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tim |
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#include <math.h>
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#include <iostream>
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using namespace std;
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#ifdef IS_MPI
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#include <mpi.h>
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#endif //is_mpi
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#include "brains/Thermo.hpp"
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#include "primitives/SRI.hpp"
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#include "integrators/Integrator.hpp"
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#include "utils/simError.h"
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#include "math/MatVec3.h"
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#ifdef IS_MPI
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#define __C
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#include "brains/mpiSimulation.hpp"
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#endif // is_mpi
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inline double roundMe( double x ){
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
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}
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Thermo::Thermo( SimInfo* the_info ) {
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info = the_info;
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int baseSeed = the_info->getSeed();
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gaussStream = new gaussianSPRNG( baseSeed );
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}
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Thermo::~Thermo(){
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delete gaussStream;
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}
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double Thermo::getKinetic(){
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
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double kinetic;
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double amass;
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double aVel[3], aJ[3], I[3][3];
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int i, j, k, kl;
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double kinetic_global;
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vector<StuntDouble *> integrableObjects = info->integrableObjects;
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kinetic = 0.0;
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kinetic_global = 0.0;
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for (kl=0; kl<integrableObjects.size(); kl++) {
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aVel = integrableObjects[kl]->getVel();
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amass = integrableObjects[kl]->getMass();
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for(j=0; j<3; j++)
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kinetic += amass*aVel[j]*aVel[j];
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if (integrableObjects[kl]->isDirectional()){
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aJ = integrableObjects[kl]->getJ();
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integrableObjects[kl]->getI( I );
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if (integrableObjects[kl]->isLinear()) {
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i = integrableObjects[kl]->linearAxis();
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j = (i+1)%3;
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k = (i+2)%3;
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kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
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} else {
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for (j=0; j<3; j++)
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kinetic += aJ[j]*aJ[j] / I[j][j];
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}
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}
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}
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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
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kinetic = kinetic * 0.5 / e_convert;
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return kinetic;
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}
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double Thermo::getPotential(){
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double potential_local;
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double potential;
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int el, nSRI;
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Molecule* molecules;
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molecules = info->molecules;
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nSRI = info->n_SRI;
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potential_local = 0.0;
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potential = 0.0;
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potential_local += info->lrPot;
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for( el=0; el<info->n_mol; el++ ){
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potential_local += molecules[el].getPotential();
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}
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// Get total potential for entire system from MPI.
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#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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return potential;
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}
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double Thermo::getTotalE(){
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double total;
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total = this->getKinetic() + this->getPotential();
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return total;
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}
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double Thermo::getTemperature(){
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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
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double temperature;
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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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double Thermo::getVolume() {
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return info->boxVol;
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}
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double Thermo::getPressure() {
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// Relies on the calculation of the full molecular pressure tensor
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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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this->getPressureTensor(press);
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
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return pressure;
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}
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double Thermo::getPressureX() {
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// Relies on the calculation of the full molecular pressure tensor
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const double p_convert = 1.63882576e8;
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double press[3][3];
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double pressureX;
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this->getPressureTensor(press);
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pressureX = p_convert * press[0][0];
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return pressureX;
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}
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double Thermo::getPressureY() {
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// Relies on the calculation of the full molecular pressure tensor
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const double p_convert = 1.63882576e8;
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double press[3][3];
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double pressureY;
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this->getPressureTensor(press);
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pressureY = p_convert * press[1][1];
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return pressureY;
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}
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double Thermo::getPressureZ() {
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// Relies on the calculation of the full molecular pressure tensor
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const double p_convert = 1.63882576e8;
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double press[3][3];
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double pressureZ;
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this->getPressureTensor(press);
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pressureZ = p_convert * press[2][2];
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return pressureZ;
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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:
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// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
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const double e_convert = 4.184e-4;
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double molmass, volume;
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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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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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// use velocities of integrableObjects and their masses:
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for (i=0; i < info->integrableObjects.size(); i++) {
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molmass = info->integrableObjects[i]->getMass();
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vcom = info->integrableObjects[i]->getVel();
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p_local[0] += molmass * (vcom[0] * vcom[0]);
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p_local[1] += molmass * (vcom[0] * vcom[1]);
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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]);
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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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// Get total for entire system from MPI.
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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++) {
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p_global[i] = p_local[i];
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}
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#endif // is_mpi
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volume = this->getVolume();
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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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void Thermo::velocitize() {
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double aVel[3], aJ[3], I[3][3];
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int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
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double vdrift[3];
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double vbar;
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
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double av2;
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double kebar;
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double temperature;
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int nobj;
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if (!info->have_target_temp) {
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sprintf( painCave.errMsg,
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"You can't resample the velocities without a targetTemp!\n"
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);
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painCave.isFatal = 1;
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painCave.severity = OOPSE_ERROR;
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simError();
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return;
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}
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nobj = info->integrableObjects.size();
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temperature = info->target_temp;
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kebar = kb * temperature * (double)info->ndfRaw /
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( 2.0 * (double)info->ndf );
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for(vr = 0; vr < nobj; vr++){
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// uses equipartition theory to solve for vbar in angstrom/fs
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av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
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vbar = sqrt( av2 );
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// picks random velocities from a gaussian distribution
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// centered on vbar
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for (j=0; j<3; j++)
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aVel[j] = vbar * gaussStream->getGaussian();
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info->integrableObjects[vr]->setVel( aVel );
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if(info->integrableObjects[vr]->isDirectional()){
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info->integrableObjects[vr]->getI( I );
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if (info->integrableObjects[vr]->isLinear()) {
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l= info->integrableObjects[vr]->linearAxis();
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m = (l+1)%3;
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n = (l+2)%3;
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aJ[l] = 0.0;
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vbar = sqrt( 2.0 * kebar * I[m][m] );
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aJ[m] = vbar * gaussStream->getGaussian();
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vbar = sqrt( 2.0 * kebar * I[n][n] );
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aJ[n] = vbar * gaussStream->getGaussian();
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} else {
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for (j = 0 ; j < 3; j++) {
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vbar = sqrt( 2.0 * kebar * I[j][j] );
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aJ[j] = vbar * gaussStream->getGaussian();
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}
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} // else isLinear
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info->integrableObjects[vr]->setJ( aJ );
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}//isDirectional
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}
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// Get the Center of Mass drift velocity.
