 |
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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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|
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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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|
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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] ); |
142 |
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|
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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] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
144 |
> |
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 |
148 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
149 |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
148 |
> |
angle = dt * ji[2] / I[2][2]; |
149 |
> |
this->rotate( 0, 1, angle, ji, A); |
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|
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// rotate about the y-axis |
152 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
153 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
152 |
> |
angle = dt2 * ji[1] / I[1][1]; |
153 |
> |
this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the x-axis |
156 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
157 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
156 |
> |
angle = dt2 * ji[0] / I[0][0]; |
157 |
> |
this->rotate( 1, 2, angle, ji, A ); |
158 |
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|
159 |
< |
dAtom->setJx( ji[0] ); |
160 |
< |
dAtom->setJy( ji[1] ); |
161 |
< |
dAtom->setJz( ji[2] ); |
162 |
< |
} |
163 |
< |
|
159 |
> |
dAtom->setJ( ji ); |
160 |
> |
dAtom->setA( A ); |
161 |
> |
} |
162 |
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} |
163 |
< |
|
163 |
> |
|
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// Scale the box after all the positions have been moved: |
165 |
< |
|
165 |
> |
|
166 |
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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
167 |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
168 |
< |
|
169 |
< |
|
168 |
> |
|
169 |
> |
bigScale = 1.0; |
170 |
> |
smallScale = 1.0; |
171 |
> |
offDiagMax = 0.0; |
172 |
> |
|
173 |
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for(i=0; i<3; i++){ |
174 |
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for(j=0; j<3; j++){ |
175 |
< |
ident[i][j] = 0.0; |
176 |
< |
eta1[i][j] = eta[3*i+j]; |
177 |
< |
eta2[i][j] = 0.0; |
175 |
> |
|
176 |
> |
// Calculate the matrix Product of the eta array (we only need |
177 |
> |
// the ij element right now): |
178 |
> |
|
179 |
> |
eta2ij = 0.0; |
180 |
|
for(k=0; k<3; k++){ |
181 |
< |
eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
181 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
182 |
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} |
183 |
< |
} |
184 |
< |
ident[i][i] = 1.0; |
185 |
< |
} |
183 |
> |
|
184 |
> |
scaleMat[i][j] = 0.0; |
185 |
> |
// identity matrix (see above): |
186 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
187 |
> |
// Taylor expansion for the exponential truncated at second order: |
188 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
189 |
|
|
190 |
< |
|
191 |
< |
info->getBoxM(hm); |
192 |
< |
|
187 |
< |
for(i=0; i<3; i++){ |
188 |
< |
for(j=0; j<3; j++){ |
189 |
< |
hmnew[i][j] = 0.0; |
190 |
< |
for(k=0; k<3; k++){ |
191 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
192 |
< |
hmnew[i][j] += hm[3*k+i] * (ident[k][j] |
193 |
< |
+ dt * eta1[k][j] |
194 |
< |
+ 0.5 * dt * dt * eta2[k][j]); |
195 |
< |
} |
190 |
> |
if (i != j) |
191 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
192 |
> |
offDiagMax = fabs(scaleMat[i][j]); |
193 |
|
} |
194 |
+ |
|
195 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
196 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
197 |
|
} |
198 |
|
|
199 |
< |
for (i = 0; i < 3; i++) { |
200 |
< |
for (j = 0; j < 3; j++) { |
201 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
202 |
< |
hm[3*j + 1] = hmnew[i][j]; |
203 |
< |
} |
199 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
200 |
> |
sprintf( painCave.errMsg, |
201 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
202 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
203 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
204 |
> |
" [%lf\t%lf\t%lf]\n" |
