| 1 |
#include <math.h> |
| 2 |
#include <iostream> |
| 3 |
using namespace std; |
| 4 |
|
| 5 |
#ifdef IS_MPI |
| 6 |
#include <mpi.h> |
| 7 |
#endif //is_mpi |
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|
| 9 |
#include "Thermo.hpp" |
| 10 |
#include "SRI.hpp" |
| 11 |
#include "Integrator.hpp" |
| 12 |
#include "simError.h" |
| 13 |
#include "MatVec3.h" |
| 14 |
#include "ConstraintManager.hpp" |
| 15 |
#include "Mat3x3d.hpp" |
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|
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#ifdef IS_MPI |
| 18 |
#define __C |
| 19 |
#include "mpiSimulation.hpp" |
| 20 |
#endif // is_mpi |
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|
| 22 |
inline double roundMe( double x ){ |
| 23 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 24 |
} |
| 25 |
|
| 26 |
Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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int baseSeed = the_info->getSeed(); |
| 29 |
|
| 30 |
gaussStream = new gaussianSPRNG( baseSeed ); |
| 31 |
|
| 32 |
cpIter = info->consMan->createPairIterator(); |
| 33 |
} |
| 34 |
|
| 35 |
Thermo::~Thermo(){ |
| 36 |
delete gaussStream; |
| 37 |
delete cpIter; |
| 38 |
} |
| 39 |
|
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double Thermo::getKinetic(){ |
| 41 |
|
| 42 |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 43 |
double kinetic; |
| 44 |
double amass; |
| 45 |
double aVel[3], aJ[3], I[3][3]; |
| 46 |
int i, j, k, kl; |
| 47 |
|
| 48 |
double kinetic_global; |
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vector<StuntDouble *> integrableObjects = info->integrableObjects; |
| 50 |
|
| 51 |
kinetic = 0.0; |
| 52 |
kinetic_global = 0.0; |
| 53 |
|
| 54 |
for (kl=0; kl<integrableObjects.size(); kl++) { |
| 55 |
integrableObjects[kl]->getVel(aVel); |
| 56 |
amass = integrableObjects[kl]->getMass(); |
| 57 |
|
| 58 |
for(j=0; j<3; j++) |
| 59 |
kinetic += amass*aVel[j]*aVel[j]; |
| 60 |
|
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if (integrableObjects[kl]->isDirectional()){ |
| 62 |
|
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integrableObjects[kl]->getJ( aJ ); |
| 64 |
integrableObjects[kl]->getI( I ); |
| 65 |
|
| 66 |
if (integrableObjects[kl]->isLinear()) { |
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i = integrableObjects[kl]->linearAxis(); |
| 68 |
j = (i+1)%3; |
| 69 |
k = (i+2)%3; |
| 70 |
kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; |
| 71 |
} else { |
| 72 |
for (j=0; j<3; j++) |
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kinetic += aJ[j]*aJ[j] / I[j][j]; |
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} |
| 75 |
} |
| 76 |
} |
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#ifdef IS_MPI |
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MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
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MPI_SUM, MPI_COMM_WORLD); |
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kinetic = kinetic_global; |
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#endif //is_mpi |
| 82 |
|
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kinetic = kinetic * 0.5 / e_convert; |
| 84 |
|
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return kinetic; |
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} |
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|
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double Thermo::getPotential(){ |
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|
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double potential_local; |
| 91 |
double potential; |
| 92 |
int el, nSRI; |
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Molecule* molecules; |
| 94 |
|
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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|
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potential_local = 0.0; |
| 99 |
potential = 0.0; |
| 100 |
potential_local += info->lrPot; |
| 101 |
|
| 102 |
for( el=0; el<info->n_mol; el++ ){ |
| 103 |
potential_local += molecules[el].getPotential(); |
| 104 |
} |
| 105 |
|
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// Get total potential for entire system from MPI. |
| 107 |
#ifdef IS_MPI |
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MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
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MPI_SUM, MPI_COMM_WORLD); |
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#else |
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potential = potential_local; |
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#endif // is_mpi |
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|
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return potential; |
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} |
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|
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double Thermo::getTotalE(){ |
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|
