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#include <cmath> |
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#include <math.h> |
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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 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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|
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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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int 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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|
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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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|
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if( theInfo->useInitXSstate ){ |
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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){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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|
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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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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} |
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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> NPTf<T>::~NPTf() { |
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|
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// empty for now |
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} |
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|
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template<typename T> void NPTf<T>::resetIntegrator() { |
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|
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int i, j; |
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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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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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T::resetIntegrator(); |
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} |
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|
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void NPTf::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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template<typename T> void NPTf<T>::evolveEtaA() { |
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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; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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double bigScale, smallScale, offDiagMax; |
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int i, j; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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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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|
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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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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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template<typename T> void NPTf<T>::evolveEtaB() { |
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|
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int 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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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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template<typename T> void NPTf<T>::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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if (i == j) { |
70 |
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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); |
73 |
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|
74 |
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vScale[i][j] = eta[i][j] + chi; |
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|
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} else { |
77 |
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|
78 |
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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vScale[i][j] = eta[i][j]; |
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|
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vScale[i][j] = eta[i][j]; |
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|
127 |
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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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|
133 |
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for( i=0; i<nAtoms; i++ ){ |
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> |
info->matVecMul3( vScale, vel, sc ); |
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> |
} |
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|
136 |
< |
atoms[i]->getVel( vel ); |
137 |
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atoms[i]->getPos( pos ); |
138 |
< |
atoms[i]->getFrc( frc ); |
136 |
> |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
137 |
> |
int i,j; |
138 |
> |
double myVel[3]; |
139 |
> |
double vScale[3][3]; |
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|
|
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mass = atoms[i]->getMass(); |
142 |
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|
143 |
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// velocity half step |
144 |
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|
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info->matVecMul3( vScale, vel, sc ); |
146 |
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|
147 |
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for (j = 0; j < 3; j++) { |
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vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
100 |
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rj[j] = pos[j]; |
