| 1 |
+ |
/* |
| 2 |
+ |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
+ |
* |
| 4 |
+ |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
+ |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
+ |
* redistribute this software in source and binary code form, provided |
| 7 |
+ |
* that the following conditions are met: |
| 8 |
+ |
* |
| 9 |
+ |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
+ |
* publication of scientific results based in part on use of the |
| 11 |
+ |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
+ |
* the article in which the program was described (Matthew |
| 13 |
+ |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
+ |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
+ |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
+ |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
+ |
* |
| 18 |
+ |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
+ |
* notice, this list of conditions and the following disclaimer. |
| 20 |
+ |
* |
| 21 |
+ |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
+ |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
+ |
* documentation and/or other materials provided with the |
| 24 |
+ |
* distribution. |
| 25 |
+ |
* |
| 26 |
+ |
* This software is provided "AS IS," without a warranty of any |
| 27 |
+ |
* kind. All express or implied conditions, representations and |
| 28 |
+ |
* warranties, including any implied warranty of merchantability, |
| 29 |
+ |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
+ |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
+ |
* be liable for any damages suffered by licensee as a result of |
| 32 |
+ |
* using, modifying or distributing the software or its |
| 33 |
+ |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
+ |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
+ |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
+ |
* damages, however caused and regardless of the theory of liability, |
| 37 |
+ |
* arising out of the use of or inability to use software, even if the |
| 38 |
+ |
* University of Notre Dame has been advised of the possibility of |
| 39 |
+ |
* such damages. |
| 40 |
+ |
*/ |
| 41 |
+ |
|
| 42 |
|
#include <math.h> |
| 43 |
|
#include <iostream> |
| 3 |
– |
using namespace std; |
| 44 |
|
|
| 45 |
|
#ifdef IS_MPI |
| 46 |
|
#include <mpi.h> |
| 47 |
|
#endif //is_mpi |
| 48 |
|
|
| 49 |
< |
#include "Thermo.hpp" |
| 50 |
< |
#include "SRI.hpp" |
| 51 |
< |
#include "Integrator.hpp" |
| 52 |
< |
#include "simError.h" |
| 13 |
< |
#include "MatVec3.h" |
| 49 |
> |
#include "brains/Thermo.hpp" |
| 50 |
> |
#include "primitives/Molecule.hpp" |
| 51 |
> |
#include "utils/simError.h" |
| 52 |
> |
#include "utils/OOPSEConstant.hpp" |
| 53 |
|
|
| 54 |
< |
#ifdef IS_MPI |
| 16 |
< |
#define __C |
| 17 |
< |
#include "mpiSimulation.hpp" |
| 18 |
< |
#endif // is_mpi |
| 54 |
> |
namespace oopse { |
| 55 |
|
|
| 56 |
< |
inline double roundMe( double x ){ |
| 57 |
< |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 58 |
< |
} |
| 56 |
> |
double Thermo::getKinetic() { |
| 57 |
> |
SimInfo::MoleculeIterator miter; |
| 58 |
> |
std::vector<StuntDouble*>::iterator iiter; |
| 59 |
> |
Molecule* mol; |
| 60 |
> |
StuntDouble* integrableObject; |
| 61 |
> |
Vector3d vel; |
| 62 |
> |
Vector3d angMom; |
| 63 |
> |
Mat3x3d I; |
| 64 |
> |
int i; |
| 65 |
> |
int j; |
| 66 |
> |
int k; |
| 67 |
> |
double kinetic = 0.0; |
| 68 |
> |
double kinetic_global = 0.0; |
| 69 |
> |
|
| 70 |
> |
