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#include <cmath> |
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#include "Atom.hpp" |
3 |
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#include "SRI.hpp" |
4 |
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#include "AbstractClasses.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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// 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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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
27 |
< |
Integrator( theInfo, the_ff ) |
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> |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
27 |
> |
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; |
31 |
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integralOfChidt = 0.0; |
32 |
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|
33 |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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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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|
42 |
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have_chi_tolerance = 0; |
43 |
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have_eta_tolerance = 0; |
44 |
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have_pos_iter_tolerance = 0; |
45 |
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|
46 |
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oldPos = new double[3*nAtoms]; |
47 |
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oldVel = new double[3*nAtoms]; |
48 |
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oldJi = new double[3*nAtoms]; |
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#ifdef IS_MPI |
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Nparticles = mpiSim->getTotAtoms(); |
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#else |
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Nparticles = theInfo->n_atoms; |
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#endif |
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|
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} |
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|
57 |
< |
void NPTf::moveA() { |
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|
59 |
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int i,j,k; |
60 |
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int atomIndex, aMatIndex; |
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> |
template<typename T> NPTf<T>::~NPTf() { |
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delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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|
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template<typename T> void NPTf<T>::moveA() { |
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|
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// new version of NPTf |
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int i, j, k; |
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DirectionalAtom* dAtom; |
68 |
< |
double Tb[3]; |
69 |
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double ji[3]; |
68 |
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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 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; |
77 |
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double press[9]; |
76 |
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double sc[3]; |
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double eta2ij; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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double bigScale, smallScale, offDiagMax; |
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double COM[3]; |
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|
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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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tStats->getPressureTensor(press); |
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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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tStats->getCOM(COM); |
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|
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//calculate scale factor of veloity |
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
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|
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if (i == j) { |
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vScale[i][j] += chi; |
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} |
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} |
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} |
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|
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eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) / |
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(NkBT*tb2); |
64 |
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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/p_convert) / |
68 |
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(NkBT*tb2); |
