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#include <cmath> |
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#include "Atom.hpp" |
| 3 |
#include "Molecule.hpp" |
| 4 |
#include "SRI.hpp" |
| 5 |
#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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|
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|
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// Basic non-isotropic thermostating and barostating via the Melchionna |
| 15 |
// 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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|
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// The NPTfm variant scales the molecular center-of-mass coordinates |
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// instead of the atomic coordinates |
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|
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template<typename T> NPTfm<T>::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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int i, j; |
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chi = 0.0; |
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integralOfChidt = 0.0; |
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|
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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|
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have_tau_thermostat = 0; |
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have_tau_barostat = 0; |
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have_target_temp = 0; |
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have_target_pressure = 0; |
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} |
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|
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template<typename T> void NPTfm<T>::moveA() { |
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|
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// int i, j, k; |
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// DirectionalAtom* dAtom; |
| 48 |
// 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 instaTemp, instaPress, instaVol; |
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// double tt2, tb2; |
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// double sc[3]; |
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// double eta2ij, smallScale, bigScale, offDiagMax; |
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// double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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|
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// int nInMol; |
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// double rc[3]; |
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|
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// /* |
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// nMols = info->n_mol; |
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// myMolecules = info->molecules; |
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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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// // first evolve chi a half step |
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|
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// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
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// for (i = 0; i < 3; i++ ) { |
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// for (j = 0; j < 3; j++ ) { |
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// if (i == j) { |
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|
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// eta[i][j] += dt2 * instaVol * |
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// (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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|
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// vScale[i][j] = eta[i][j] + chi; |
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|
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// } else { |
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|
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// eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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|
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// vScale[i][j] = eta[i][j]; |
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|