for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
| 71 |
> |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 72 |
> |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 73 |
|
|
| 74 |
< |
Thermo::Thermo( SimInfo* the_info ) { |
| 75 |
< |
info = the_info; |
| 26 |
< |
int baseSeed = the_info->getSeed(); |
| 27 |
< |
|
| 28 |
< |
gaussStream = new gaussianSPRNG( baseSeed ); |
| 29 |
< |
} |
| 74 |
> |
double mass = integrableObject->getMass(); |
| 75 |
> |
Vector3d vel = integrableObject->getVel(); |
| 76 |
|
|
| 77 |
< |
Thermo::~Thermo(){ |
| 32 |
< |
delete gaussStream; |
| 33 |
< |
} |
| 77 |
> |
kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 78 |
|
|
| 79 |
< |
double Thermo::getKinetic(){ |
| 79 |
> |
if (integrableObject->isDirectional()) { |
| 80 |
> |
angMom = integrableObject->getJ(); |
| 81 |
> |
I = integrableObject->getI(); |
| 82 |
|
|
| 83 |
< |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 84 |
< |
double kinetic; |
| 85 |
< |
double amass; |
| 86 |
< |
double aVel[3], aJ[3], I[3][3]; |
| 87 |
< |
int i, j, k, kl; |
| 88 |
< |
|
| 89 |
< |
double kinetic_global; |
| 90 |
< |
vector<StuntDouble *> integrableObjects = info->integrableObjects; |
| 91 |
< |
|
| 92 |
< |
kinetic = 0.0; |
| 93 |
< |
kinetic_global = 0.0; |
| 48 |
< |
|
| 49 |
< |
for (kl=0; kl<integrableObjects.size(); kl++) { |
| 50 |
< |
integrableObjects[kl]->getVel(aVel); |
| 51 |
< |
amass = integrableObjects[kl]->getMass(); |
| 52 |
< |
|
| 53 |
< |
for(j=0; j<3; j++) |
| 54 |
< |
kinetic += amass*aVel[j]*aVel[j]; |
| 55 |
< |
|
| 56 |
< |
if (integrableObjects[kl]->isDirectional()){ |
| 57 |
< |
|
| 58 |
< |
integrableObjects[kl]->getJ( aJ ); |
| 59 |
< |
integrableObjects[kl]->getI( I ); |
| 60 |
< |
|
| 61 |
< |
if (integrableObjects[kl]->isLinear()) { |
| 62 |
< |
i = integrableObjects[kl]->linearAxis(); |
| 63 |
< |
j = (i+1)%3; |
| 64 |
< |
k = (i+2)%3; |
| 65 |
< |
kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; |
| 66 |
< |
} else { |
| 67 |
< |
for (j=0; j<3; j++) |
| 68 |
< |
kinetic += aJ[j]*aJ[j] / I[j][j]; |
| 83 |
> |
if (integrableObject->isLinear()) { |
| 84 |
> |
i = integrableObject->linearAxis(); |
| 85 |
> |
j = (i + 1) % 3; |
| 86 |
> |
k = (i + 2) % 3; |
| 87 |
> |
kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k); |
| 88 |
> |
} else { |
| 89 |
> |
kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) |
| 90 |
> |
+ angMom[2]*angMom[2]/I(2, 2); |
| 91 |
> |
} |
| 92 |
> |
} |
| 93 |
> |
|
| 94 |
|
} |
| 95 |
< |
} |
| 96 |
< |
} |
| 95 |
> |
} |
| 96 |
> |
|
| 97 |
|
#ifdef IS_MPI |
| 73 |
– |
MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
| 74 |
– |
MPI_SUM, MPI_COMM_WORLD); |
| 75 |
– |
kinetic = kinetic_global; |
| 76 |
– |
#endif //is_mpi |
| 77 |
– |
|
| 78 |
– |
kinetic = kinetic * 0.5 / e_convert; |
| 98 |
|
|
| 99 |
< |
return kinetic; |
| 100 |
< |
} |
| 99 |
> |
MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM, |
| 100 |
> |
MPI_COMM_WORLD); |
| 101 |
> |
kinetic = kinetic_global; |
| 102 |
|
|
| 103 |
< |
double Thermo::getPotential(){ |
| 84 |
< |
|
| 85 |
< |
double potential_local; |
| 86 |
< |
double potential; |
| 87 |
< |
int el, nSRI; |
| 88 |
< |
Molecule* molecules; |
| 103 |
> |
#endif //is_mpi |
| 104 |
|
|
| 105 |
< |
molecules = info->molecules; |
| 91 |
< |
nSRI = info->n_SRI; |
| 105 |
> |
kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
| 106 |
|
|
| 107 |
< |
potential_local = 0.0; |
| 94 |
< |
potential = 0.0; |
| 95 |
< |