69 |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
70 |
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eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
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eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
72 |
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eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) / |
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(NkBT*tb2); |
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|
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//evolve velocity half step |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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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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|
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scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
86 |
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scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
87 |
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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); |
90 |
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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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|
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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]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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|
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// position whole step |
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mass = atoms[i]->getMass(); |
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|
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info->matVecMul3( vScale, vel, sc ); |
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|
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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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> |
for (j=0; j < 3; j++) { |
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// velocity half step |
114 |
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vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
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} |
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|
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< |
info->wrapVector(rj); |
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|
105 |
< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
106 |
< |
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
107 |
< |
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
108 |
< |
|
109 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
110 |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
111 |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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atoms[i]->setVel( vel ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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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(); |
120 |
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Tb[1] = dAtom->getTy(); |
121 |
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Tb[2] = dAtom->getTz(); |
122 |
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|
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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ji[0] = dAtom->getJx(); |
131 |
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ji[1] = dAtom->getJy(); |
132 |
< |
ji[2] = dAtom->getJz(); |
130 |
> |
dAtom->getJ( ji ); |
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> |
|
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> |
for (j=0; j < 3; j++) |
133 |
> |
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); |
132 |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
133 |
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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); |
139 |
> |
dAtom->getI(I); |
140 |
> |
|
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// rotate about the x-axis |
142 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
143 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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< |
|
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> |
angle = dt2 * ji[0] / I[0][0]; |
143 |
> |
this->rotate( 1, 2, angle, ji, A ); |
144 |
> |
|
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// rotate about the y-axis |
146 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
147 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
146 |
> |
angle = dt2 * ji[1] / I[1][1]; |
147 |
> |
this->rotate( 2, 0, angle, ji, A ); |
148 |
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|
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// rotate about the z-axis |
150 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
151 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
150 |
> |
angle = dt * ji[2] / I[2][2]; |
151 |
> |
this->rotate( 0, 1, angle, ji, A); |
152 |
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|
153 |
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// rotate about the y-axis |