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// } |
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// } |
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// } |
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|
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|
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// for (i = 0; i < nMols; i++) { |
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|
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// myMolecules[i].getCOM(rc); |
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|
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// nInMol = myMolecules[i].getNAtoms(); |
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// myAtoms = myMolecules[i].getMyAtoms(); |
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|
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// // find the minimum image coordinates of the molecular centers of mass: |
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|
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// info->wrapVector(rc); |
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|
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// for( j=0; j< nInMol; j++ ){ |
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|
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// if(myAtoms[j] != NULL) { |
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|
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// myAtoms[j]->getVel( vel ); |
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// myAtoms[j]->getPos( pos ); |
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// myAtoms[j]->getFrc( frc ); |
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|
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// mass = myAtoms[j]->getMass(); |
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|
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// // velocity half step |
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|
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// info->matVecMul3( vScale, vel, sc ); |
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|
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// for (k = 0; k < 3; k++) |
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// vel[k] += dt2 * ((frc[k] / mass) * eConvert - sc[k]); |
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|
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// myAtoms[j]->setVel( vel ); |
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|
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// // position whole step |
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|
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// info->matVecMul3( eta, rc, sc ); |
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|
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// for (k = 0; k < 3; k++ ) |
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// pos[k] += dt * (vel[k] + sc[k]); |
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|
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// myAtoms[j]->setPos( pos ); |
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|
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// if( myAtoms[j]->isDirectional() ){ |
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|
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// dAtom = (DirectionalAtom *)myAtoms[j]; |
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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 (k=0; k < 3; k++) |
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// ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*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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// } |
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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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|
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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 |
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// // 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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// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
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// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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// } |
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|