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double total; |
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|
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total = this->getKinetic() + this->getPotential(); |
| 122 |
return total; |
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} |
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|
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double Thermo::getTemperature(){ |
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|
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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
| 128 |
double temperature; |
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|
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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
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} |
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|
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double Thermo::getVolume() { |
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|
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return info->boxVol; |
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} |
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|
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double Thermo::getPressure() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressure; |
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|
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this->getPressureTensor(press); |
| 148 |
|
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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|
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return pressure; |
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} |
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|
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double Thermo::getPressureX() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
| 159 |
double press[3][3]; |
| 160 |
double pressureX; |
| 161 |
|
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this->getPressureTensor(press); |
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|
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pressureX = p_convert * press[0][0]; |
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|
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return pressureX; |
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} |
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|
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double Thermo::getPressureY() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
| 174 |
double press[3][3]; |
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double pressureY; |
| 176 |
|
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this->getPressureTensor(press); |
| 178 |
|
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pressureY = p_convert * press[1][1]; |
| 180 |
|
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return pressureY; |
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} |
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|
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double Thermo::getPressureZ() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
| 189 |
double press[3][3]; |
| 190 |
double pressureZ; |
| 191 |
|
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this->getPressureTensor(press); |
| 193 |
|
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pressureZ = p_convert * press[2][2]; |
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|
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return pressureZ; |
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} |
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|
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|
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void Thermo::getPressureTensor(double press[3][3]){ |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
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// routine derived via viral theorem description in: |
| 203 |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
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|
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const double e_convert = 4.184e-4; |
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|
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double molmass, volume; |
| 208 |
double vcom[3]; |
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double p_local[9], p_global[9]; |
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int i, j, k; |
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|
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for (i=0; i < 9; i++) { |
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p_local[i] = 0.0; |
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p_global[i] = 0.0; |
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} |
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|
