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#include <stdlib.h> |
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#include <math.h> |
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#include <string.h> |
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|
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.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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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
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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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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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NPT( theInfo, the_ff ) |
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{ |
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int i; |
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chi = 0.0; |
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for(i = 0; i < 9; i++) eta[i] = 0.0; |
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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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GenericData* data; |
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double *etaArray; |
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int i,j; |
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|
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void NPTi::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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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 angle; |
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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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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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eta[i][j] = 0.0; |
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oldEta[i][j] = 0.0; |
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} |
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} |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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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 < 9; i++) { |
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eta[i] += dt2 * ( instaVol * (sigma[i] - targetPressure*identMat[i])) |
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/ (NkBT*tb2)); |
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data != NULL){ |
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|
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int test = data->getDarray(etaArray); |
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|
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if( test == 9 ){ |
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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] = etaArray[3*i+j]; |
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oldEta[i][j] = eta[i][j]; |
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} |
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} |
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delete[] etaArray; |
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} |
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else |
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std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test |
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<< ").\n" |
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<< " Simulation wil proceed with eta = 0;\n"; |
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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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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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NPTf::~NPTf() { |
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|
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// position whole step |
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// empty for now |
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} |
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for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
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rj[0] = pos[j]; |
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rj[1] = pos[j+1]; |
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rj[2] = pos[j+2]; |
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void NPTf::resetIntegrator() { |
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info->wrapVector(rj); |
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int i, j; |
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pos[j] += dt * (vel[j] + eta*rj[0]); |
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pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
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pos[j+2] += dt * (vel[j+2] + eta*rj[2]); |
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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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// Scale the box after all the positions have been moved: |
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NPT::resetIntegrator(); |
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} |
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info->scaleBox(exp(dt*eta)); |
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|
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if( atoms[i]->isDirectional() ){ |
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void NPTf::evolveEtaA() { |
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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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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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int i, j; |
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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|