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// if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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// sprintf( painCave.errMsg, |
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// "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]); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } else if (offDiagMax > 0.1) { |
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// sprintf( painCave.errMsg, |
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// "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 236 |
// " Check your tauBarostat, as it is probably too small!\n\n" |
| 237 |
// " scaleMat = [%lf\t%lf\t%lf]\n" |
| 238 |
// " [%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]); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } else { |
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// info->getBoxM(hm); |
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// info->matMul3(hm, scaleMat, hmnew); |
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// info->setBoxM(hmnew); |
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// } |
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// */ |
| 251 |
|
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// tt2 = tauThermostat * tauThermostat; |
| 253 |
// tb2 = tauBarostat * tauBarostat; |
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|
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// instaTemp = tStats->getTemperature(); |
| 256 |
// tStats->getPressureTensor(press); |
| 257 |
// instaVol = tStats->getVolume(); |
| 258 |
|
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// tStats->getCOM(COM); |
| 260 |
|
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// //calculate scale factor of veloity |
| 262 |
// for (i = 0; i < 3; i++ ) { |
| 263 |
// for (j = 0; j < 3; j++ ) { |
| 264 |
// vScale[i][j] = eta[i][j]; |
| 265 |
|
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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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|
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// for (i = 0; i < nMols; i++) { |
| 274 |
|
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// myMolecules[i].getCOM(rc); |
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|
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// nInMol = myMolecules[i].getNAtoms(); |
| 278 |
// myAtoms = myMolecules[i].getMyAtoms(); |
| 279 |
|
| 280 |
|
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// for( j=0; j< nInMol; j++ ){ |
| 282 |
|
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// if(myAtoms[j] != NULL) { |
| 284 |
|
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// myAtoms[j]->getVel( vel ); |
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// myAtoms[j]->getFrc( frc ); |
| 287 |
|
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// mass = myAtoms[j]->getMass(); |
| 289 |
|
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// // velocity half step |
| 291 |
|
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// info->matVecMul3( vScale, vel, sc ); |
| 293 |
|
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// for (k = 0; k < 3; k++) |
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// vel[k] += dt2 * ((frc[k] / mass) * eConvert - sc[k]); |
| 296 |
|
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// myAtoms[j]->setVel( vel ); |
| 298 |
|
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// if( myAtoms[j]->isDirectional() ){ |
| 300 |
|
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// dAtom = (DirectionalAtom *)myAtoms[j]; |
| 302 |
|
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// // get and convert the torque to body frame |
| 304 |
|
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// dAtom->getTrq( Tb ); |
| 306 |
// dAtom->lab2Body( Tb ); |
| 307 |
|
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// // get the angular momentum, and propagate a half step |
| 309 |
|
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// dAtom->getJ( ji ); |
| 311 |
|
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// for (k=0; k < 3; k++) |
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// ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*chi); |
| 314 |
|
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// // use the angular velocities to propagate the rotation matrix a |
| 316 |
// // full time step |
| 317 |
|
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// dAtom->getA(A); |
| 319 |
// dAtom->getI(I); |
| 320 |
|
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// // rotate about the x-axis |
