| 1 |
#include <cmath> |
| 2 |
#include "Atom.hpp" |
| 3 |
#include "SRI.hpp" |
| 4 |
#include "AbstractClasses.hpp" |
| 5 |
#include "SimInfo.hpp" |
| 6 |
#include "ForceFields.hpp" |
| 7 |
#include "Thermo.hpp" |
| 8 |
#include "ReadWrite.hpp" |
| 9 |
#include "Integrator.hpp" |
| 10 |
#include "simError.h" |
| 11 |
|
| 12 |
|
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// Basic non-isotropic thermostating and barostating via the Melchionna |
| 14 |
// modification of the Hoover algorithm: |
| 15 |
// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 17 |
// Molec. Phys., 78, 533. |
| 18 |
// |
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// and |
| 20 |
// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 24 |
T( theInfo, the_ff ) |
| 25 |
{ |
| 26 |
int i, j; |
| 27 |
chi = 0.0; |
| 28 |
integralOfChidt = 0.0; |
| 29 |
|
| 30 |
for(i = 0; i < 3; i++) |
| 31 |
for (j = 0; j < 3; j++) |
| 32 |
eta[i][j] = 0.0; |
| 33 |
|
| 34 |
have_tau_thermostat = 0; |
| 35 |
have_tau_barostat = 0; |
| 36 |
have_target_temp = 0; |
| 37 |
have_target_pressure = 0; |
| 38 |
|
| 39 |
have_chi_tolerance = 0; |
| 40 |
have_eta_tolerance = 0; |
| 41 |
have_pos_iter_tolerance = 0; |
| 42 |
|
| 43 |
oldPos = new double[3*nAtoms]; |
| 44 |
oldVel = new double[3*nAtoms]; |
| 45 |
oldJi = new double[3*nAtoms]; |
| 46 |
#ifdef IS_MPI |
| 47 |
Nparticles = mpiSim->getTotAtoms(); |
| 48 |
#else |
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Nparticles = theInfo->n_atoms; |
| 50 |
#endif |
| 51 |
} |
| 52 |
|
| 53 |
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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|
| 61 |
int i, j, k; |
| 62 |
DirectionalAtom* dAtom; |
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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]; |
| 69 |
double instaTemp, instaPress, instaVol; |
| 70 |
double tt2, tb2; |
| 71 |
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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|
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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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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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|
| 91 |
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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//evolve velocity half step |
| 98 |
for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getVel( vel ); |
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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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info->matVecMul3( vScale, vel, sc ); |
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|
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for (j=0; j < 3; j++) { |
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// velocity half step (use chi from previous step here): |
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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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|
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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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// get and convert the torque to body frame |
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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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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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// 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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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] / 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] / 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 |
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angle = dt * ji[2] / I[2][2]; |
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this->rotate( 0, 1, angle, ji, A); |
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|
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// rotate about the y-axis |
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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 x-axis |
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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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dAtom->setJ( ji ); |
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dAtom->setA( A ); |
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} |
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} |
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|
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// advance chi half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
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//calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
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|
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//advance eta half step |
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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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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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else |
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eta[i][j] += dt2 * instaVol * press[i][j] / ( NkBT*tb2); |
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} |
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|
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//save the old positions |
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for(i = 0; i < nAtoms; i++){ |
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atoms[i]->getPos(pos); |