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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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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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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oldEta[i][j] = eta[i][j]; |
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} |
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|
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void NPTi::moveB( void ){ |
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int i,j,k; |
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int atomIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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void NPTf::evolveEtaB() { |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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int i,j; |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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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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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and complete the angular momentum |
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// half step |
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|
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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|
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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prevEta[i][j] = eta[i][j]; |
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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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eta[i][j] = oldEta[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] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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} |
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} |
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} |
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} |
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|
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int NPTi::readyCheck() { |
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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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< |
"NPTi error: You can't use the NPTi 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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void NPTf::getVelScaleA(double sc[3], double vel[3]) { |
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int i,j; |
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double vScale[3][3]; |
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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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vScale[i][j] = eta[i][j]; |
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|
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if (i == j) { |
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vScale[i][j] += chi; |
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} |
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} |
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} |
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|
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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPTi error: You can't use the NPTi integrator\n" |
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" without a targetPressure!\n" |
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); |
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painCave.isFatal = 1; |
| 142 |
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simError(); |
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return -1; |
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info->matVecMul3( vScale, vel, sc ); |
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} |
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|
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void NPTf::getVelScaleB(double sc[3], int index ){ |
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int i,j; |
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double myVel[3]; |
| 142 |
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double vScale[3][3]; |
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|
| 144 |
> |
// std::cerr << "velScaleB chi = " << chi << "\n"; |
| 145 |
> |
|
| 146 |
> |
for (i = 0; i < 3; i++ ) { |
| 147 |
> |
for (j = 0; j < 3; j++ ) { |
| 148 |
> |
vScale[i][j] = eta[i][j]; |
| 149 |
> |
|
| 150 |
> |
if (i == j) { |
| 151 |
> |
vScale[i][j] += chi; |
| 152 |
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} |
| 153 |
> |
} |
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|
} |
| 155 |
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|
| 156 |
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// We must set tauThermostat. |
| 157 |
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|
| 158 |
< |
if (!have_tau_thermostat) { |
| 155 |
> |
|
| 156 |
> |
for (j = 0; j < 3; j++) |
| 157 |
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myVel[j] = oldVel[3*index + j]; |
| 158 |
> |
|
| 159 |
> |
// std::cerr << "velScaleB = \n" |
| 160 |
> |
// << "[ " << vScale[0][0] << " , " << vScale[0][1] << " , " << vScale[0][2] << "]\n" |
| 161 |
> |
// << "[ " << vScale[1][0] << " , " << vScale[1][1] << " , " << vScale[1][2] << "]\n" |
| 162 |
> |
// << "[ " << vScale[2][0] << " , " << vScale[2][1] << " , " << vScale[2][2] << "]\n\n"; |
| 163 |
> |
|
| 164 |
> |
|
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// std::cerr << "myVel " << index << " in => " |
| 166 |
> |
// << myVel[0] << ", " << myVel[1] << ", " << myVel[2] << "\n"; |
| 167 |
> |
|
| 168 |
> |
info->matVecMul3( vScale, myVel, sc ); |
| 169 |
> |
|
| 170 |
> |
// std::cerr << "sc " << index << " out => " |
| 171 |
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// << sc[0] << ", " << sc[1] << ", " << sc[2] << "\n"; |
| 172 |
> |
