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gezelter |
576 |
#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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gezelter |
578 |
// Basic non-isotropic thermostating and barostating via the Melchionna |
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gezelter |
576 |
// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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gezelter |
577 |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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gezelter |
576 |
Integrator( theInfo, the_ff ) |
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{ |
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int i; |
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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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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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gezelter |
577 |
void NPTf::moveA() { |
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gezelter |
576 |
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int i,j,k; |
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int atomIndex, aMatIndex; |
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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 rj[3]; |
| 42 |
gezelter |
578 |
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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gezelter |
576 |
double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double angle; |
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gezelter |
577 |
double press[9]; |
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const double p_convert = 1.63882576e8; |
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gezelter |
576 |
|
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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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gezelter |
577 |
tStats->getPressureTensor(press); |
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for (i=0; i < 9; i++) press[i] *= p_convert; |
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gezelter |
576 |
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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gezelter |
577 |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
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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); |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
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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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gezelter |
576 |
for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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// velocity half step |
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gezelter |
577 |
|
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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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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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vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
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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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gezelter |
576 |
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gezelter |
577 |
vel[atomIndex] = vx; |
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vel[atomIndex+1] = vy; |
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vel[atomIndex+2] = vz; |
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gezelter |
576 |
// position whole step |
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gezelter |
577 |
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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gezelter |
576 |
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gezelter |
577 |
info->wrapVector(rj); |
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gezelter |
576 |
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gezelter |
577 |
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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gezelter |
576 |
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gezelter |
577 |
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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gezelter |
576 |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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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->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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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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// 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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// 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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// 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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// 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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// 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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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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} |
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} |
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gezelter |
577 |
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// Scale the box after all the positions have been moved: |
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gezelter |
578 |
// 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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gezelter |
577 |
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gezelter |
578 |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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ident[i][j] = 0.0; |
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eta1[i][j] = eta[3*i+j]; |
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eta2[i][j] = 0.0; |
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for(k=0; k<3; k++){ |
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eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
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} |
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} |
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ident[i][i] = 1.0; |
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} |
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gezelter |
577 |
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info->getBoxM(hm); |
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gezelter |
578 |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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hmnew[i][j] = 0.0; |
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for(k=0; k<3; k++){ |
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// remember that hmat has transpose ordering for Fortran compat: |
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hmnew[i][j] += hm[3*k+i] * (ident[k][j] |
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+ dt * eta1[k][j] |
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+ 0.5 * dt * dt * eta2[k][j]); |
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} |
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} |
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} |
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gezelter |
577 |
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gezelter |
578 |
for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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// remember that hmat has transpose ordering for Fortran compat: |
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hm[3*j + 1] = hmnew[i][j]; |
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} |
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} |
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gezelter |
577 |
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gezelter |
578 |
info->setBoxM(hm); |
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gezelter |
576 |
} |
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gezelter |
578 |
void NPTf::moveB( void ){ |
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gezelter |
576 |
int i,j,k; |
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int atomIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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gezelter |
578 |
double press[9]; |
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double instaTemp, instaVol; |
| 218 |
gezelter |
576 |
double tt2, tb2; |
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gezelter |
578 |
double vx, vy, vz; |
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double scx, scy, scz; |
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const double p_convert = 1.63882576e8; |
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gezelter |
576 |
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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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gezelter |
578 |
tStats->getPressureTensor(press); |
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for (i=0; i < 9; i++) press[i] *= p_convert; |
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gezelter |
576 |
instaVol = tStats->getVolume(); |
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gezelter |
578 |
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// first evolve chi a half step |
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gezelter |
576 |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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gezelter |
578 |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
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eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
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eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
| 240 |
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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); |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
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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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| 247 |
gezelter |
576 |
for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
| 249 |
gezelter |
578 |
|
| 250 |
gezelter |
576 |
// velocity half step |
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| 252 |
gezelter |
578 |
vx = vel[atomIndex]; |
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vy = vel[atomIndex+1]; |
| 254 |
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vz = vel[atomIndex+2]; |
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| 256 |
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scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
| 257 |
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scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
| 258 |
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scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
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| 260 |
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vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
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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); |
| 263 |
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| 264 |
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vel[atomIndex] = vx; |
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vel[atomIndex+1] = vy; |
| 266 |
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vel[atomIndex+2] = vz; |
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| 268 |
gezelter |
576 |
if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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| 272 |
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// get and convert the torque to body frame |
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| 274 |
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
| 276 |
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Tb[2] = dAtom->getTz(); |
| 277 |
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| 278 |
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dAtom->lab2Body( Tb ); |
| 279 |
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| 280 |
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// get the angular momentum, and complete the angular momentum |
| 281 |
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// half step |
| 282 |
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| 283 |
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ji[0] = dAtom->getJx(); |
| 284 |
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ji[1] = dAtom->getJy(); |
| 285 |
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ji[2] = dAtom->getJz(); |
| 286 |
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| 287 |
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 288 |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 289 |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 290 |
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| 291 |
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dAtom->setJx( ji[0] ); |
| 292 |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
| 294 |
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} |
| 295 |
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} |
| 296 |
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} |
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| 298 |
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int NPTi::readyCheck() { |
| 299 |
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| 300 |
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// First check to see if we have a target temperature. |
| 301 |
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// Not having one is fatal. |
| 302 |
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| 303 |
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if (!have_target_temp) { |
| 304 |
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sprintf( painCave.errMsg, |
| 305 |
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"NPTi error: You can't use the NPTi integrator\n" |
| 306 |
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" without a targetTemp!\n" |
| 307 |
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); |
| 308 |
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painCave.isFatal = 1; |
| 309 |
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simError(); |
| 310 |
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return -1; |
| 311 |
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} |
| 312 |
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| 313 |
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if (!have_target_pressure) { |
| 314 |
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sprintf( painCave.errMsg, |
| 315 |
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"NPTi error: You can't use the NPTi integrator\n" |
| 316 |
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" without a targetPressure!\n" |
| 317 |
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); |
| 318 |
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painCave.isFatal = 1; |
| 319 |
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simError(); |
| 320 |
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return -1; |
| 321 |
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} |
| 322 |
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| 323 |
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// We must set tauThermostat. |
| 324 |
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| 325 |
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if (!have_tau_thermostat) { |
| 326 |
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sprintf( painCave.errMsg, |
| 327 |
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"NPTi error: If you use the NPTi\n" |
| 328 |
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" integrator, you must set tauThermostat.\n"); |
| 329 |
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painCave.isFatal = 1; |
| 330 |
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simError(); |
| 331 |
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return -1; |
| 332 |
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} |
| 333 |
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| 334 |
|
|
// We must set tauBarostat. |
| 335 |
|
|
|
| 336 |
|
|
if (!have_tau_barostat) { |
| 337 |
|
|
sprintf( painCave.errMsg, |
| 338 |
|
|
"NPTi error: If you use the NPTi\n" |
| 339 |
|
|
" integrator, you must set tauBarostat.\n"); |
| 340 |
|
|
painCave.isFatal = 1; |
| 341 |
|
|
simError(); |
| 342 |
|
|
return -1; |
| 343 |
|
|
} |
| 344 |
|
|
|
| 345 |
|
|
// We need NkBT a lot, so just set it here: |
| 346 |
|
|
|
| 347 |
|
|
NkBT = (double)info->ndf * kB * targetTemp; |
| 348 |
|
|
|
| 349 |
|
|
return 1; |
| 350 |
|
|
} |