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for(j = 0; j < 3; j++) |
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oldPos[i*3 + j] = pos[j]; |
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} |
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|
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//the first estimation of r(t+dt) is equal to r(t) |
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|
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for(k = 0; k < 4; k ++){ |
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|
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for(i =0 ; i < nAtoms; i++){ |
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|
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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|
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for(j = 0; j < 3; j++) |
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rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
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|
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info->matVecMul3( eta, rj, sc ); |
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|
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
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|
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atoms[i]->setPos( pos ); |
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|
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} |
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|
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} |
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|
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|
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// Scale the box after all the positions have been moved: |
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|
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// 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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|
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bigScale = 1.0; |
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smallScale = 1.0; |
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offDiagMax = 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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|
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// Calculate the matrix Product of the eta array (we only need |
| 222 |
// the ij element right now): |
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|
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eta2ij = 0.0; |
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for(k=0; k<3; k++){ |
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eta2ij += eta[i][k] * eta[k][j]; |
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} |
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|
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scaleMat[i][j] = 0.0; |
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// identity matrix (see above): |
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if (i == j) scaleMat[i][j] = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
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|
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if (i != j) |
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if (fabs(scaleMat[i][j]) > offDiagMax) |
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offDiagMax = fabs(scaleMat[i][j]); |
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} |
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|
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if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 241 |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
| 243 |
|
| 244 |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
| 246 |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 254 |
painCave.isFatal = 1; |
| 255 |
simError(); |
| 256 |
} else if (offDiagMax > 0.1) { |
| 257 |
sprintf( painCave.errMsg, |
| 258 |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 259 |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 260 |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 261 |
" [%lf\t%lf\t%lf]\n" |
| 262 |
" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 266 |
painCave.isFatal = 1; |
| 267 |
simError(); |
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} else { |
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info->getBoxM(hm); |
| 270 |
info->matMul3(hm, scaleMat, hmnew); |
| 271 |
info->setBoxM(hmnew); |
| 272 |
} |
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|
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} |
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|
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template<typename T> void NPTf<T>::moveB( void ){ |
| 277 |
|
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int i, j, k; |
| 279 |
DirectionalAtom* dAtom; |
| 280 |
double Tb[3], ji[3]; |
| 281 |
double vel[3], frc[3]; |
| 282 |
double mass; |
| 283 |
|
| 284 |
double instaTemp, instaPress, instaVol; |
| 285 |
double tt2, tb2; |
| 286 |
double sc[3]; |
| 287 |
double press[3][3], vScale[3][3]; |
| 288 |
double oldChi, prevChi; |
| 289 |
double oldEta[3][3], preEta[3][3], diffEta; |
| 290 |
|
| 291 |
tt2 = tauThermostat * tauThermostat; |
| 292 |
tb2 = tauBarostat * tauBarostat; |
| 293 |
|
| 294 |
|
| 295 |
// Set things up for the iteration: |
| 296 |
|
| 297 |
oldChi = chi; |
| 298 |
|
| 299 |
for(i = 0; i < 3; i++) |
| 300 |
for(j = 0; j < 3; j++) |
| 301 |
oldEta[i][j] = eta[i][j]; |
| 302 |
|
| 303 |
for( i=0; i<nAtoms; i++ ){ |
| 304 |
|
| 305 |
atoms[i]->getVel( vel ); |
| 306 |
|
| 307 |
for (j=0; j < 3; j++) |
| 308 |
oldVel[3*i + j] = vel[j]; |