potential_local += info->lrPot; |
| 96 |
< |
|
| 97 |
< |
for( el=0; el<info->n_mol; el++ ){ |
| 98 |
< |
potential_local += molecules[el].getPotential(); |
| 107 |
> |
return kinetic; |
| 108 |
|
} |
| 109 |
|
|
| 110 |
< |
// Get total potential for entire system from MPI. |
| 111 |
< |
#ifdef IS_MPI |
| 112 |
< |
MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
| 113 |
< |
MPI_SUM, MPI_COMM_WORLD); |
| 114 |
< |
#else |
| 106 |
< |
potential = potential_local; |
| 107 |
< |
#endif // is_mpi |
| 110 |
> |
double Thermo::getPotential() { |
| 111 |
> |
double potential = 0.0; |
| 112 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 113 |
> |
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 114 |
> |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 115 |
|
|
| 116 |
< |
return potential; |
| 110 |
< |
} |
| 116 |
> |
// Get total potential for entire system from MPI. |
| 117 |
|
|
| 118 |
< |
double Thermo::getTotalE(){ |
| 118 |
> |
#ifdef IS_MPI |
| 119 |
|
|
| 120 |
< |
double total; |
| 120 |
> |
MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 121 |
> |
MPI_COMM_WORLD); |
| 122 |
|
|
| 123 |
< |
total = this->getKinetic() + this->getPotential(); |
| 117 |
< |
return total; |
| 118 |
< |
} |
| 123 |
> |
#else |
| 124 |
|
|
| 125 |
< |
double Thermo::getTemperature(){ |
| 125 |
> |
potential = potential_local; |
| 126 |
|
|
| 127 |
< |
const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
| 123 |
< |
double temperature; |
| 127 |
> |
#endif // is_mpi |
| 128 |
|
|
| 129 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
| 130 |
< |
return temperature; |
| 127 |
< |
} |
| 129 |
> |
return potential; |
| 130 |
> |
} |
| 131 |
|
|
| 132 |
< |
double Thermo::getVolume() { |
| 132 |
> |
double Thermo::getTotalE() { |
| 133 |
> |
double total; |
| 134 |
|
|
| 135 |
< |
return info->boxVol; |
| 136 |
< |
} |
| 135 |
> |
total = this->getKinetic() + this->getPotential(); |
| 136 |
> |
return total; |
| 137 |
> |
} |
| 138 |
|
|
| 139 |
< |
double Thermo::getPressure() { |
| 139 |
> |
double Thermo::getTemperature() { |
| 140 |
> |
|
| 141 |
> |
double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb ); |
| 142 |
> |
return temperature; |
| 143 |
> |
} |
| 144 |
|
|
| 145 |
< |
// Relies on the calculation of the full molecular pressure tensor |
| 146 |
< |
|
| 147 |
< |
const double p_convert = 1.63882576e8; |
| 148 |
< |
double press[3][3]; |
| 140 |
< |
double pressure; |
| 145 |
> |
double Thermo::getVolume() { |
| 146 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 147 |
> |
return curSnapshot->getVolume(); |
| 148 |
> |
} |
| 149 |
|
|
| 150 |
< |
this->getPressureTensor(press); |
| 150 |
> |
double Thermo::getPressure() { |
| 151 |
|
|
| 152 |
< |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 152 |
> |
// Relies on the calculation of the full molecular pressure tensor |
| 153 |
|
|
| 146 |
– |
return pressure; |
| 147 |
– |
} |
| 154 |
|
|
| 155 |
< |
double Thermo::getPressureX() { |
| 155 |
> |
Mat3x3d tensor; |
| 156 |
> |
double pressure; |
| 157 |
|
|
| 158 |
< |
// Relies on the calculation of the full molecular pressure tensor |
| 152 |
< |
|
| 153 |
< |
const double p_convert = 1.63882576e8; |
| 154 |
< |
double press[3][3]; |
| 155 |
< |
double pressureX; |
| 158 |
> |
tensor = getPressureTensor(); |
| 159 |
|
|
| 160 |
< |
this->getPressureTensor(press); |
| 160 |
> |
pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
| 161 |
|
|
| 162 |
< |
pressureX = p_convert * press[0][0]; |
| 162 |