} |
| 173 |
> |
|
| 174 |
> |
void NPTf::getPosScale(double pos[3], double COM[3], |
| 175 |
> |
int index, double sc[3]){ |
| 176 |
> |
int j; |
| 177 |
> |
double rj[3]; |
| 178 |
> |
|
| 179 |
> |
for(j=0; j<3; j++) |
| 180 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 181 |
> |
|
| 182 |
> |
info->matVecMul3( eta, rj, sc ); |
| 183 |
> |
} |
| 184 |
> |
|
| 185 |
> |
void NPTf::scaleSimBox( void ){ |
| 186 |
> |
|
| 187 |
> |
int i,j,k; |
| 188 |
> |
double scaleMat[3][3]; |
| 189 |
> |
double eta2ij; |
| 190 |
> |
double bigScale, smallScale, offDiagMax; |
| 191 |
> |
double hm[3][3], hmnew[3][3]; |
| 192 |
> |
|
| 193 |
> |
|
| 194 |
> |
|
| 195 |
> |
// Scale the box after all the positions have been moved: |
| 196 |
> |
|
| 197 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 198 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 199 |
> |
|
| 200 |
> |
bigScale = 1.0; |
| 201 |
> |
smallScale = 1.0; |
| 202 |
> |
offDiagMax = 0.0; |
| 203 |
> |
|
| 204 |
> |
for(i=0; i<3; i++){ |
| 205 |
> |
for(j=0; j<3; j++){ |
| 206 |
> |
|
| 207 |
> |
// Calculate the matrix Product of the eta array (we only need |
| 208 |
> |
// the ij element right now): |
| 209 |
> |
|
| 210 |
> |
eta2ij = 0.0; |
| 211 |
> |
for(k=0; k<3; k++){ |
| 212 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
| 213 |
> |
} |
| 214 |
> |
|
| 215 |
> |
scaleMat[i][j] = 0.0; |
| 216 |
> |
// identity matrix (see above): |
| 217 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
| 218 |
> |
// Taylor expansion for the exponential truncated at second order: |
| 219 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 220 |
> |
|
| 221 |
> |
if (i != j) |
| 222 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 223 |
> |
offDiagMax = fabs(scaleMat[i][j]); |
| 224 |
> |
} |
| 225 |
> |
|
| 226 |
> |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 227 |
> |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 231 |
|
sprintf( painCave.errMsg, |
| 232 |
< |
"NPTi error: If you use the NPTi\n" |
| 233 |
< |
" integrator, you must set tauThermostat.\n"); |
| 232 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 233 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 234 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 235 |
> |
" [%lf\t%lf\t%lf]\n" |
| 236 |
> |
" [%lf\t%lf\t%lf]\n", |
| 237 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 238 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 239 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 240 |
|
painCave.isFatal = 1; |
| 241 |
|
simError(); |
| 242 |
< |
return -1; |
| 234 |
< |
} |
| 235 |
< |
|
| 236 |
< |
// We must set tauBarostat. |
| 237 |
< |
|
| 238 |
< |
if (!have_tau_barostat) { |
| 242 |
> |
} else if (offDiagMax > 0.1) { |
| 243 |
|
sprintf( painCave.errMsg, |
| 244 |
< |
"NPTi error: If you use the NPTi\n" |
| 245 |
< |
" integrator, you must set tauBarostat.\n"); |
| 244 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 245 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 246 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 247 |
> |
" [%lf\t%lf\t%lf]\n" |
| 248 |
> |
" [%lf\t%lf\t%lf]\n", |
| 249 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 250 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 251 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 252 |
|
painCave.isFatal = 1; |
| 253 |
|
simError(); |
| 254 |
< |
return -1; |
| 255 |
< |
} |
| 254 |
> |
} else { |
| 255 |
> |
info->getBoxM(hm); |
| 256 |
> |
info->matMul3(hm, scaleMat, hmnew); |
| 257 |
> |
info->setBoxM(hmnew); |
| 258 |
> |
} |
| 259 |
> |
} |
| 260 |
|
|
| 261 |
< |
// We need NkBT a lot, so just set it here: |
| 261 |
> |
bool NPTf::etaConverged() { |
| 262 |
> |
int i; |
| 263 |
> |
double diffEta, sumEta; |
| 264 |
|
|
| 265 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
| 265 |
> |
sumEta = 0; |
| 266 |
> |
for(i = 0; i < 3; i++) |
| 267 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 268 |
|
|
| 269 |
< |
return 1; |
| 269 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
| 270 |
> |
|
| 271 |
> |
return ( diffEta <= etaTolerance ); |
| 272 |
|
} |
| 273 |
+ |
|
| 274 |
+ |
double NPTf::getConservedQuantity(void){ |
| 275 |
+ |
|
| 276 |
+ |
double conservedQuantity; |
| 277 |
+ |
double totalEnergy; |
| 278 |
+ |
double thermostat_kinetic; |
| 279 |
+ |
double thermostat_potential; |
| 280 |
+ |
double barostat_kinetic; |
| 281 |
+ |
double barostat_potential; |
| 282 |
+ |
double trEta; |
| 283 |
+ |
double a[3][3], b[3][3]; |
| 284 |
+ |
|
| 285 |
+ |
totalEnergy = tStats->getTotalE(); |
| 286 |
+ |
|
| 287 |
+ |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 288 |
+ |
(2.0 * eConvert); |
| 289 |
+ |
|
| 290 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 291 |
+ |
|
| 292 |
+ |
info->transposeMat3(eta, a); |
| 293 |
+ |
info->matMul3(a, eta, b); |
| 294 |
+ |
trEta = info->matTrace3(b); |
| 295 |
+ |
|
| 296 |
+ |
barostat_kinetic = NkBT * tb2 * trEta / |
| 297 |
+ |
(2.0 * eConvert); |
| 298 |
+ |
|
| 299 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 300 |
+ |
eConvert; |
| 301 |
+ |
|
| 302 |
+ |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 303 |
+ |
barostat_kinetic + barostat_potential; |
| 304 |
+ |
|
| 305 |
+ |
// cout.width(8); |
| 306 |
+ |
// cout.precision(8); |
| 307 |
+ |
|
| 308 |
+ |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 309 |
+ |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 310 |
+ |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 311 |
+ |
|
| 312 |
+ |
return conservedQuantity; |
| 313 |
+ |
|
| 314 |
+ |
} |
| 315 |
+ |
|
| 316 |
+ |
char* NPTf::getAdditionalParameters(void){ |
| 317 |
+ |
|
| 318 |
+ |
sprintf(addParamBuffer, |
| 319 |
+ |
"\t%G\t%G;" |
| 320 |
+ |
"\t%G\t%G\t%G;" |
| 321 |
+ |
"\t%G\t%G\t%G;" |
| 322 |
+ |
"\t%G\t%G\t%G;", |
| 323 |
+ |
chi, integralOfChidt, |
| 324 |
+ |
eta[0][0], eta[0][1], eta[0][2], |
| 325 |
+ |
eta[1][0], eta[1][1], eta[1][2], |
| 326 |
+ |
eta[2][0], eta[2][1], eta[2][2] |
| 327 |
+ |
); |
| 328 |
+ |
|
| 329 |
+ |
return addParamBuffer; |
| 330 |
+ |
} |