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// use velocities of integrableObjects and their masses: |
| 218 |
|
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for (i=0; i < info->integrableObjects.size(); i++) { |
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|
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molmass = info->integrableObjects[i]->getMass(); |
| 222 |
|
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info->integrableObjects[i]->getVel(vcom); |
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|
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p_local[0] += molmass * (vcom[0] * vcom[0]); |
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p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 227 |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
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p_local[3] += molmass * (vcom[1] * vcom[0]); |
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p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 230 |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
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p_local[6] += molmass * (vcom[2] * vcom[0]); |
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p_local[7] += molmass * (vcom[2] * vcom[1]); |
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p_local[8] += molmass * (vcom[2] * vcom[2]); |
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|
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} |
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|
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// Get total for entire system from MPI. |
| 238 |
|
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#ifdef IS_MPI |
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MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
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#else |
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for (i=0; i<9; i++) { |
| 243 |
p_global[i] = p_local[i]; |
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} |
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#endif // is_mpi |
| 246 |
|
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volume = this->getVolume(); |
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|
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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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k = 3*i + j; |
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press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
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} |
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} |
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} |
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|
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void Thermo::velocitize() { |
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|
| 261 |
double aVel[3], aJ[3], I[3][3]; |
| 262 |
int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
| 263 |
double vdrift[3]; |
| 264 |
double vbar; |
| 265 |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 266 |
double av2; |
| 267 |
double kebar; |
| 268 |
double temperature; |
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int nobj; |
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|
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nobj = info->integrableObjects.size(); |
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|
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temperature = info->target_temp; |
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|
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kebar = kb * temperature * (double)info->ndfRaw / |
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( 2.0 * (double)info->ndf ); |
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|
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for(vr = 0; vr < nobj; vr++){ |
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|
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// uses equipartition theory to solve for vbar in angstrom/fs |
| 281 |
|
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av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
| 283 |
vbar = sqrt( av2 ); |
| 284 |
|
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// picks random velocities from a gaussian distribution |
| 286 |
// centered on vbar |
| 287 |
|
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for (j=0; j<3; j++) |
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aVel[j] = vbar * gaussStream->getGaussian(); |
| 290 |
|
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info->integrableObjects[vr]->setVel( aVel ); |
| 292 |
|
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if(info->integrableObjects[vr]->isDirectional()){ |
| 294 |
|
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info->integrableObjects[vr]->getI( I ); |
| 296 |
|
| 297 |
if (info->integrableObjects[vr]->isLinear()) { |
| 298 |