> |
return pressure; |
| 163 |
> |
} |
| 164 |
|
|
| 165 |
< |
return pressureX; |
| 162 |
< |
} |
| 165 |
> |
double Thermo::getPressure(int direction) { |
| 166 |
|
|
| 167 |
< |
double Thermo::getPressureY() { |
| 167 |
> |
// Relies on the calculation of the full molecular pressure tensor |
| 168 |
|
|
| 169 |
< |
// Relies on the calculation of the full molecular pressure tensor |
| 170 |
< |
|
| 171 |
< |
const double p_convert = 1.63882576e8; |
| 169 |
< |
double press[3][3]; |
| 170 |
< |
double pressureY; |
| 169 |
> |
|
| 170 |
> |
Mat3x3d tensor; |
| 171 |
> |
double pressure; |
| 172 |
|
|
| 173 |
< |
this->getPressureTensor(press); |
| 173 |
> |
tensor = getPressureTensor(); |
| 174 |
|
|
| 175 |
< |
pressureY = p_convert * press[1][1]; |
| 175 |
> |
pressure = OOPSEConstant::pressureConvert * tensor(direction, direction); |
| 176 |
|
|
| 177 |
< |
return pressureY; |
| 178 |
< |
} |
| 177 |
> |
return pressure; |
| 178 |
> |
} |
| 179 |
|
|
| 179 |
– |
double Thermo::getPressureZ() { |
| 180 |
|
|
| 181 |
– |
// Relies on the calculation of the full molecular pressure tensor |
| 182 |
– |
|
| 183 |
– |
const double p_convert = 1.63882576e8; |
| 184 |
– |
double press[3][3]; |
| 185 |
– |
double pressureZ; |
| 181 |
|
|
| 182 |
< |
this->getPressureTensor(press); |
| 182 |
> |
Mat3x3d Thermo::getPressureTensor() { |
| 183 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 184 |
> |
// routine derived via viral theorem description in: |
| 185 |
> |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 186 |
> |
Mat3x3d pressureTensor; |
| 187 |
> |
Mat3x3d p_local(0.0); |
| 188 |
> |
Mat3x3d p_global(0.0); |
| 189 |
|
|
| 190 |
< |
pressureZ = p_convert * press[2][2]; |
| 190 |
> |
SimInfo::MoleculeIterator i; |
| 191 |
> |
std::vector<StuntDouble*>::iterator j; |
| 192 |
> |
Molecule* mol; |
| 193 |
> |
StuntDouble* integrableObject; |
| 194 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 195 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 196 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 197 |
|
|
| 198 |
< |
return pressureZ; |
| 199 |
< |
} |
| 200 |
< |
|
| 201 |
< |
|
| 202 |
< |
void Thermo::getPressureTensor(double press[3][3]){ |
| 196 |
< |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 197 |
< |
// routine derived via viral theorem description in: |
| 198 |
< |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 199 |
< |
|
| 200 |
< |
const double e_convert = 4.184e-4; |
| 201 |
< |
|
| 202 |
< |
double molmass, volume; |
| 203 |
< |
double vcom[3]; |
| 204 |
< |
double p_local[9], p_global[9]; |
| 205 |
< |
int i, j, k; |
| 206 |
< |
|
| 207 |
< |
for (i=0; i < 9; i++) { |
| 208 |
< |
p_local[i] = 0.0; |
| 209 |
< |
p_global[i] = 0.0; |
| 210 |
< |
} |
| 211 |
< |
|
| 212 |
< |
// use velocities of integrableObjects and their masses: |
| 213 |
< |
|
| 214 |
< |
for (i=0; i < info->integrableObjects.size(); i++) { |
| 215 |
< |
|
| 216 |
< |
molmass = info->integrableObjects[i]->getMass(); |
| 198 |
> |
double mass = integrableObject->getMass(); |
| 199 |
> |
Vector3d vcom = integrableObject->getVel(); |
| 200 |
> |
p_local += mass * outProduct(vcom, vcom); |
| 201 |
> |
} |
| 202 |
> |
} |
| 203 |
|
|
| 218 |
– |
info->integrableObjects[i]->getVel(vcom); |
| 219 |
– |
|
| 220 |
– |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
| 221 |
– |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 222 |
– |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
| 223 |
