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#include <cmath> |
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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|
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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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// 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; |
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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 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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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" |
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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 { |
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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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} |
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|
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template<typename T> void NPTfm<T>::moveB( void ){ |
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|
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int i, j; |
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DirectionalAtom* dAtom; |
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double Tb[3], ji[3]; |
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double vel[3], frc[3]; |
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double mass; |
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|
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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 press[3][3], vScale[3][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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// 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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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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// 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 (j = 0; j < 3; j++) { |
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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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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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dAtom->setJ( ji ); |
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|
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} |
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} |
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} |
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|
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template<typename T> void NPTfm<T>::resetIntegrator() { |
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int i,j; |
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|
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chi = 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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|
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template<typename T> int NPTfm<T>::readyCheck() { |
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|
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//check parent's readyCheck() first |
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if (T::readyCheck() == -1) |
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return -1; |
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|
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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|
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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NPTfm error: You can't use the NPTfm integrator\n" |
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" without a targetTemp!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPTfm error: You can't use the NPTfm integrator\n" |
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" without a targetPressure!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauThermostat. |
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|
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NPTfm error: If you use the NPTfm\n" |
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" integrator, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauBarostat. |
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|
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if (!have_tau_barostat) { |
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sprintf( painCave.errMsg, |
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"NPTfm error: If you use the NPTfm\n" |
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" integrator, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We need NkBT a lot, so just set it here: |
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|
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NkBT = (double)info->ndf * kB * targetTemp; |
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|
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return 1; |
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} |
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|
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template<typename T> double NPTfm<T>::getConservedQuantity(void){ |
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|
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double conservedQuantity; |
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double tb2; |
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double trEta; |
| 406 |
|
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//HNVE |
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conservedQuantity = tStats->getTotalE(); |
| 409 |
|
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//HNVT |
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conservedQuantity += (info->getNDF() * kB * targetTemp * |
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(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0)) / eConvert ; |
| 413 |
|
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//HNPT |
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tb2 = tauBarostat *tauBarostat; |
| 416 |
|
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trEta = info->matTrace3(eta); |
| 418 |
|
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conservedQuantity += (targetPressure * tStats->getVolume() / p_convert + |
| 420 |
3*NkBT/2 * tb2 * trEta * trEta) / eConvert; |
| 421 |
|
| 422 |
return conservedQuantity; |
| 423 |
} |