| 309 |
|
| 310 |
if( atoms[i]->isDirectional() ){ |
| 311 |
|
| 312 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 313 |
|
| 314 |
dAtom->getJ( ji ); |
| 315 |
|
| 316 |
for (j=0; j < 3; j++) |
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oldJi[3*i + j] = ji[j]; |
| 318 |
|
| 319 |
} |
| 320 |
} |
| 321 |
|
| 322 |
// do the iteration: |
| 323 |
|
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instaVol = tStats->getVolume(); |
| 325 |
|
| 326 |
for (k=0; k < 4; k++) { |
| 327 |
|
| 328 |
instaTemp = tStats->getTemperature(); |
| 329 |
tStats->getPressureTensor(press); |
| 330 |
|
| 331 |
// evolve chi another half step using the temperature at t + dt/2 |
| 332 |
|
| 333 |
prevChi = chi; |
| 334 |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 335 |
|
| 336 |
for(i = 0; i < 3; i++) |
| 337 |
for(j = 0; j < 3; j++) |
| 338 |
preEta[i][j] = eta[i][j]; |
| 339 |
|
| 340 |
//advance eta half step and calculate scale factor for velocity |
| 341 |
for(i = 0; i < 3; i ++) |
| 342 |
for(j = 0; j < 3; j++){ |
| 343 |
if( i == j){ |
| 344 |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 345 |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 346 |
vScale[i][j] = eta[i][j] + chi; |
| 347 |
} |
| 348 |
else |
| 349 |
{ |
| 350 |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 351 |
vScale[i][j] = eta[i][j]; |
| 352 |
} |
| 353 |
} |
| 354 |
|
| 355 |
//advance velocity half step |
| 356 |
for( i=0; i<nAtoms; i++ ){ |
| 357 |
|
| 358 |
atoms[i]->getFrc( frc ); |
| 359 |
atoms[i]->getVel(vel); |
| 360 |
|
| 361 |
mass = atoms[i]->getMass(); |
| 362 |
|
| 363 |
info->matVecMul3( vScale, vel, sc ); |
| 364 |
|
| 365 |
for (j=0; j < 3; j++) { |
| 366 |
// velocity half step (use chi from previous step here): |
| 367 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 368 |
} |
| 369 |
|
| 370 |
atoms[i]->setVel( vel ); |
| 371 |
|
| 372 |
if( atoms[i]->isDirectional() ){ |
| 373 |
|
| 374 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 375 |
|
| 376 |
// get and convert the torque to body frame |
| 377 |
|
| 378 |
dAtom->getTrq( Tb ); |
| 379 |
dAtom->lab2Body( Tb ); |
| 380 |
|
| 381 |
for (j=0; j < 3; j++) |
| 382 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 383 |
|
| 384 |
dAtom->setJ( ji ); |
| 385 |
} |
| 386 |
} |
| 387 |
|
| 388 |
|
| 389 |
diffEta = 0; |
| 390 |
for(i = 0; i < 3; i++) |
| 391 |
diffEta += pow(preEta[i][i] - eta[i][i], 2); |
| 392 |
|
| 393 |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
| 394 |
break; |
| 395 |
} |
| 396 |
|
| 397 |
//calculate integral of chida |
| 398 |
integralOfChidt += dt2*chi; |
| 399 |
|
| 400 |
|
| 401 |
} |
| 402 |
|
| 403 |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 404 |
int i,j; |
| 405 |
|
| 406 |
chi = 0.0; |
| 407 |
|
| 408 |
for(i = 0; i < 3; i++) |
| 409 |
for (j = 0; j < 3; j++) |
| 410 |
eta[i][j] = 0.0; |
| 411 |
|
| 412 |
} |
| 413 |
|
| 414 |
template<typename T> int NPTf<T>::readyCheck() { |
| 415 |
|
| 416 |
//check parent's readyCheck() first |
| 417 |
if (T::readyCheck() == -1) |
| 418 |
return -1; |
| 419 |
|
| 420 |
// First check to see if we have a target temperature. |
| 421 |
// Not having one is fatal. |
| 422 |
|
| 423 |
if (!have_target_temp) { |
| 424 |
sprintf( painCave.errMsg, |
| 425 |
"NPTf error: You can't use the NPTf integrator\n" |
| 426 |
" without a targetTemp!\n" |
| 427 |
); |
| 428 |
painCave.isFatal = 1; |
| 429 |
simError(); |
| 430 |
return -1; |
| 431 |
} |
| 432 |
|
| 433 |
if (!have_target_pressure) { |
| 434 |
sprintf( painCave.errMsg, |
| 435 |
"NPTf error: You can't use the NPTf integrator\n" |
| 436 |
" without a targetPressure!\n" |
| 437 |
); |
| 438 |
painCave.isFatal = 1; |
| 439 |
simError(); |
| 440 |
return -1; |
| 441 |
} |
| 442 |
|
| 443 |
// We must set tauThermostat. |
| 444 |
|
| 445 |
if (!have_tau_thermostat) { |
| 446 |
sprintf( painCave.errMsg, |
| 447 |
"NPTf error: If you use the NPTf\n" |
| 448 |
" integrator, you must set tauThermostat.\n"); |
| 449 |
painCave.isFatal = 1; |
| 450 |
simError(); |
| 451 |
return -1; |
| 452 |
} |
| 453 |
|
| 454 |
// We must set tauBarostat. |
| 455 |
|
| 456 |
if (!have_tau_barostat) { |
| 457 |
sprintf( painCave.errMsg, |
| 458 |
"NPTf error: If you use the NPTf\n" |
| 459 |
" integrator, you must set tauBarostat.\n"); |
| 460 |
painCave.isFatal = 1; |
| 461 |
simError(); |
| 462 |
return -1; |
| 463 |
} |
| 464 |
|
| 465 |
// We need NkBT a lot, so just set it here: |
| 466 |
|
| 467 |
NkBT = (double)Nparticles * kB * targetTemp; |
| 468 |
fkBT = (double)info->ndf * kB * targetTemp; |
| 469 |
|
| 470 |
return 1; |
| 471 |
} |
| 472 |
|
| 473 |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 474 |
|
| 475 |
double conservedQuantity; |
| 476 |
double tb2; |
| 477 |
double trEta; |
| 478 |
double U; |
| 479 |
double thermo; |
| 480 |
double integral; |
| 481 |
double baro; |
| 482 |
double PV; |
| 483 |
|
| 484 |
U = tStats->getTotalE(); |
| 485 |
thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 486 |
|
| 487 |
tb2 = tauBarostat * tauBarostat; |
| 488 |
trEta = info->matTrace3(eta); |
| 489 |
baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert; |
| 490 |
|
| 491 |
integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert; |
| 492 |
|
| 493 |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 494 |
|
| 495 |
|
| 496 |
cout.width(8); |
| 497 |
cout.precision(8); |
| 498 |
|
| 499 |
cout << info->getTime() << "\t" |
| 500 |
<< chi << "\t" |
| 501 |
<< trEta << "\t" |
| 502 |
<< U << "\t" |
| 503 |
<< thermo << "\t" |
| 504 |
<< baro << "\t" |
| 505 |
<< integral << "\t" |
| 506 |
<< PV << "\t" |
| 507 |
<< U+thermo+integral+PV+baro << endl; |
| 508 |
|
| 509 |
conservedQuantity = U+thermo+integral+PV+baro; |
| 510 |
return conservedQuantity; |
| 511 |
|
| 512 |
} |
