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#include <cmath> |
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#include "Atom.hpp" |
| 3 |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( 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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|
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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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|
| 39 |
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void NPTf::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; |
| 42 |
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DirectionalAtom* dAtom; |
| 43 |
< |
double Tb[3]; |
| 44 |
< |
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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> |
|
| 48 |
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double rj[3]; |
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– |
double ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3]; |
| 43 |
– |
double hm[9]; |
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double vx, vy, vz; |
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– |
double scx, scy, scz; |
| 49 |
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double instaTemp, instaPress, instaVol; |
| 50 |
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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; |
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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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|
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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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|
| 58 |
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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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< |
|
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eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
| 68 |
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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); |
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eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
| 72 |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
| 73 |
< |
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; |
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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; |
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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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|
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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]; |
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rj[2] = pos[atomIndex+2]; |
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|
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info->wrapVector(rj); |
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|
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< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
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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); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
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< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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> |
for (j = 0; j < 3; j++ ) |
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> |
pos[j] += dt * (vel[j] + sc[j]); |
| 113 |
> |
|
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> |
atoms[i]->setPos( pos ); |
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|
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if( atoms[i]->isDirectional() ){ |
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// get and convert the torque to body frame |
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|
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< |
Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
| 122 |
< |
Tb[2] = dAtom->getTz(); |
| 123 |
< |
|
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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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< |
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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> |
|
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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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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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|
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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] ); |
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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] ); |
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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 |
| 147 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 148 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 147 |
> |
angle = dt * ji[2] / I[2][2]; |
| 148 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 149 |
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|
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// rotate about the y-axis |
| 151 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 152 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 151 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 152 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 153 |
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|
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// rotate about the x-axis |
| 155 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 156 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 155 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 156 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 157 |
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|
| 158 |
< |
dAtom->setJx( ji[0] ); |
| 159 |
< |
dAtom->setJy( ji[1] ); |
| 160 |
< |
dAtom->setJz( ji[2] ); |
| 162 |
< |
} |
| 163 |
< |
|
| 158 |
> |
dAtom->setJ( ji ); |
| 159 |
> |
dAtom->setA( A ); |
| 160 |
> |
} |
| 161 |
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} |
| 162 |
< |
|
| 162 |
> |
|
| 163 |
|
// Scale the box after all the positions have been moved: |
| 164 |
< |
|
| 164 |
> |
|
| 165 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 166 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 167 |
< |
|
| 168 |
< |
|
| 167 |
> |
|
| 168 |
> |
bigScale = 1.0; |
| 169 |
> |
smallScale = 1.0; |
| 170 |
> |
offDiagMax = 0.0; |
| 171 |
> |
|
| 172 |
|
for(i=0; i<3; i++){ |
| 173 |
|
for(j=0; j<3; j++){ |
| 174 |
< |
ident[i][j] = 0.0; |
| 175 |
< |
eta1[i][j] = eta[3*i+j]; |
| 176 |
< |
eta2[i][j] = 0.0; |
| 177 |
< |
for(k=0; k<3; k++){ |
| 178 |
< |
eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
| 179 |
< |
} |
| 180 |
< |
} |
| 181 |
< |
ident[i][i] = 1.0; |
| 182 |
< |
} |
| 183 |
< |
|
| 184 |
< |
|
| 185 |
< |
info->getBoxM(hm); |
| 186 |
< |
|
| 187 |
< |
for(i=0; i<3; i++){ |
| 188 |
< |
for(j=0; j<3; j++){ |
| 189 |
< |
hmnew[i][j] = 0.0; |
| 174 |
> |
|
| 175 |
> |
// Calculate the matrix Product of the eta array (we only need |
| 176 |
> |
// the ij element right now): |
| 177 |
> |
|
| 178 |
> |
eta2ij = 0.0; |
| 179 |
|
for(k=0; k<3; k++){ |
| 180 |
< |
// 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]); |
| 180 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
| 181 |
|
} |
| 182 |
+ |
|
| 183 |
+ |
scaleMat[i][j] = 0.0; |
| 184 |
+ |
// identity matrix (see above): |
| 185 |
+ |
if (i == j) scaleMat[i][j] = 1.0; |
| 186 |
+ |
// Taylor expansion for the exponential truncated at second order: |
| 187 |
+ |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 188 |
+ |
|
| 189 |
+ |
if (i != j) |
| 190 |
+ |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 191 |
+ |
offDiagMax = fabs(scaleMat[i][j]); |
| 192 |
+ |
|
| 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; |
| 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 |
|
|