154 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
155 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
154 |
> |
angle = dt2 * ji[1] / I[1][1]; |
155 |
> |
this->rotate( 2, 0, angle, ji, A ); |
156 |
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|
157 |
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// rotate about the x-axis |
158 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
159 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
158 |
> |
angle = dt2 * ji[0] / I[0][0]; |
159 |
> |
this->rotate( 1, 2, angle, ji, A ); |
160 |
|
|
161 |
< |
dAtom->setJx( ji[0] ); |
162 |
< |
dAtom->setJy( ji[1] ); |
163 |
< |
dAtom->setJz( ji[2] ); |
161 |
> |
dAtom->setJ( ji ); |
162 |
> |
dAtom->setA( A ); |
163 |
> |
} |
164 |
> |
} |
165 |
> |
|
166 |
> |
// advance chi half step |
167 |
> |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
168 |
> |
|
169 |
> |
// calculate the integral of chidt |
170 |
> |
integralOfChidt += dt2*chi; |
171 |
> |
|
172 |
> |
// advance eta half step |
173 |
> |
|
174 |
> |
for(i = 0; i < 3; i ++) |
175 |
> |
for(j = 0; j < 3; j++){ |
176 |
> |
if( i == j) |
177 |
> |
eta[i][j] += dt2 * instaVol * |
178 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
179 |
> |
else |
180 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
181 |
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} |
182 |
|
|
183 |
+ |
//save the old positions |
184 |
+ |
for(i = 0; i < nAtoms; i++){ |
185 |
+ |
atoms[i]->getPos(pos); |
186 |
+ |
for(j = 0; j < 3; j++) |
187 |
+ |
oldPos[i*3 + j] = pos[j]; |
188 |
|
} |
189 |
+ |
|
190 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
191 |
+ |
|
192 |
+ |
for(k = 0; k < 4; k ++){ |
193 |
|
|
194 |
< |
// Scale the box after all the positions have been moved: |
194 |
> |
for(i =0 ; i < nAtoms; i++){ |
195 |
|
|
196 |
< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
197 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
196 |
> |
atoms[i]->getVel(vel); |
197 |
> |
atoms[i]->getPos(pos); |
198 |
|
|
199 |
+ |
for(j = 0; j < 3; j++) |
200 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
201 |
+ |
|
202 |
+ |
info->matVecMul3( eta, rj, sc ); |
203 |
+ |
|
204 |
+ |
for(j = 0; j < 3; j++) |
205 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
206 |
|
|
207 |
< |
for(i=0; i<3; i++){ |
208 |
< |
for(j=0; j<3; j++){ |
173 |
< |
ident[i][j] = 0.0; |
174 |
< |
eta1[i][j] = eta[3*i+j]; |
175 |
< |
eta2[i][j] = 0.0; |
176 |
< |
for(k=0; k<3; k++){ |
177 |
< |
eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
178 |
< |
} |
207 |
> |
atoms[i]->setPos( pos ); |
208 |
> |
|
209 |
|
} |
180 |
– |
ident[i][i] = 1.0; |
181 |
– |
} |
210 |
|
|
211 |
< |
|
212 |
< |
info->getBoxM(hm); |
211 |
> |
if (nConstrained) { |
212 |
> |
constrainA(); |
213 |
> |
} |
214 |
> |
} |
215 |
> |
|
216 |
|
|
217 |
+ |
// Scale the box after all the positions have been moved: |
218 |
+ |
|
219 |
+ |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
220 |
+ |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
221 |
+ |
|
222 |
+ |
bigScale = 1.0; |
223 |
+ |
smallScale = 1.0; |
224 |
+ |
offDiagMax = 0.0; |
225 |
+ |
|
226 |
|
for(i=0; i<3; i++){ |
227 |
< |
for(j=0; j<3; j++){ |
228 |
< |
hmnew[i][j] = 0.0; |
227 |
> |
for(j=0; j<3; j++){ |
228 |
> |
|
229 |
> |
// Calculate the matrix Product of the eta array (we only need |
230 |
> |
// the ij element right now): |
231 |
> |
|
232 |
> |
eta2ij = 0.0; |
233 |
|
for(k=0; k<3; k++){ |
234 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
191 |
< |
hmnew[i][j] += hm[3*k+i] * (ident[k][j] |
192 |
< |
+ dt * eta1[k][j] |
193 |
< |
+ 0.5 * dt * dt * eta2[k][j]); |
234 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
235 |
|
} |
236 |
+ |
|
237 |
+ |
scaleMat[i][j] = 0.0; |
238 |
+ |
// identity matrix (see above): |
239 |
+ |
if (i == j) scaleMat[i][j] = 1.0; |
240 |
+ |
// Taylor expansion for the exponential truncated at second order: |
241 |
+ |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
242 |
+ |
|
243 |
+ |
if (i != j) |
244 |
+ |
if (fabs(scaleMat[i][j]) > offDiagMax) |
245 |
+ |
offDiagMax = fabs(scaleMat[i][j]); |
246 |
|
} |
247 |
+ |
|
248 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
249 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
250 |
|
} |
251 |
|
|
252 |
< |
for (i = 0; i < 3; i++) { |
253 |
< |
for (j = 0; j < 3; j++) { |
254 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
255 |
< |
hm[3*j + i] = hmnew[i][j]; |
256 |
< |
} |
252 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
253 |
> |
sprintf( painCave.errMsg, |
254 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
255 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
256 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
257 |
> |
" [%lf\t%lf\t%lf]\n" |
258 |
> |
" [%lf\t%lf\t%lf]\n", |
259 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
260 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
261 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
262 |
> |
painCave.isFatal = 1; |
263 |
> |
simError(); |
264 |
> |
} else if (offDiagMax > 0.1) { |
265 |
> |
sprintf( painCave.errMsg, |
266 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
267 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
268 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
269 |
> |