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getCOMVel(vdrift);
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// Corrects for the center of mass drift.
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// sums all the momentum and divides by total mass.
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for(vd = 0; vd < nobj; vd++){
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aVel = info->integrableObjects[vd]->getVel();
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for (j=0; j < 3; j++)
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aVel[j] -= vdrift[j];
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info->integrableObjects[vd]->setVel( aVel );
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}
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}
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void Thermo::getCOMVel(double vdrift[3]){
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double mtot, mtot_local;
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double aVel[3], amass;
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double vdrift_local[3];
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int vd, j;
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int nobj;
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nobj = info->integrableObjects.size();
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mtot_local = 0.0;
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vdrift_local[0] = 0.0;
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vdrift_local[1] = 0.0;
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vdrift_local[2] = 0.0;
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for(vd = 0; vd < nobj; vd++){
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amass = info->integrableObjects[vd]->getMass();
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aVel = info->integrableObjects[vd]->getVel();
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for(j = 0; j < 3; j++)
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vdrift_local[j] += aVel[j] * amass;
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mtot_local += amass;
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}
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#ifdef IS_MPI
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MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
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MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
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#else
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mtot = mtot_local;
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for(vd = 0; vd < 3; vd++) {
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vdrift[vd] = vdrift_local[vd];
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}
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380 |
|
|
#endif
|
381 |
|
|
|
382 |
|
|
for (vd = 0; vd < 3; vd++) {
|
383 |
|
|
vdrift[vd] = vdrift[vd] / mtot;
|
384 |
|
|
}
|
385 |
|
|
|
386 |
|
|
}
|
387 |
|
|
|
388 |
|
|
void Thermo::getCOM(double COM[3]){
|
389 |
|
|
|
390 |
|
|
double mtot, mtot_local;
|
391 |
|
|
double aPos[3], amass;
|
392 |
|
|
double COM_local[3];
|
393 |
|
|
int i, j;
|
394 |
|
|
int nobj;
|
395 |
|
|
|
396 |
|
|
mtot_local = 0.0;
|
397 |
|
|
COM_local[0] = 0.0;
|
398 |
|
|
COM_local[1] = 0.0;
|
399 |
|
|
COM_local[2] = 0.0;
|
400 |
|
|
|
401 |
|
|
nobj = info->integrableObjects.size();
|
402 |
|
|
for(i = 0; i < nobj; i++){
|
403 |
|
|
|
404 |
|
|
amass = info->integrableObjects[i]->getMass();
|
405 |
|
|
aPos = info->integrableObjects[i]->getPos();
|
406 |
|
|
|
407 |
|
|
for(j = 0; j < 3; j++)
|
408 |
|
|
COM_local[j] += aPos[j] * amass;
|
409 |
|
|
|
410 |
|
|
mtot_local += amass;
|
411 |
|
|
}
|
412 |
|
|
|
413 |
|
|
#ifdef IS_MPI
|
414 |
|
|
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
|
415 |
|
|
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
|
416 |
|
|
#else
|
417 |
|
|
mtot = mtot_local;
|
418 |
|
|
for(i = 0; i < 3; i++) {
|
419 |
|
|
COM[i] = COM_local[i];
|
420 |
|
|
}
|
421 |
|
|
#endif
|
422 |
|
|
|
423 |
|
|
for (i = 0; i < 3; i++) {
|
424 |
|
|
COM[i] = COM[i] / mtot;
|
425 |
|
|
}
|
426 |
|
|
}
|
427 |
|
|
|
428 |
|
|
void Thermo::removeCOMdrift() {
|
429 |
|
|
double vdrift[3], aVel[3];
|
430 |
|
|
int vd, j, nobj;
|
431 |
|
|
|
432 |
|
|
nobj = info->integrableObjects.size();
|
433 |
|
|
|
434 |
|
|
// Get the Center of Mass drift velocity.
|
435 |
|
|
|
436 |
|
|
getCOMVel(vdrift);
|
437 |
|
|
|
438 |
|
|
// Corrects for the center of mass drift.
|
439 |
|
|
// sums all the momentum and divides by total mass.
|
440 |
|
|
|
441 |
|
|
for(vd = 0; vd < nobj; vd++){
|
442 |
|
|
|
443 |
|
|
aVel = info->integrableObjects[vd]->getVel();
|
444 |
|
|
|
445 |
|
|
for (j=0; j < 3; j++)
|
446 |
|
|
aVel[j] -= vdrift[j];
|
447 |
|
|
|
448 |
|
|
info->integrableObjects[vd]->setVel( aVel );
|
449 |
|
|
}
|
450 |
|
|
}
|