205 |
> |
" [%lf\t%lf\t%lf]\n", |
206 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
207 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
208 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
209 |
> |
painCave.isFatal = 1; |
210 |
> |
simError(); |
211 |
> |
} else if (offDiagMax > 0.1) { |
212 |
> |
sprintf( painCave.errMsg, |
213 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
214 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
215 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
216 |
> |
" [%lf\t%lf\t%lf]\n" |
217 |
> |
" [%lf\t%lf\t%lf]\n", |
218 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
219 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
220 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
221 |
> |
painCave.isFatal = 1; |
222 |
> |
simError(); |
223 |
> |
} else { |
224 |
> |
info->getBoxM(hm); |
225 |
> |
info->matMul3(hm, scaleMat, hmnew); |
226 |
> |
info->setBoxM(hmnew); |
227 |
|
} |
205 |
– |
|
206 |
– |
info->setBoxM(hm); |
228 |
|
|
229 |
|
} |
230 |
|
|
231 |
< |
void NPTf::moveB( void ){ |
232 |
< |
int i,j,k; |
233 |
< |
int atomIndex; |
231 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
232 |
> |
|
233 |
> |
int i, j; |
234 |
|
DirectionalAtom* dAtom; |
235 |
< |
double Tb[3]; |
236 |
< |
double ji[3]; |
237 |
< |
double press[9]; |
238 |
< |
double instaTemp, instaVol; |
235 |
> |
double Tb[3], ji[3]; |
236 |
> |
double vel[3], frc[3]; |
237 |
> |
double mass; |
238 |
> |
|
239 |
> |
double instaTemp, instaPress, instaVol; |
240 |
|
double tt2, tb2; |
241 |
< |
double vx, vy, vz; |
242 |
< |
double scx, scy, scz; |
221 |
< |
const double p_convert = 1.63882576e8; |
241 |
> |
double sc[3]; |
242 |
> |
double press[3][3], vScale[3][3]; |
243 |
|
|
244 |
|
tt2 = tauThermostat * tauThermostat; |
245 |
|
tb2 = tauBarostat * tauBarostat; |
246 |
|
|
247 |
|
instaTemp = tStats->getTemperature(); |
248 |
|
tStats->getPressureTensor(press); |
228 |
– |
|
229 |
– |
for (i=0; i < 9; i++) press[i] *= p_convert; |
230 |
– |
|
249 |
|
instaVol = tStats->getVolume(); |
250 |
|
|
251 |
|
// first evolve chi a half step |
252 |
|
|
253 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
254 |
|
|
255 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
256 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
257 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
240 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
241 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
242 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
243 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
244 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
245 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
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++ ){ |
248 |
– |
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 |
+ |
|
283 |
+ |
info->matVecMul3( vScale, vel, sc ); |
284 |
|
|
285 |
< |
vx = vel[atomIndex]; |
286 |
< |
vy = vel[atomIndex+1]; |
287 |
< |
vz = vel[atomIndex+2]; |
255 |
< |
|
256 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
257 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
258 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
259 |
< |
|
260 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
261 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
262 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
285 |
> |
for (j = 0; j < 3; j++) { |
286 |
> |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
287 |
> |
} |
288 |
|
|
289 |
< |
vel[atomIndex] = vx; |
265 |
< |
vel[atomIndex+1] = vy; |
266 |
< |
vel[atomIndex+2] = vz; |
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(); |
275 |
< |
Tb[1] = dAtom->getTy(); |
276 |
< |
Tb[2] = dAtom->getTz(); |
277 |
< |
|
297 |
> |
dAtom->getTrq( Tb ); |
298 |
|
dAtom->lab2Body( Tb ); |
299 |
|
|
300 |
< |
// get the angular momentum, and complete the angular momentum |
281 |
< |
// half step |
300 |
> |
// get the angular momentum, and propagate a half step |
301 |
|
|
302 |
< |
ji[0] = dAtom->getJx(); |
284 |
< |
ji[1] = dAtom->getJy(); |
285 |
< |
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); |
289 |
< |
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] ); |
294 |
< |
} |
307 |
> |
dAtom->setJ( ji ); |
308 |
> |
|
309 |
> |
} |
310 |
|
} |
311 |
|
} |
312 |
|
|
313 |
< |
int NPTf::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. |
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 |
+ |
} |