| 1 |
< |
#include <math.h> |
| 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 "integrators/NVT.hpp" |
| 43 |
> |
#include "primitives/Molecule.hpp" |
| 44 |
> |
#include "utils/simError.h" |
| 45 |
> |
#include "utils/OOPSEConstant.hpp" |
| 46 |
|
|
| 47 |
< |
#include "Atom.hpp" |
| 4 |
< |
#include "SRI.hpp" |
| 5 |
< |
#include "AbstractClasses.hpp" |
| 6 |
< |
#include "SimInfo.hpp" |
| 7 |
< |
#include "ForceFields.hpp" |
| 8 |
< |
#include "Thermo.hpp" |
| 9 |
< |
#include "ReadWrite.hpp" |
| 10 |
< |
#include "Integrator.hpp" |
| 11 |
< |
#include "simError.h" |
| 47 |
> |
namespace oopse { |
| 48 |
|
|
| 49 |
+ |
NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) { |
| 50 |
|
|
| 51 |
< |
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 51 |
> |
Globals* simParams = info_->getSimParams(); |
| 52 |
|
|
| 53 |
< |
template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff): |
| 54 |
< |
T( theInfo, the_ff ) |
| 55 |
< |
{ |
| 56 |
< |
GenericData* data; |
| 20 |
< |
DoubleData * chiValue; |
| 21 |
< |
DoubleData * integralOfChidtValue; |
| 22 |
< |
|
| 23 |
< |
chiValue = NULL; |
| 24 |
< |
integralOfChidtValue = NULL; |
| 25 |
< |
|
| 26 |
< |
chi = 0.0; |
| 27 |
< |
have_tau_thermostat = 0; |
| 28 |
< |
have_target_temp = 0; |
| 29 |
< |
have_chi_tolerance = 0; |
| 30 |
< |
integralOfChidt = 0.0; |
| 31 |
< |
|
| 32 |
< |
|
| 33 |
< |
if( theInfo->useInitXSstate ){ |
| 34 |
< |
|
| 35 |
< |
// retrieve chi and integralOfChidt from simInfo |
| 36 |
< |
data = info->getProperty(CHIVALUE_ID); |
| 37 |
< |
if(data){ |
| 38 |
< |
chiValue = dynamic_cast<DoubleData*>(data); |
| 53 |
> |
if (!simParams->getUseIntialExtendedSystemState()) { |
| 54 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 55 |
> |
currSnapshot->setChi(0.0); |
| 56 |
> |
currSnapshot->setIntegralOfChiDt(0.0); |
| 57 |
|
} |
| 58 |
|
|
| 59 |
< |
data = info->getProperty(INTEGRALOFCHIDT_ID); |
| 60 |
< |
if(data){ |
| 61 |
< |
integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
| 59 |
> |
if (!simParams->haveTargetTemp()) { |
| 60 |
> |
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
| 61 |
> |
painCave.isFatal = 1; |
| 62 |
> |
painCave.severity = OOPSE_ERROR; |
| 63 |
> |
simError(); |
| 64 |
> |
} else { |
| 65 |
> |
targetTemp_ = simParams->getTargetTemp(); |
| 66 |
|
} |
| 45 |
– |
|
| 46 |
– |
// chi and integralOfChidt should appear by pair |
| 47 |
– |
if(chiValue && integralOfChidtValue){ |
| 48 |
– |
chi = chiValue->getData(); |
| 49 |
– |
integralOfChidt = integralOfChidtValue->getData(); |
| 50 |
– |
} |
| 51 |
– |
} |
| 67 |
|
|
| 68 |
< |
oldVel = new double[3*integrableObjects.size()]; |
| 54 |
< |
oldJi = new double[3*integrableObjects.size()]; |
| 55 |
< |
} |
| 68 |
> |
// We must set tauThermostat_. |
| 69 |
|
|
| 70 |
< |
template<typename T> NVT<T>::~NVT() { |
| 71 |
< |
delete[] oldVel; |
| 72 |
< |
delete[] oldJi; |
| 60 |
< |
} |
| 70 |
> |
if (!simParams->haveTauThermostat()) { |