141 |
> |
for (i = 0; i < 3; i++ ) { |
142 |
> |
for (j = 0; j < 3; j++ ) { |
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> |
vScale[i][j] = eta[i][j]; |
144 |
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|
145 |
> |
if (i == j) { |
146 |
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vScale[i][j] += chi; |
147 |
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} |
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} |
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} |
150 |
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|
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atoms[i]->setVel( vel ); |
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for (j = 0; j < 3; j++) |
152 |
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myVel[j] = oldVel[3*index + j]; |
153 |
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|
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// position whole step |
154 |
> |
info->matVecMul3( vScale, myVel, sc ); |
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> |
} |
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|
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info->wrapVector(rj); |
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> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
158 |
> |
int index, double sc[3]){ |
159 |
> |
int j; |
160 |
> |
double rj[3]; |
161 |
|
|
162 |
< |
info->matVecMul3( eta, rj, sc ); |
162 |
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for(j=0; j<3; j++) |
163 |
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rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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|
|
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for (j = 0; j < 3; j++ ) |
166 |
< |
pos[j] += dt * (vel[j] + sc[j]); |
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> |
info->matVecMul3( eta, rj, sc ); |
166 |
> |
} |
167 |
|
|
168 |
< |
atoms[i]->setPos( pos ); |
115 |
< |
|
116 |
< |
if( atoms[i]->isDirectional() ){ |
168 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
169 |
|
|
170 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
171 |
< |
|
172 |
< |
// get and convert the torque to body frame |
173 |
< |
|
174 |
< |
dAtom->getTrq( Tb ); |
123 |
< |
dAtom->lab2Body( Tb ); |
124 |
< |
|
125 |
< |
// get the angular momentum, and propagate a half step |
170 |
> |
int i,j,k; |
171 |
> |
double scaleMat[3][3]; |
172 |
> |
double eta2ij; |
173 |
> |
double bigScale, smallScale, offDiagMax; |
174 |
> |
double hm[3][3], hmnew[3][3]; |
175 |
|
|
127 |
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dAtom->getJ( ji ); |
176 |
|
|
129 |
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for (j=0; j < 3; j++) |
130 |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
131 |
– |
|
132 |
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// use the angular velocities to propagate the rotation matrix a |
133 |
– |
// full time step |
177 |
|
|
178 |
< |
dAtom->getA(A); |
136 |
< |
dAtom->getI(I); |
137 |
< |
|
138 |
< |
// rotate about the x-axis |
139 |
< |
angle = dt2 * ji[0] / I[0][0]; |
140 |
< |
this->rotate( 1, 2, angle, ji, A ); |
178 |
> |
// Scale the box after all the positions have been moved: |
179 |
|
|
142 |
– |
// rotate about the y-axis |
143 |
– |
angle = dt2 * ji[1] / I[1][1]; |
144 |
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this->rotate( 2, 0, angle, ji, A ); |
145 |
– |
|
146 |
– |
// rotate about the z-axis |
147 |
– |
angle = dt * ji[2] / I[2][2]; |
148 |
– |
this->rotate( 0, 1, angle, ji, A); |
149 |
– |
|
150 |
– |
// rotate about the y-axis |
151 |
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angle = dt2 * ji[1] / I[1][1]; |
152 |
– |
this->rotate( 2, 0, angle, ji, A ); |
153 |
– |
|
154 |
– |
// rotate about the x-axis |
155 |
– |
angle = dt2 * ji[0] / I[0][0]; |
156 |
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this->rotate( 1, 2, angle, ji, A ); |
157 |
– |
|
158 |
– |
dAtom->setJ( ji ); |
159 |
– |
dAtom->setA( A ); |
160 |
– |
} |
161 |
– |
} |
162 |
– |
|
163 |
– |
// Scale the box after all the positions have been moved: |
164 |
– |
|
180 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
181 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
182 |
< |
|
182 |
> |
|
183 |
|
bigScale = 1.0; |
184 |
|
smallScale = 1.0; |
185 |
|
offDiagMax = 0.0; |
186 |
< |
|
186 |
> |
|
187 |
|
for(i=0; i<3; i++){ |
188 |
|
for(j=0; j<3; j++){ |
189 |
< |
|
189 |
> |
|
190 |
|
// Calculate the matrix Product of the eta array (we only need |
191 |
|
// the ij element right now): |
192 |
< |
|
192 |
> |
|
193 |
|
eta2ij = 0.0; |
194 |
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for(k=0; k<3; k++){ |
195 |
|
eta2ij += eta[i][k] * eta[k][j]; |
196 |
|
} |
197 |
< |
|
197 |
> |
|
198 |
|
scaleMat[i][j] = 0.0; |
199 |
|
// identity matrix (see above): |
200 |
|
if (i == j) scaleMat[i][j] = 1.0; |
202 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
203 |
|
|
204 |
|
if (i != j) |
205 |
< |
if (fabs(scaleMat[i][j]) > offDiagMax) |
205 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
206 |
|
offDiagMax = fabs(scaleMat[i][j]); |
192 |
– |
|
207 |
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} |
208 |
|
|
209 |
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if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
210 |
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if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
211 |
|
} |
212 |
< |
|
213 |
< |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
212 |
> |
|
213 |
> |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
214 |
|
sprintf( painCave.errMsg, |
215 |
< |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
215 |
> |
"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
216 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
217 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
218 |
|
" [%lf\t%lf\t%lf]\n" |
222 |
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
223 |
|
painCave.isFatal = 1; |
224 |
|
simError(); |
225 |
< |
} else if (offDiagMax > 0.1) { |
225 |
> |
} else if (offDiagMax > 0.01) { |