|
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l= info->integrableObjects[vr]->linearAxis(); |
| 300 |
m = (l+1)%3; |
| 301 |
n = (l+2)%3; |
| 302 |
|
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aJ[l] = 0.0; |
| 304 |
vbar = sqrt( 2.0 * kebar * I[m][m] ); |
| 305 |
aJ[m] = vbar * gaussStream->getGaussian(); |
| 306 |
vbar = sqrt( 2.0 * kebar * I[n][n] ); |
| 307 |
aJ[n] = vbar * gaussStream->getGaussian(); |
| 308 |
|
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} else { |
| 310 |
for (j = 0 ; j < 3; j++) { |
| 311 |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 312 |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 313 |
} |
| 314 |
} // else isLinear |
| 315 |
|
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info->integrableObjects[vr]->setJ( aJ ); |
| 317 |
|
| 318 |
}//isDirectional |
| 319 |
|
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} |
| 321 |
|
| 322 |
// Get the Center of Mass drift velocity. |
| 323 |
|
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getCOMVel(vdrift); |
| 325 |
|
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// Corrects for the center of mass drift. |
| 327 |
// sums all the momentum and divides by total mass. |
| 328 |
|
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for(vd = 0; vd < nobj; vd++){ |
| 330 |
|
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info->integrableObjects[vd]->getVel(aVel); |
| 332 |
|
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for (j=0; j < 3; j++) |
| 334 |
aVel[j] -= vdrift[j]; |
| 335 |
|
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info->integrableObjects[vd]->setVel( aVel ); |
| 337 |
} |
| 338 |
|
| 339 |
} |
| 340 |
|
| 341 |
void Thermo::getCOMVel(double vdrift[3]){ |
| 342 |
|
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double mtot, mtot_local; |
| 344 |
double aVel[3], amass; |
| 345 |
double vdrift_local[3]; |
| 346 |
int vd, j; |
| 347 |
int nobj; |
| 348 |
|
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nobj = info->integrableObjects.size(); |
| 350 |
|
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mtot_local = 0.0; |
| 352 |
vdrift_local[0] = 0.0; |
| 353 |
vdrift_local[1] = 0.0; |
| 354 |
vdrift_local[2] = 0.0; |
| 355 |
|
| 356 |
for(vd = 0; vd < nobj; vd++){ |
| 357 |
|
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amass = info->integrableObjects[vd]->getMass(); |
| 359 |
info->integrableObjects[vd]->getVel( aVel ); |
| 360 |
|
| 361 |
for(j = 0; j < 3; j++) |
| 362 |
vdrift_local[j] += aVel[j] * amass; |
| 363 |
|
| 364 |
mtot_local += amass; |
| 365 |
} |
| 366 |
|
| 367 |
#ifdef IS_MPI |
| 368 |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 369 |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 370 |
#else |
| 371 |
mtot = mtot_local; |
| 372 |
for(vd = 0; vd < 3; vd++) { |
| 373 |
vdrift[vd] = vdrift_local[vd]; |
| 374 |
} |
| 375 |
#endif |
| 376 |
|
| 377 |
for (vd = 0; vd < 3; vd++) { |
| 378 |
vdrift[vd] = vdrift[vd] / mtot; |
| 379 |
} |
| 380 |
|
| 381 |
} |
| 382 |
|
| 383 |
void Thermo::getCOM(double COM[3]){ |
| 384 |
|
| 385 |
double mtot, mtot_local; |
| 386 |
double aPos[3], amass; |
| 387 |
double COM_local[3]; |
| 388 |
int i, j; |
| 389 |
int nobj; |
| 390 |
|
| 391 |
mtot_local = 0.0; |
| 392 |
COM_local[0] = 0.0; |
| 393 |
COM_local[1] = 0.0; |
| 394 |
COM_local[2] = 0.0; |
| 395 |
|
| 396 |
nobj = info->integrableObjects.size(); |
| 397 |
for(i = 0; i < nobj; i++){ |
| 398 |
|
| 399 |
amass = info->integrableObjects[i]->getMass(); |
| 400 |
info->integrableObjects[i]->getPos( aPos ); |
| 401 |
|
| 402 |
for(j = 0; j < 3; j++) |
| 403 |
COM_local[j] += aPos[j] * amass; |
| 404 |
|
| 405 |
mtot_local += amass; |
| 406 |
} |
| 407 |
|
| 408 |
#ifdef IS_MPI |
| 409 |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 410 |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 411 |
#else |
| 412 |
mtot = mtot_local; |
| 413 |
for(i = 0; i < 3; i++) { |
| 414 |
COM[i] = COM_local[i]; |
| 415 |
} |
| 416 |
#endif |
| 417 |
|
| 418 |
for (i = 0; i < 3; i++) { |
| 419 |
COM[i] = COM[i] / mtot; |
| 420 |
} |
| 421 |
} |
| 422 |
|
| 423 |
void Thermo::removeCOMdrift() { |
| 424 |
double vdrift[3], aVel[3]; |
| 425 |
int vd, j, nobj; |
| 426 |
|
| 427 |
nobj = info->integrableObjects.size(); |
| 428 |
|
| 429 |
// Get the Center of Mass drift velocity. |
| 430 |
|
| 431 |
getCOMVel(vdrift); |
| 432 |
|
| 433 |
// Corrects for the center of mass drift. |
| 434 |
// sums all the momentum and divides by total mass. |
| 435 |
|
| 436 |
for(vd = 0; vd < nobj; vd++){ |
| 437 |
|
| 438 |
info->integrableObjects[vd]->getVel(aVel); |
| 439 |
|
| 440 |
for (j=0; j < 3; j++) |
| 441 |
aVel[j] -= vdrift[j]; |
| 442 |
|
| 443 |
info->integrableObjects[vd]->setVel( aVel ); |
| 444 |
} |
| 445 |
} |
| 446 |
|
| 447 |
void Thermo::removeAngularMomentum(){ |
| 448 |
Vector3d vcom; |
| 449 |
Vector3d qcom; |
| 450 |
Vector3d pos; |
| 451 |
Vector3d vel; |
| 452 |
double mass; |
| 453 |
double xx; |
| 454 |
double yy; |
| 455 |
double zz; |