" [%lf\t%lf\t%lf]\n" |
270 |
> |
" [%lf\t%lf\t%lf]\n", |
271 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
272 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
273 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
274 |
> |
painCave.isFatal = 1; |
275 |
> |
simError(); |
276 |
> |
} else { |
277 |
> |
info->getBoxM(hm); |
278 |
> |
info->matMul3(hm, scaleMat, hmnew); |
279 |
> |
info->setBoxM(hmnew); |
280 |
|
} |
204 |
– |
|
205 |
– |
info->setBoxM(hm); |
281 |
|
|
282 |
|
} |
283 |
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|
284 |
< |
void NPTf::moveB( void ){ |
285 |
< |
int i,j,k; |
286 |
< |
int atomIndex; |
284 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
285 |
> |
|
286 |
> |
//new version of NPTf |
287 |
> |
int i, j, k; |
288 |
|
DirectionalAtom* dAtom; |
289 |
< |
double Tb[3]; |
290 |
< |
double ji[3]; |
291 |
< |
double press[9]; |
292 |
< |
double instaTemp, instaVol; |
289 |
> |
double Tb[3], ji[3]; |
290 |
> |
double vel[3], myVel[3], frc[3]; |
291 |
> |
double mass; |
292 |
> |
|
293 |
> |
double instaTemp, instaPress, instaVol; |
294 |
|
double tt2, tb2; |
295 |
< |
double vx, vy, vz; |
296 |
< |
double scx, scy, scz; |
297 |
< |
const double p_convert = 1.63882576e8; |
295 |
> |
double sc[3]; |
296 |
> |
double press[3][3], vScale[3][3]; |
297 |
> |
double oldChi, prevChi; |
298 |
> |
double oldEta[3][3], prevEta[3][3], diffEta; |
299 |
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|
300 |
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tt2 = tauThermostat * tauThermostat; |
301 |
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tb2 = tauBarostat * tauBarostat; |
302 |
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|
303 |
< |
instaTemp = tStats->getTemperature(); |
304 |
< |
tStats->getPressureTensor(press); |
305 |
< |
instaVol = tStats->getVolume(); |
228 |
< |
|
229 |
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// first evolve chi a half step |
303 |
> |
// Set things up for the iteration: |
304 |
> |
|
305 |
> |
oldChi = chi; |
306 |
|
|
307 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
308 |
< |
|
309 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) / |
234 |
< |
(NkBT*tb2); |
235 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
236 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
237 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
238 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) / |
239 |
< |
(NkBT*tb2); |
240 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
241 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
242 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
243 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) / |
244 |
< |
(NkBT*tb2); |
307 |
> |
for(i = 0; i < 3; i++) |
308 |
> |
for(j = 0; j < 3; j++) |
309 |
> |
oldEta[i][j] = eta[i][j]; |
310 |
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|
311 |
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for( i=0; i<nAtoms; i++ ){ |
247 |
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atomIndex = i * 3; |
312 |
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|
313 |
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// velocity half step |
313 |
> |
atoms[i]->getVel( vel ); |
314 |
> |
|
315 |
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for (j=0; j < 3; j++) |
316 |
> |
oldVel[3*i + j] = vel[j]; |
317 |
> |
|
318 |
> |
if( atoms[i]->isDirectional() ){ |
319 |
> |
|
320 |
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dAtom = (DirectionalAtom *)atoms[i]; |
321 |
> |
|
322 |
> |
dAtom->getJ( ji ); |
323 |
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|
324 |
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for (j=0; j < 3; j++) |
325 |
> |
oldJi[3*i + j] = ji[j]; |
326 |
> |
|
327 |
> |
} |
328 |
> |
} |
329 |
> |
|
330 |
> |
// do the iteration: |
331 |
> |
|
332 |
> |
instaVol = tStats->getVolume(); |
333 |
> |
|
334 |
> |
for (k=0; k < 4; k++) { |
335 |
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|
336 |
< |
vx = vel[atomIndex]; |
337 |
< |
vy = vel[atomIndex+1]; |
338 |
< |
vz = vel[atomIndex+2]; |
336 |
> |
instaTemp = tStats->getTemperature(); |
337 |
> |
tStats->getPressureTensor(press); |
338 |
> |
|
339 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
340 |
> |
|
341 |
> |
prevChi = chi; |
342 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
343 |
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|
344 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
345 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
346 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
258 |
< |
|
259 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
260 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
261 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
344 |
> |
for(i = 0; i < 3; i++) |
345 |
> |
for(j = 0; j < 3; j++) |
346 |
> |
prevEta[i][j] = eta[i][j]; |
347 |
|
|
348 |
< |
vel[atomIndex] = vx; |
349 |
< |
vel[atomIndex+1] = vy; |
350 |
< |
vel[atomIndex+2] = vz; |
348 |
> |
//advance eta half step and calculate scale factor for velocity |
349 |
> |
|
350 |
> |
for(i = 0; i < 3; i ++) |
351 |
> |
for(j = 0; j < 3; j++){ |
352 |
> |
if( i == j) { |
353 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