– |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
| 224 |
– |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 225 |
– |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
| 226 |
– |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 227 |
– |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 228 |
– |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 229 |
– |
|
| 230 |
– |
} |
| 231 |
– |
|
| 232 |
– |
// Get total for entire system from MPI. |
| 233 |
– |
|
| 204 |
|
#ifdef IS_MPI |
| 205 |
< |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 205 |
> |
MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 206 |
|
#else |
| 207 |
< |
for (i=0; i<9; i++) { |
| 238 |
< |
p_global[i] = p_local[i]; |
| 239 |
< |
} |
| 207 |
> |
p_global = p_local; |
| 208 |
|
#endif // is_mpi |
| 209 |
|
|
| 210 |
< |
volume = this->getVolume(); |
| 210 |
> |
double volume = this->getVolume(); |
| 211 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 212 |
> |
Mat3x3d tau = curSnapshot->statData.getTau(); |
| 213 |
|
|
| 214 |
+ |
pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
| 215 |
|
|
| 216 |
< |
|
| 246 |
< |
for(i = 0; i < 3; i++) { |
| 247 |
< |
for (j = 0; j < 3; j++) { |
| 248 |
< |
k = 3*i + j; |
| 249 |
< |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
| 250 |
< |
} |
| 216 |
> |
return pressureTensor; |
| 217 |
|
} |
| 252 |
– |
} |
| 218 |
|
|
| 219 |
< |
void Thermo::velocitize() { |
| 220 |
< |
|
| 221 |
< |
double aVel[3], aJ[3], I[3][3]; |
| 257 |
< |
int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
| 258 |
< |
double vdrift[3]; |
| 259 |
< |
double vbar; |
| 260 |
< |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 261 |
< |
double av2; |
| 262 |
< |
double kebar; |
| 263 |
< |
double temperature; |
| 264 |
< |
int nobj; |
| 265 |
< |
|
| 266 |
< |
if (!info->have_target_temp) { |
| 267 |
< |
sprintf( painCave.errMsg, |
| 268 |
< |
"You can't resample the velocities without a targetTemp!\n" |
| 269 |
< |
); |
| 270 |
< |
painCave.isFatal = 1; |
| 271 |
< |
painCave.severity = OOPSE_ERROR; |
| 272 |
< |
simError(); |
| 273 |
< |
return; |
| 274 |
< |
} |
| 275 |
< |
|
| 276 |
< |
nobj = info->integrableObjects.size(); |
| 277 |
< |
|
| 278 |
< |
temperature = info->target_temp; |
| 279 |
< |
|
| 280 |
< |
kebar = kb * temperature * (double)info->ndfRaw / |
| 281 |
< |
( 2.0 * (double)info->ndf ); |
| 282 |
< |
|
| 283 |
< |
for(vr = 0; vr < nobj; vr++){ |
| 219 |
> |
void Thermo::saveStat(){ |
| 220 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 221 |
> |
Stats& stat = currSnapshot->statData; |
| 222 |
|
|
| 223 |
< |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 223 |
> |
stat[Stats::KINETIC_ENERGY] = getKinetic(); |
| 224 |
> |
stat[Stats::POTENTIAL_ENERGY] = getPotential(); |
| 225 |
> |
stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ; |
| 226 |
> |
stat[Stats::TEMPERATURE] = getTemperature(); |
| 227 |
> |
stat[Stats::PRESSURE] = getPressure(); |
| 228 |
> |
stat[Stats::VOLUME] = getVolume(); |
| 229 |
|
|
| 230 |
< |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
| 231 |
< |
vbar = sqrt( av2 ); |
| 230 |
> |
Mat3x3d tensor =getPressureTensor(); |
| 231 |
> |
stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0); |
| 232 |
> |
stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1); |
| 233 |
> |
stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2); |
| 234 |
|
|
| 290 |
– |
// picks random velocities from a gaussian distribution |
| 291 |
– |
