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#include <math.h> |
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ExtendedSystem::ExtendedSystem( SimInfo &info ) { |
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// get what information we need from the SimInfo object |
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entry_plug = &info; |
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nAtoms = info.n_atoms; |
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atoms = info.atoms; |
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nMols = info.n_mol; |
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molecules = info.molecules; |
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} |
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ExtendedSystem::~ExtendedSystem() { |
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} |
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void ExtendedSystem::nose_hoover_nvt( double ke, double dt, double temp ){ |
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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int i, j, degrees_freedom; |
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double ke, dt, temp, kB; |
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double keconverter, NkBT, zetaScale, ke_temp; |
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double vxi, vyi, vzi, jxi, jyi, jzi; |
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degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
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kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
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keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K |
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ke_temp = ke * keconverter; |
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NkBT = degrees_freedom*kB*temp; |
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// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin & |
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// qmass is set in the parameter file |
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zeta = zeta + dt*((ke_temp*2 - NkBT)/qmass); |
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zetaScale = zeta * dt; |
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// perform thermostat scaling on linear velocities and angular momentum |
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for(i = 0, i < nmol; i++ ) { |
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vxi = vx(i)*zetaScale; |
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vyi = vy(i)*zetaScale; |
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vzi = vz(i)*zetaScale; |
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jxi = jx(i)*zetaScale; |
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jyi = jy(i)*zetaScale; |
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jzi = jz(i)*zetaScale; |
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vx(i) = vx(i) - vxi; |
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vy(i) = vy(i) - vyi; |
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vz(i) = vz(i) - vzi; |
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jx(i) = jx(i) - jxi; |
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jy(i) = jy(i) - jyi; |
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jz(i) = jz(i) - jzi; |
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} |
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} |
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void ExtendedSystem::nose_hoover_anderson_npt(double pressure, double ke, double dt, |
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double temp ) { |
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// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500 |
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int i, j, degrees_freedom; |
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double pressure, dt, temp, pressure_units, epsilonScale; |
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double ke, kB, vxi, vyi, vzi, pressure_ext; |
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double boxx_old, boxy_old, boxz_old; |
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double keconverter, NkBT, zetaScale, ke_temp; |
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double jxi, jyi, jzi, scale; |
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kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
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pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
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degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
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keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K |
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pressure_ext = pressure * pressure_units; |
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volume = boxx*boxy*boxz; |
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ke_temp = ke * keconverter; |
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NkBT = degrees_freedom*kB*temp; |
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// propogate the strain rate |
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epsilon_dot += dt * ( (p_mol - pressure_ext)*volume |
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/ (tau_relax*tau_relax * kB * temp) ); |
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// determine the change in cell volume |
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scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0)); |
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volume = volume * pow(scale, 3.0); |
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// perform affine transform to update positions with volume fluctuations |
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affine_transform( scale ); |
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// save old lengths and update box size |
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boxx_old = boxx; |
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boxy_old = boxy; |
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boxz_old = boxz; |
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boxx = boxx_old*scale; |
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boxy = boxy_old*scale; |
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boxz = boxz_old*scale; |
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epsilonScale = epsilon_dot * dt; |
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// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
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// qmass is set in the parameter file |
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zeta += dt * ( (ke_temp*2 - NkBT) / qmass ); |
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zetaScale = zeta * dt; |
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// apply barostating and thermostating to velocities and angular momenta |
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for (i=0; i < nmol; i++) { |
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vxi = vx(i)*epsilonScale; |
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vyi = vy(i)*epsilonScale; |
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vzi = vz(i)*epsilonScale; |
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vxi = vxi + vx(i)*zetaScale; |
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vyi = vyi + vy(i)*zetaScale; |
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vzi = vzi + vz(i)*zetaScale; |
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jxi = jx(i)*zetaScale; |
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jyi = jy(i)*zetaScale; |
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jzi = jz(i)*zetaScale; |
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vx(i) = vx(i) - vxi; |
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vy(i) = vy(i) - vyi; |
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vz(i) = vz(i) - vzi; |
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jx(i) = jx(i) - jxi; |
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jy(i) = jy(i) - jyi; |
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jz(i) = jz(i) - jzi; |
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} |
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} |
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void ExtendedSystem::affine_transform( double scale ){ |
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int i; |
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double boxx_old, boxy_old, boxz_old, percentScale; |
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double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi; |
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double[3] r; |
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// first determine the scaling factor from the box size change |
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percentScale = (boxx - boxx_old)/boxx_old; |
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for (i=0; i < nMols; i++) { |
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molecules[i]->getCOM(r); |
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// find the minimum image coordinates of the molecular centers of mass: |
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boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5); |
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boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0); |
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boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0); |
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boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0); |
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rxi = rx(i) - boxx_num; |
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ryi = ry(i) - boxy_num; |
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rzi = rz(i) - boxz_num; |
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// update the minimum image coordinates using the scaling factor |
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rxi = rxi + rxi*percentScale; |
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ryi = ryi + ryi*percentScale; |
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rzi = rzi + rzi*percentScale; |
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rx(i) = rxi + boxx_num; |
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ry(i) = ryi + boxy_num; |
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rz(i) = rzi + boxz_num; |
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} |
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} |