354 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
355 |
> |
vScale[i][j] = eta[i][j] + chi; |
356 |
> |
} else { |
357 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
358 |
> |
vScale[i][j] = eta[i][j]; |
359 |
> |
} |
360 |
> |
} |
361 |
|
|
362 |
< |
if( atoms[i]->isDirectional() ){ |
362 |
> |
for( i=0; i<nAtoms; i++ ){ |
363 |
> |
|
364 |
> |
atoms[i]->getFrc( frc ); |
365 |
> |
atoms[i]->getVel(vel); |
366 |
|
|
367 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
367 |
> |
mass = atoms[i]->getMass(); |
368 |
> |
|
369 |
> |
for (j = 0; j < 3; j++) |
370 |
> |
myVel[j] = oldVel[3*i + j]; |
371 |
|
|
372 |
< |
// get and convert the torque to body frame |
372 |
> |
info->matVecMul3( vScale, myVel, sc ); |
373 |
|
|
374 |
< |
Tb[0] = dAtom->getTx(); |
375 |
< |
Tb[1] = dAtom->getTy(); |
376 |
< |
Tb[2] = dAtom->getTz(); |
374 |
> |
// velocity half step |
375 |
> |
for (j=0; j < 3; j++) { |
376 |
> |
// velocity half step (use chi from previous step here): |
377 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
378 |
> |
} |
379 |
|
|
380 |
< |
dAtom->lab2Body( Tb ); |
380 |
> |
atoms[i]->setVel( vel ); |
381 |
|
|
382 |
< |
// get the angular momentum, and complete the angular momentum |
383 |
< |
// half step |
382 |
> |
if( atoms[i]->isDirectional() ){ |
383 |
> |
|
384 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
385 |
> |
|
386 |
> |
// get and convert the torque to body frame |
387 |
> |
|
388 |
> |
dAtom->getTrq( Tb ); |
389 |
> |
dAtom->lab2Body( Tb ); |
390 |
> |
|
391 |
> |
for (j=0; j < 3; j++) |
392 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
393 |
|
|
394 |
< |
ji[0] = dAtom->getJx(); |
395 |
< |
ji[1] = dAtom->getJy(); |
284 |
< |
ji[2] = dAtom->getJz(); |
285 |
< |
|
286 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
287 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
288 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
289 |
< |
|
290 |
< |
dAtom->setJx( ji[0] ); |
291 |
< |
dAtom->setJy( ji[1] ); |
292 |
< |
dAtom->setJz( ji[2] ); |
394 |
> |
dAtom->setJ( ji ); |
395 |
> |
} |
396 |
|
} |
397 |
+ |
|
398 |
+ |
if (nConstrained) { |
399 |
+ |
constrainB(); |
400 |
+ |
} |
401 |
+ |
|
402 |
+ |
diffEta = 0; |
403 |
+ |
for(i = 0; i < 3; i++) |
404 |
+ |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
405 |
+ |
|
406 |
+ |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
407 |
+ |
break; |
408 |
|
} |
409 |
+ |
|
410 |
+ |
//calculate integral of chidt |
411 |
+ |
integralOfChidt += dt2*chi; |
412 |
+ |
|
413 |
|
} |
414 |
|
|
415 |
< |
int NPTf::readyCheck() { |
415 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
416 |
> |
int i,j; |
417 |
> |
|
418 |
> |
chi = 0.0; |
419 |
> |
|
420 |
> |
for(i = 0; i < 3; i++) |
421 |
> |
for (j = 0; j < 3; j++) |
422 |
> |
eta[i][j] = 0.0; |
423 |
> |
|
424 |
> |
} |
425 |
> |
|
426 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
427 |
> |
|
428 |
> |
//check parent's readyCheck() first |
429 |
> |
if (T::readyCheck() == -1) |
430 |
> |
return -1; |
431 |
|
|
432 |
|
// First check to see if we have a target temperature. |
433 |
|
// Not having one is fatal. |
474 |
|
return -1; |
475 |
|
} |
476 |
|
|
477 |
< |
// We need NkBT a lot, so just set it here: |
477 |
> |
|
478 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
479 |
> |
// of particles, so no subtraction or addition of constraints or |
480 |
> |
// orientational degrees of freedom: |
481 |
> |
|
482 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
483 |
> |
|
484 |
> |
// fkBT is used because the thermostat operates on more degrees of freedom |
485 |
> |
// than the barostat (when there are particles with orientational degrees |
486 |
> |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
487 |
> |
|
488 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
489 |
|
|
346 |
– |
NkBT = (double)info->ndf * kB * targetTemp; |
347 |
– |
|
490 |
|
return 1; |
491 |
|
} |
492 |
+ |
|
493 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
494 |
+ |
|
495 |
+ |
double conservedQuantity; |
496 |
+ |
double Energy; |
497 |
+ |
double thermostat_kinetic; |
498 |
+ |
double thermostat_potential; |
499 |
+ |
double barostat_kinetic; |
500 |
+ |
double barostat_potential; |
501 |
+ |
double trEta; |
502 |
+ |
double a[3][3], b[3][3]; |
503 |
+ |
|
504 |
+ |
Energy = tStats->getTotalE(); |
505 |
+ |
|
506 |
+ |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
507 |
+ |
(2.0 * eConvert); |
508 |
+ |
|
509 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
510 |
+ |
|
511 |
+ |
info->transposeMat3(eta, a); |
512 |
+ |
info->matMul3(a, eta, b); |
513 |
+ |
trEta = info->matTrace3(b); |
514 |
+ |
|
515 |
+ |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
516 |
+ |
(2.0 * eConvert); |
517 |
+ |
|
518 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
519 |
+ |
eConvert; |
520 |
+ |
|
521 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
522 |
+ |
barostat_kinetic + barostat_potential; |
523 |
+ |
|
524 |
+ |
cout.width(8); |
525 |
+ |
cout.precision(8); |
526 |
+ |
|
527 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
528 |
+ |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
529 |
+ |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
530 |
+ |
|
531 |
+ |
return conservedQuantity; |
532 |
+ |
} |