// centered on vbar |
| 235 |
|
|
| 236 |
< |
for (j=0; j<3; j++) |
| 237 |
< |
aVel[j] = vbar * gaussStream->getGaussian(); |
| 236 |
> |
/**@todo need refactorying*/ |
| 237 |
> |
//Conserved Quantity is set by integrator and time is set by setTime |
| 238 |
|
|
| 296 |
– |
info->integrableObjects[vr]->setVel( aVel ); |
| 297 |
– |
|
| 298 |
– |
if(info->integrableObjects[vr]->isDirectional()){ |
| 299 |
– |
|
| 300 |
– |
info->integrableObjects[vr]->getI( I ); |
| 301 |
– |
|
| 302 |
– |
if (info->integrableObjects[vr]->isLinear()) { |
| 303 |
– |
|
| 304 |
– |
l= info->integrableObjects[vr]->linearAxis(); |
| 305 |
– |
m = (l+1)%3; |
| 306 |
– |
n = (l+2)%3; |
| 307 |
– |
|
| 308 |
– |
aJ[l] = 0.0; |
| 309 |
– |
vbar = sqrt( 2.0 * kebar * I[m][m] ); |
| 310 |
– |
aJ[m] = vbar * gaussStream->getGaussian(); |
| 311 |
– |
vbar = sqrt( 2.0 * kebar * I[n][n] ); |
| 312 |
– |
aJ[n] = vbar * gaussStream->getGaussian(); |
| 313 |
– |
|
| 314 |
– |
} else { |
| 315 |
– |
for (j = 0 ; j < 3; j++) { |
| 316 |
– |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 317 |
– |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 318 |
– |
} |
| 319 |
– |
} // else isLinear |
| 320 |
– |
|
| 321 |
– |
info->integrableObjects[vr]->setJ( aJ ); |
| 322 |
– |
|
| 323 |
– |
}//isDirectional |
| 324 |
– |
|
| 239 |
|
} |
| 240 |
|
|
| 241 |
< |
// Get the Center of Mass drift velocity. |
| 328 |
< |
|
| 329 |
< |
getCOMVel(vdrift); |
| 330 |
< |
|
| 331 |
< |
// Corrects for the center of mass drift. |
| 332 |
< |
// sums all the momentum and divides by total mass. |
| 333 |
< |
|
| 334 |
< |
for(vd = 0; vd < nobj; vd++){ |
| 335 |
< |
|
| 336 |
< |
info->integrableObjects[vd]->getVel(aVel); |
| 337 |
< |
|
| 338 |
< |
for (j=0; j < 3; j++) |
| 339 |
< |
aVel[j] -= vdrift[j]; |
| 340 |
< |
|
| 341 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
| 342 |
< |
} |
| 343 |
< |
|
| 344 |
< |
} |
| 345 |
< |
|
| 346 |
< |
void Thermo::getCOMVel(double vdrift[3]){ |
| 347 |
< |
|
| 348 |
< |
double mtot, mtot_local; |
| 349 |
< |
double aVel[3], amass; |
| 350 |
< |
double vdrift_local[3]; |
| 351 |
< |
int vd, j; |
| 352 |
< |
int nobj; |
| 353 |
< |
|
| 354 |
< |
nobj = info->integrableObjects.size(); |
| 355 |
< |
|
| 356 |
< |
mtot_local = 0.0; |
| 357 |
< |
vdrift_local[0] = 0.0; |
| 358 |
< |
vdrift_local[1] = 0.0; |
| 359 |
< |
vdrift_local[2] = 0.0; |
| 360 |
< |
|
| 361 |
< |
for(vd = 0; vd < nobj; vd++){ |
| 362 |
< |
|
| 363 |
< |
amass = info->integrableObjects[vd]->getMass(); |
| 364 |
< |
info->integrableObjects[vd]->getVel( aVel ); |
| 365 |
< |
|
| 366 |
< |
for(j = 0; j < 3; j++) |
| 367 |
< |
vdrift_local[j] += aVel[j] * amass; |
| 368 |
< |
|
| 369 |
< |
mtot_local += amass; |
| 370 |
< |
} |
| 371 |
< |
|
| 372 |
< |
#ifdef IS_MPI |
| 373 |
< |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 374 |
< |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 375 |
< |
#else |
| 376 |
< |
mtot = mtot_local; |
| 377 |
< |
for(vd = 0; vd < 3; vd++) { |
| 378 |
< |
vdrift[vd] = vdrift_local[vd]; |
| 379 |
< |
} |
| 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 |
< |
info->integrableObjects[i]->getPos( aPos ); |
| 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 |
< |
info->integrableObjects[vd]->getVel(aVel); |
| 444 |
< |
|
| 445 |
< |
for (j=0; j < 3; j++) |
| 446 |
< |
aVel[j] -= vdrift[j]; |
| 447 |
< |
|
| 448 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
| 449 |
< |
} |
| 450 |
< |
} |
| 241 |
> |
} //end namespace oopse |