226 |
|
sprintf( painCave.errMsg, |
227 |
< |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
227 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
228 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
229 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
230 |
|
" [%lf\t%lf\t%lf]\n" |
239 |
|
info->matMul3(hm, scaleMat, hmnew); |
240 |
|
info->setBoxM(hmnew); |
241 |
|
} |
228 |
– |
|
242 |
|
} |
243 |
|
|
244 |
< |
void NPTf::moveB( void ){ |
244 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
245 |
> |
int i; |
246 |
> |
double diffEta, sumEta; |
247 |
|
|
248 |
< |
int i, j; |
249 |
< |
DirectionalAtom* dAtom; |
250 |
< |
double Tb[3], ji[3]; |
236 |
< |
double vel[3], frc[3]; |
237 |
< |
double mass; |
248 |
> |
sumEta = 0; |
249 |
> |
for(i = 0; i < 3; i++) |
250 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
251 |
|
|
252 |
< |
double instaTemp, instaPress, instaVol; |
240 |
< |
double tt2, tb2; |
241 |
< |
double sc[3]; |
242 |
< |
double press[3][3], vScale[3][3]; |
243 |
< |
|
244 |
< |
tt2 = tauThermostat * tauThermostat; |
245 |
< |
tb2 = tauBarostat * tauBarostat; |
252 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
253 |
|
|
254 |
< |
instaTemp = tStats->getTemperature(); |
255 |
< |
tStats->getPressureTensor(press); |
249 |
< |
instaVol = tStats->getVolume(); |
250 |
< |
|
251 |
< |
// first evolve chi a half step |
252 |
< |
|
253 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
254 |
< |
|
255 |
< |
for (i = 0; i < 3; i++ ) { |
256 |
< |
for (j = 0; j < 3; j++ ) { |
257 |
< |
if (i == j) { |
254 |
> |
return ( diffEta <= etaTolerance ); |
255 |
> |
} |
256 |
|
|
257 |
< |
eta[i][j] += dt2 * instaVol * |
260 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
257 |
> |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
258 |
|
|
259 |
< |
vScale[i][j] = eta[i][j] + chi; |
260 |
< |
|
261 |
< |
} else { |
262 |
< |
|
263 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
259 |
> |
double conservedQuantity; |
260 |
> |
double totalEnergy; |
261 |
> |
double thermostat_kinetic; |
262 |
> |
double thermostat_potential; |
263 |
> |
double barostat_kinetic; |
264 |
> |
double barostat_potential; |
265 |
> |
double trEta; |
266 |
> |
double a[3][3], b[3][3]; |
267 |
|
|
268 |
< |
vScale[i][j] = eta[i][j]; |
269 |
< |
|
270 |
< |
} |
271 |
< |
} |
272 |
< |
} |
268 |
> |
totalEnergy = tStats->getTotalE(); |
269 |
|
|
270 |
< |
for( i=0; i<nAtoms; i++ ){ |
270 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
271 |
> |
(2.0 * eConvert); |
272 |
|
|
273 |
< |
atoms[i]->getVel( vel ); |
277 |
< |
atoms[i]->getFrc( frc ); |
273 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
274 |
|
|
275 |
< |
mass = atoms[i]->getMass(); |
276 |
< |
|
277 |
< |
// velocity half step |
282 |
< |
|
283 |
< |
info->matVecMul3( vScale, vel, sc ); |
284 |
< |
|
285 |
< |
for (j = 0; j < 3; j++) { |
286 |
< |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
287 |
< |
} |
275 |
> |
info->transposeMat3(eta, a); |
276 |
> |
info->matMul3(a, eta, b); |
277 |
> |
trEta = info->matTrace3(b); |
278 |
|
|
279 |
< |
atoms[i]->setVel( vel ); |
280 |
< |
|
291 |
< |
if( atoms[i]->isDirectional() ){ |
279 |
> |
barostat_kinetic = NkBT * tb2 * trEta / |
280 |
> |
(2.0 * eConvert); |
281 |
|
|
282 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
283 |
< |
|
295 |
< |
// get and convert the torque to body frame |
296 |
< |
|
297 |
< |
dAtom->getTrq( Tb ); |
298 |
< |
dAtom->lab2Body( Tb ); |
299 |
< |
|
300 |
< |
// get the angular momentum, and propagate a half step |
301 |
< |
|
302 |
< |
dAtom->getJ( ji ); |
303 |
< |
|
304 |
< |
for (j=0; j < 3; j++) |
305 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
306 |
< |
|
307 |
< |
dAtom->setJ( ji ); |
282 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
283 |
> |
eConvert; |
284 |
|
|
285 |
< |
} |
286 |
< |
} |
311 |
< |
} |
285 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
286 |
> |
barostat_kinetic + barostat_potential; |
287 |
|
|
288 |
< |
int NPTf::readyCheck() { |
314 |
< |
|
315 |
< |
// First check to see if we have a target temperature. |
316 |
< |
// Not having one is fatal. |
317 |
< |
|
318 |
< |
if (!have_target_temp) { |
319 |
< |
sprintf( painCave.errMsg, |
320 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
321 |
< |
" without a targetTemp!\n" |
322 |
< |
); |
323 |
< |
painCave.isFatal = 1; |
324 |
< |
simError(); |
325 |
< |
return -1; |
326 |
< |
} |
288 |
> |
return conservedQuantity; |
289 |
|
|
290 |
< |
if (!have_target_pressure) { |
329 |
< |
sprintf( painCave.errMsg, |
330 |
< |
"NPTf error: You can't use the NPTf integrator\n" |
331 |
< |
" without a targetPressure!\n" |
332 |
< |
); |
333 |
< |
painCave.isFatal = 1; |
334 |
< |
simError(); |
335 |
< |
return -1; |
336 |
< |
} |
337 |
< |
|
338 |
< |
// We must set tauThermostat. |
339 |
< |
|
340 |
< |
if (!have_tau_thermostat) { |
341 |
< |
sprintf( painCave.errMsg, |
342 |
< |
"NPTf error: If you use the NPTf\n" |
343 |
< |
" integrator, you must set tauThermostat.\n"); |
344 |
< |
painCave.isFatal = 1; |
345 |
< |
simError(); |
346 |
< |
return -1; |
347 |
< |
} |
290 |
> |
} |
291 |
|
|
292 |
< |
// We must set tauBarostat. |
293 |
< |
|
294 |
< |
if (!have_tau_barostat) { |
295 |
< |
sprintf( painCave.errMsg, |
353 |
< |
"NPTf error: If you use the NPTf\n" |
354 |
< |
" integrator, you must set tauBarostat.\n"); |
355 |
< |
painCave.isFatal = 1; |
356 |
< |
simError(); |
357 |
< |
return -1; |
358 |
< |
} |
292 |
> |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
293 |
> |
string parameters; |
294 |
> |
const int BUFFERSIZE = 2000; // size of the read buffer |
295 |
> |
char buffer[BUFFERSIZE]; |
296 |
|
|
297 |
< |
// We need NkBT a lot, so just set it here: |
297 |
> |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
298 |
> |
parameters += buffer; |
299 |
|
|
300 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
300 |
> |
for(int i = 0; i < 3; i++){ |
301 |
> |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
302 |
> |
parameters += buffer; |
303 |
> |
} |
304 |
|
|
305 |
< |
return 1; |
305 |
> |
return parameters; |
306 |
> |
|
307 |
|
} |