| 456 |
double xy; |
| 457 |
double xz; |
| 458 |
double yz; |
| 459 |
Vector3d localAngMom; |
| 460 |
Vector3d angMom; |
| 461 |
Vector3d omega; |
| 462 |
vector<StuntDouble *> integrableObjects; |
| 463 |
double localInertiaVec[9]; |
| 464 |
double inertiaVec[9]; |
| 465 |
vector<Vector3d> qMinusQCom; |
| 466 |
vector<Vector3d> vMinusVCom; |
| 467 |
Mat3x3d inertiaMat; |
| 468 |
Mat3x3d inverseInertiaMat; |
| 469 |
|
| 470 |
integrableObjects = info->integrableObjects; |
| 471 |
qMinusQCom.resize(integrableObjects.size()); |
| 472 |
vMinusVCom.resize(integrableObjects.size()); |
| 473 |
|
| 474 |
getCOM(qcom.vec); |
| 475 |
getCOMVel(vcom.vec); |
| 476 |
|
| 477 |
//initialize components for inertia tensor |
| 478 |
xx = 0.0; |
| 479 |
yy = 0.0; |
| 480 |
zz = 0.0; |
| 481 |
xy = 0.0; |
| 482 |
xz = 0.0; |
| 483 |
yz = 0.0; |
| 484 |
|
| 485 |
//build components of Inertia tensor |
| 486 |
// |
| 487 |
// [ Ixx -Ixy -Ixz ] |
| 488 |
// J = | -Iyx Iyy -Iyz | |
| 489 |
// [ -Izx -Iyz Izz ] |
| 490 |
//See Fowles and Cassidy Chapter 9 or Goldstein Chapter 5 |
| 491 |
for(size_t i = 0; i < integrableObjects.size(); i++){ |
| 492 |
integrableObjects[i]->getPos(pos.vec); |
| 493 |
integrableObjects[i]->getVel(vel.vec); |
| 494 |
mass = integrableObjects[i]->getMass(); |
| 495 |
|
| 496 |
qMinusQCom[i] = pos - qcom; |
| 497 |
info->wrapVector(qMinusQCom[i].vec); |
| 498 |
|
| 499 |
vMinusVCom[i] = vel - vcom; |
| 500 |
|
| 501 |
//compute moment of inertia coefficents |
| 502 |
xx += qMinusQCom[i].x * qMinusQCom[i].x * mass; |
| 503 |
yy += qMinusQCom[i].y * qMinusQCom[i].y * mass; |
| 504 |
zz += qMinusQCom[i].z * qMinusQCom[i].z * mass; |
| 505 |
|
| 506 |
// compute products of inertia |
| 507 |
xy += qMinusQCom[i].x * qMinusQCom[i].y * mass; |
| 508 |
xz += qMinusQCom[i].x * qMinusQCom[i].z * mass; |
| 509 |
yz += qMinusQCom[i].y * qMinusQCom[i].z * mass; |
| 510 |
|
| 511 |
localAngMom += crossProduct(qMinusQCom[i] , vMinusVCom[i] ) * mass; |
| 512 |
|
| 513 |
} |
| 514 |
|
| 515 |
localInertiaVec[0] =yy+zz; |
| 516 |
localInertiaVec[1] = -xy; |
| 517 |
localInertiaVec[2] = -xz; |
| 518 |
localInertiaVec[3] = -xy; |
| 519 |
localInertiaVec[4] = xx+zz; |
| 520 |
localInertiaVec[5] = -yz; |
| 521 |
localInertiaVec[6] = -xz; |
| 522 |
localInertiaVec[7] = -yz; |
| 523 |
localInertiaVec[8] = xx+yy; |
| 524 |
|
| 525 |
//Sum and distribute inertia and angmom arrays |
| 526 |
#ifdef MPI |
| 527 |
|
| 528 |
MPI_Allreduce(localInertiaVec, inertiaVec, 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 529 |
|
| 530 |
MPI_Allreduce(localAngMom.vec, angMom.vec, 3, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 531 |
|
| 532 |
inertiaMat.element[0][0] = inertiaVec[0]; |
| 533 |
inertiaMat.element[0][1] = inertiaVec[1]; |
| 534 |
inertiaMat.element[0][2] = inertiaVec[2]; |
| 535 |
|
| 536 |
inertiaMat.element[1][0] = inertiaVec[3]; |
| 537 |
inertiaMat.element[1][1] = inertiaVec[4]; |
| 538 |
inertiaMat.element[1][2] = inertiaVec[5]; |
| 539 |
|
| 540 |
inertiaMat.element[2][0] = inertiaVec[6]; |
| 541 |
inertiaMat.element[2][1] = inertiaVec[7]; |
| 542 |
inertiaMat.element[2][2] = inertiaVec[8]; |
| 543 |
|
| 544 |
#else |
| 545 |
|
| 546 |
inertiaMat.element[0][0] = localInertiaVec[0]; |
| 547 |
inertiaMat.element[0][1] = localInertiaVec[1]; |
| 548 |
inertiaMat.element[0][2] = localInertiaVec[2]; |
| 549 |
|
| 550 |
inertiaMat.element[1][0] = localInertiaVec[3]; |
| 551 |
inertiaMat.element[1][1] = localInertiaVec[4]; |
| 552 |
inertiaMat.element[1][2] = localInertiaVec[5]; |
| 553 |
|
| 554 |
inertiaMat.element[2][0] = localInertiaVec[6]; |
| 555 |
inertiaMat.element[2][1] = localInertiaVec[7]; |
| 556 |
inertiaMat.element[2][2] = localInertiaVec[8]; |
| 557 |
|
| 558 |
angMom = localAngMom; |
| 559 |
#endif |
| 560 |
|
| 561 |
//invert the moment of inertia tensor by LU-decomposition / backsolving: |
| 562 |
|
| 563 |
inverseInertiaMat = inertiaMat.inverse(); |
| 564 |
|
| 565 |
//calculate the angular velocities: omega = I^-1 . L |
| 566 |
|
| 567 |
omega = inverseInertiaMat * angMom; |
| 568 |
|
| 569 |
//subtract out center of mass velocity and angular momentum from |
| 570 |
//particle velocities |
| 571 |
|
| 572 |
for(size_t i = 0; i < integrableObjects.size(); i++){ |
| 573 |
vel = vMinusVCom[i] - crossProduct(omega, qMinusQCom[i]); |
| 574 |
integrableObjects[i]->setVel(vel.vec); |
| 575 |
} |
| 576 |
} |
| 577 |
|
| 578 |
double Thermo::getConsEnergy(){ |
| 579 |
ConstraintPair* consPair; |
| 580 |
double totConsEnergy; |
| 581 |
double bondLen2; |
| 582 |
double dist; |
| 583 |
double lamda; |
| 584 |
|
| 585 |
totConsEnergy = 0; |
| 586 |
|
| 587 |
for(cpIter->first(); !cpIter->isEnd(); cpIter->next()){ |
| 588 |
consPair = cpIter->currentItem(); |
| 589 |
bondLen2 = consPair->getBondLength2(); |
| 590 |
lamda = consPair->getLamda(); |
| 591 |
//dist = consPair->getDistance(); |
| 592 |
|
| 593 |
//totConsEnergy += lamda * (dist*dist - bondLen2); |
| 594 |
} |
| 595 |
|
| 596 |
return totConsEnergy; |
| 597 |
} |
| 598 |
|
| 599 |
|