| 322 |
// angle = dt2 * ji[0] / I[0][0]; |
| 323 |
// this->rotate( 1, 2, angle, ji, A ); |
| 324 |
|
| 325 |
// // rotate about the y-axis |
| 326 |
// angle = dt2 * ji[1] / I[1][1]; |
| 327 |
// this->rotate( 2, 0, angle, ji, A ); |
| 328 |
|
| 329 |
// // rotate about the z-axis |
| 330 |
// angle = dt * ji[2] / I[2][2]; |
| 331 |
// this->rotate( 0, 1, angle, ji, A); |
| 332 |
|
| 333 |
// // rotate about the y-axis |
| 334 |
// angle = dt2 * ji[1] / I[1][1]; |
| 335 |
// this->rotate( 2, 0, angle, ji, A ); |
| 336 |
|
| 337 |
// // rotate about the x-axis |
| 338 |
// angle = dt2 * ji[0] / I[0][0]; |
| 339 |
// this->rotate( 1, 2, angle, ji, A ); |
| 340 |
|
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// dAtom->setJ( ji ); |
| 342 |
// dAtom->setA( A ); |
| 343 |
// } |
| 344 |
// } |
| 345 |
// } |
| 346 |
// } |
| 347 |
|
| 348 |
|
| 349 |
// // advance chi half step |
| 350 |
// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 351 |
|
| 352 |
// //calculate the integral of chidt |
| 353 |
// integralOfChidt += dt2*chi; |
| 354 |
|
| 355 |
// //advance eta half step |
| 356 |
// for(i = 0; i < 3; i ++) |
| 357 |
// for(j = 0; j < 3; j++){ |
| 358 |
// if( i == j) |
| 359 |
// eta[i][j] += dt2 * instaVol * |
| 360 |
// (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 361 |
// else |
| 362 |
// eta[i][j] += dt2 * instaVol * press[i][j] / ( NkBT*tb2); |
| 363 |
// } |
| 364 |
|
| 365 |
// //save the old positions |
| 366 |
// for(i = 0; i < nAtoms; i++){ |
| 367 |
// atoms[i]->getPos(pos); |
| 368 |
// for(j = 0; j < 3; j++) |
| 369 |
// oldPos[i*3 + j] = pos[j]; |
| 370 |
// } |
| 371 |
|
| 372 |
// //the first estimation of r(t+dt) is equal to r(t) |
| 373 |
|
| 374 |
// for(k = 0; k < 4; k ++){ |
| 375 |
|
| 376 |
// for(i =0 ; i < nAtoms; i++){ |
| 377 |
|
| 378 |
// atoms[i]->getVel(vel); |
| 379 |
// atoms[i]->getPos(pos); |
| 380 |
|
| 381 |
// for(j = 0; j < 3; j++) |
| 382 |
// rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
| 383 |
|
| 384 |
// info->matVecMul3( eta, rj, sc ); |
| 385 |
|
| 386 |
// for(j = 0; j < 3; j++) |
| 387 |
// pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 388 |
|
| 389 |
// atoms[i]->setPos( pos ); |
| 390 |
|
| 391 |
// } |
| 392 |
|
| 393 |
// } |
| 394 |
|
| 395 |
|
| 396 |
// // Scale the box after all the positions have been moved: |
| 397 |
|
| 398 |
// // Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 399 |
// // Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 400 |
|
| 401 |
// bigScale = 1.0; |
| 402 |
// smallScale = 1.0; |
| 403 |
// offDiagMax = 0.0; |
| 404 |
|
| 405 |
// for(i=0; i<3; i++){ |
| 406 |
// for(j=0; j<3; j++){ |
| 407 |
|
| 408 |
// // Calculate the matrix Product of the eta array (we only need |
| 409 |
// // the ij element right now): |
| 410 |
|
| 411 |
// eta2ij = 0.0; |
| 412 |
// for(k=0; k<3; k++){ |
| 413 |
// eta2ij += eta[i][k] * eta[k][j]; |
| 414 |
// } |
| 415 |
|
| 416 |
// scaleMat[i][j] = 0.0; |
| 417 |
// // identity matrix (see above): |
| 418 |
// if (i == j) scaleMat[i][j] = 1.0; |
| 419 |
// // Taylor expansion for the exponential truncated at second order: |
| 420 |
// scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 421 |
|
| 422 |
// if (i != j) |
| 423 |
// if (fabs(scaleMat[i][j]) > offDiagMax) |
| 424 |
// offDiagMax = fabs(scaleMat[i][j]); |
| 425 |
// } |
| 426 |
|
| 427 |
// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 428 |
// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 429 |
// } |
| 430 |
|
| 431 |
// if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 432 |
// sprintf( painCave.errMsg, |
| 433 |
// "NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 434 |
// " Check your tauBarostat, as it is probably too small!\n\n" |
| 435 |
// " scaleMat = [%lf\t%lf\t%lf]\n" |
| 436 |
// " [%lf\t%lf\t%lf]\n" |
| 437 |
// " [%lf\t%lf\t%lf]\n", |
| 438 |
// scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 439 |
// scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 440 |
// scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 441 |
// painCave.isFatal = 1; |
| 442 |
// simError(); |
| 443 |
// } else if (offDiagMax > 0.1) { |
| 444 |
// sprintf( painCave.errMsg, |
| 445 |
// "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 446 |
// " Check your tauBarostat, as it is probably too small!\n\n" |
| 447 |
// " scaleMat = [%lf\t%lf\t%lf]\n" |
| 448 |
// " [%lf\t%lf\t%lf]\n" |
| 449 |
// " [%lf\t%lf\t%lf]\n", |
| 450 |
// scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 451 |
// scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 452 |
// scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 453 |
// painCave.isFatal = 1; |
| 454 |
// simError(); |
| 455 |
// } else { |
| 456 |
// info->getBoxM(hm); |
| 457 |
// info->matMul3(hm, scaleMat, hmnew); |
| 458 |
// info->setBoxM(hmnew); |
| 459 |
// } |
| 460 |
|
| 461 |
|
| 462 |
|
| 463 |
} |
| 464 |
|
| 465 |
template<typename T> void NPTfm<T>::moveB( void ){ |
| 466 |
|
| 467 |
// int i, j; |
| 468 |
// DirectionalAtom* dAtom; |
| 469 |
// double Tb[3], ji[3]; |
| 470 |
// double vel[3], frc[3]; |
| 471 |
// double mass; |
| 472 |
|
| 473 |
// double instaTemp, instaPress, instaVol; |
| 474 |
// double tt2, tb2; |
| 475 |
// double sc[3]; |
| 476 |
// double press[3][3], vScale[3][3]; |
| 477 |
// double oldChi, prevChi; |
| 478 |
// double oldEta[3][3], preEta[3][3], diffEta; |
| 479 |
|
| 480 |
// /* |
| 481 |
// tt2 = tauThermostat * tauThermostat; |
| 482 |
// tb2 = tauBarostat * tauBarostat; |
| 483 |
|
| 484 |
// instaTemp = tStats->getTemperature(); |
| 485 |
// tStats->getPressureTensor(press); |
| 486 |
// instaVol = tStats->getVolume(); |
| 487 |
|
| 488 |
// // first evolve chi a half step |
| 489 |
|
| 490 |
// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 491 |
|
| 492 |
// for (i = 0; i < 3; i++ ) { |
| 493 |
// for (j = 0; j < 3; j++ ) { |
| 494 |
// if (i == j) { |
| 495 |
|
| 496 |
// eta[i][j] += dt2 * instaVol * |
| 497 |
// (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 498 |
|
| 499 |
// vScale[i][j] = eta[i][j] + chi; |
| 500 |
|
| 501 |
// } else { |
| 502 |
|
| 503 |
// eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 504 |
|
| 505 |
// vScale[i][j] = eta[i][j]; |
| 506 |
|
| 507 |
// } |
| 508 |
// } |
| 509 |
// } |
| 510 |
|
| 511 |
// for( i=0; i<nAtoms; i++ ){ |
| 512 |
|
| 513 |
// atoms[i]->getVel( vel ); |
| 514 |
// atoms[i]->getFrc( frc ); |
| 515 |
|
| 516 |
// mass = atoms[i]->getMass(); |
| 517 |
|
| 518 |
// // velocity half step |
| 519 |
|
| 520 |
// info->matVecMul3( vScale, vel, sc ); |
| 521 |
|
| 522 |
// for (j = 0; j < 3; j++) { |
| 523 |
// vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 524 |
// } |
| 525 |
|
| 526 |
// atoms[i]->setVel( vel ); |
| 527 |
|
| 528 |
// if( atoms[i]->isDirectional() ){ |
| 529 |
|
| 530 |
// dAtom = (DirectionalAtom *)atoms[i]; |
| 531 |
|
| 532 |
// // get and convert the torque to body frame |
| 533 |
|
| 534 |
// dAtom->getTrq( Tb ); |
| 535 |
// dAtom->lab2Body( Tb ); |
| 536 |
|
| 537 |
// // get the angular momentum, and propagate a half step |
| 538 |
|
| 539 |
// dAtom->getJ( ji ); |
| 540 |
|
| 541 |
// for (j=0; j < 3; j++) |
| 542 |
// ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 543 |
|
| 544 |
// dAtom->setJ( ji ); |
| 545 |
|
| 546 |
// } |
| 547 |
// } |
| 548 |
// */ |
| 549 |
|
| 550 |
// tt2 = tauThermostat * tauThermostat; |
| 551 |
// tb2 = tauBarostat * tauBarostat; |
| 552 |
|
| 553 |
|
| 554 |
// // Set things up for the iteration: |
| 555 |
|
| 556 |
// oldChi = chi; |
| 557 |
|
| 558 |
// for(i = 0; i < 3; i++) |
| 559 |
// for(j = 0; j < 3; j++) |
| 560 |
// oldEta[i][j] = eta[i][j]; |
| 561 |
|
| 562 |
// for( i=0; i<nAtoms; i++ ){ |
| 563 |
|
| 564 |
// atoms[i]->getVel( vel ); |
| 565 |
|
| 566 |
// for (j=0; j < 3; j++) |
| 567 |
// oldVel[3*i + j] = vel[j]; |
| 568 |
|
| 569 |
// if( atoms[i]->isDirectional() ){ |
| 570 |
|
| 571 |
// dAtom = (DirectionalAtom *)atoms[i]; |
| 572 |
|
| 573 |
// dAtom->getJ( ji ); |
| 574 |
|
| 575 |
// for (j=0; j < 3; j++) |
| 576 |
// oldJi[3*i + j] = ji[j]; |
| 577 |
|
| 578 |
// } |
| 579 |
// } |
| 580 |
|
| 581 |
// // do the iteration: |
| 582 |
|
| 583 |
// instaVol = tStats->getVolume(); |
| 584 |
|
| 585 |
// for (k=0; k < 4; k++) { |
| 586 |
|
| 587 |
// instaTemp = tStats->getTemperature(); |
| 588 |
// tStats->getPressureTensor(press); |
| 589 |
|
| 590 |
// // evolve chi another half step using the temperature at t + dt/2 |
| 591 |
|
| 592 |
// prevChi = chi; |
| 593 |
// chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 594 |
|
| 595 |
// for(i = 0; i < 3; i++) |
| 596 |
// for(j = 0; j < 3; j++) |
| 597 |
// preEta[i][j] = eta[i][j]; |
| 598 |
|
| 599 |
// //advance eta half step and calculate scale factor for velocity |
| 600 |
// for(i = 0; i < 3; i ++) |
| 601 |
// for(j = 0; j < 3; j++){ |
| 602 |
// if( i == j){ |
| 603 |
// eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 604 |
// (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 605 |
// vScale[i][j] = eta[i][j] + chi; |
| 606 |
// } |
| 607 |
// else |
| 608 |
// { |
| 609 |
// eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 610 |
// vScale[i][j] = eta[i][j]; |
| 611 |
// } |
| 612 |
// } |
| 613 |
|
| 614 |
// //advance velocity half step |
| 615 |
// for( i=0; i<nAtoms; i++ ){ |
| 616 |
|
| 617 |
// atoms[i]->getFrc( frc ); |
| 618 |
// atoms[i]->getVel(vel); |
| 619 |
|
| 620 |
// mass = atoms[i]->getMass(); |
| 621 |
|
| 622 |
// info->matVecMul3( vScale, vel, sc ); |
| 623 |
|
| 624 |
// for (j=0; j < 3; j++) { |
| 625 |
// // velocity half step (use chi from previous step here): |
| 626 |
// vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 627 |
// } |
| 628 |
|
| 629 |
// atoms[i]->setVel( vel ); |
| 630 |
|
| 631 |
// if( atoms[i]->isDirectional() ){ |
| 632 |
|
| 633 |
// dAtom = (DirectionalAtom *)atoms[i]; |
| 634 |
|
| 635 |
// // get and convert the torque to body frame |
| 636 |
|
| 637 |
// dAtom->getTrq( Tb ); |
| 638 |
// dAtom->lab2Body( Tb ); |
| 639 |
|
| 640 |
// for (j=0; j < 3; j++) |
| 641 |
// ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 642 |
|
| 643 |
// dAtom->setJ( ji ); |
| 644 |
// } |
| 645 |
// } |
| 646 |
|
| 647 |
|
| 648 |
// diffEta = 0; |
| 649 |
// for(i = 0; i < 3; i++) |
| 650 |
// diffEta += pow(preEta[i][i] - eta[i][i], 2); |
| 651 |
|
| 652 |
// if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
| 653 |
// break; |
| 654 |
// } |
| 655 |
|
| 656 |
// //calculate integral of chida |
| 657 |
// integralOfChidt += dt2*chi; |
| 658 |
} |
| 659 |
|
| 660 |
template<typename T> void NPTfm<T>::resetIntegrator() { |
| 661 |
int i,j; |
| 662 |
|
| 663 |
chi = 0.0; |
| 664 |
|
| 665 |
for(i = 0; i < 3; i++) |
| 666 |
for (j = 0; j < 3; j++) |
| 667 |
eta[i][j] = 0.0; |
| 668 |
} |
| 669 |
|
| 670 |
template<typename T> int NPTfm<T>::readyCheck() { |
| 671 |
|
| 672 |
//check parent's readyCheck() first |
| 673 |
if (T::readyCheck() == -1) |
| 674 |
return -1; |
| 675 |
|
| 676 |
// First check to see if we have a target temperature. |
| 677 |
// Not having one is fatal. |
| 678 |
|
| 679 |
if (!have_target_temp) { |
| 680 |
sprintf( painCave.errMsg, |
| 681 |
"NPTfm error: You can't use the NPTfm integrator\n" |
| 682 |
" without a targetTemp!\n" |
| 683 |
); |
| 684 |
painCave.isFatal = 1; |
| 685 |
simError(); |
| 686 |
return -1; |
| 687 |
} |
| 688 |
|
| 689 |
if (!have_target_pressure) { |
| 690 |
sprintf( painCave.errMsg, |
| 691 |
"NPTfm error: You can't use the NPTfm integrator\n" |
| 692 |
" without a targetPressure!\n" |
| 693 |
); |
| 694 |
painCave.isFatal = 1; |
| 695 |
simError(); |
| 696 |
return -1; |
| 697 |
} |
| 698 |
|
| 699 |
// We must set tauThermostat. |
| 700 |
|
| 701 |
if (!have_tau_thermostat) { |
| 702 |
sprintf( painCave.errMsg, |
| 703 |
"NPTfm error: If you use the NPTfm\n" |
| 704 |
" integrator, you must set tauThermostat.\n"); |
| 705 |
painCave.isFatal = 1; |
| 706 |
simError(); |
| 707 |
return -1; |
| 708 |
} |
| 709 |
|
| 710 |
// We must set tauBarostat. |
| 711 |
|
| 712 |
if (!have_tau_barostat) { |
| 713 |
sprintf( painCave.errMsg, |
| 714 |
"NPTfm error: If you use the NPTfm\n" |
| 715 |
" integrator, you must set tauBarostat.\n"); |
| 716 |
painCave.isFatal = 1; |
| 717 |
simError(); |
| 718 |
return -1; |
| 719 |
} |
| 720 |
|
| 721 |
// We need NkBT a lot, so just set it here: |
| 722 |
|
| 723 |
NkBT = (double)info->ndf * kB * targetTemp; |
| 724 |
|
| 725 |
return 1; |
| 726 |
} |
| 727 |
|
| 728 |
template<typename T> double NPTfm<T>::getConservedQuantity(void){ |
| 729 |
|
| 730 |
|
| 731 |
// double conservedQuantity; |
| 732 |
// double tb2; |
| 733 |
// double trEta; |
| 734 |
// double E_NPT; |
| 735 |
// double U; |
| 736 |
// double TS; |
| 737 |
// double PV; |
| 738 |
// double extra; |
| 739 |
|
| 740 |
// U = tStats->getTotalE(); |
| 741 |
|
| 742 |
// TS = fkBT * |
| 743 |
// (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 744 |
|
| 745 |
// PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 746 |
|
| 747 |
// tb2 = tauBarostat * tauBarostat; |
| 748 |
|
| 749 |
// trEta = info->matTrace3(eta); |
| 750 |
|
| 751 |
// extra = (fkBT * tb2 * trEta * trEta / 2.0 ) / eConvert; |
| 752 |
|
| 753 |
// cout.width(8); |
| 754 |
// cout.precision(8); |
| 755 |
|
| 756 |
// cout << info->getTime() << "\t" |
| 757 |
// << chi << "\t" |
| 758 |
// << trEta << "\t" |
| 759 |
// << U << "\t" |
| 760 |
// << TS << "\t" |
| 761 |
// << PV << "\t" |
| 762 |
// << extra << "\t" |
| 763 |
// << U+TS+PV+extra << endl; |
| 764 |
|
| 765 |
// conservedQuantity = U+TS+PV+extra; |
| 766 |
// return conservedQuantity; |
| 767 |
} |