| 71 |
> |
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
| 72 |
> |
"\tintegrator, you must set tauThermostat_.\n"); |
| 73 |
|
|
| 74 |
< |
template<typename T> void NVT<T>::moveA() { |
| 74 |
> |
painCave.severity = OOPSE_ERROR; |
| 75 |
> |
painCave.isFatal = 1; |
| 76 |
> |
simError(); |
| 77 |
> |
} else { |
| 78 |
> |
tauThermostat_ = simParams->getTauThermostat(); |
| 79 |
> |
} |
| 80 |
|
|
| 81 |
< |
int i, j; |
| 82 |
< |
DirectionalAtom* dAtom; |
| 66 |
< |
double Tb[3], ji[3]; |
| 67 |
< |
double mass; |
| 68 |
< |
double vel[3], pos[3], frc[3]; |
| 81 |
> |
update(); |
| 82 |
> |
} |
| 83 |
|
|
| 84 |
< |
double instTemp; |
| 84 |
> |
void NVT::doUpdate() { |
| 85 |
> |
oldVel_.resize(info_->getNIntegrableObjects()); |
| 86 |
> |
oldJi_.resize(info_->getNIntegrableObjects()); |
| 87 |
> |
} |
| 88 |
> |
void NVT::moveA() { |
| 89 |
> |
SimInfo::MoleculeIterator i; |
| 90 |
> |
Molecule::IntegrableObjectIterator j; |
| 91 |
> |
Molecule* mol; |
| 92 |
> |
StuntDouble* integrableObject; |
| 93 |
> |
Vector3d Tb; |
| 94 |
> |
Vector3d ji; |
| 95 |
> |
RealType mass; |
| 96 |
> |
Vector3d vel; |
| 97 |
> |
Vector3d pos; |
| 98 |
> |
Vector3d frc; |
| 99 |
|
|
| 100 |
< |
// We need the temperature at time = t for the chi update below: |
| 100 |
> |
RealType chi = currentSnapshot_->getChi(); |
| 101 |
> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 102 |
> |
|
| 103 |
> |
// We need the temperature at time = t for the chi update below: |
| 104 |
|
|
| 105 |
< |
instTemp = tStats->getTemperature(); |
| 105 |
> |
RealType instTemp = thermo.getTemperature(); |
| 106 |
|
|
| 107 |
< |
for( i=0; i < integrableObjects.size(); i++ ){ |
| 107 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 108 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 109 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 110 |
|
|
| 111 |
< |
integrableObjects[i]->getVel( vel ); |
| 112 |
< |
integrableObjects[i]->getPos( pos ); |
| 113 |
< |
integrableObjects[i]->getFrc( frc ); |
| 111 |
> |
vel = integrableObject->getVel(); |
| 112 |
> |
pos = integrableObject->getPos(); |
| 113 |
> |
frc = integrableObject->getFrc(); |
| 114 |
|
|
| 115 |
< |
mass = integrableObjects[i]->getMass(); |
| 115 |
> |
mass = integrableObject->getMass(); |
| 116 |
|
|
| 117 |
< |
for (j=0; j < 3; j++) { |
| 118 |
< |
// velocity half step (use chi from previous step here): |
| 119 |
< |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
| 120 |
< |
// position whole step |
| 121 |
< |
pos[j] += dt * vel[j]; |
| 122 |
< |
} |
| 117 |
> |
// velocity half step (use chi from previous step here): |
| 118 |
> |
//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
| 119 |
> |
vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
| 120 |
> |
|
| 121 |
> |
// position whole step |
| 122 |
> |
//pos[j] += dt * vel[j]; |
| 123 |
> |
pos += dt * vel; |
| 124 |
|
|
| 125 |
< |
integrableObjects[i]->setVel( vel ); |
| 126 |
< |
integrableObjects[i]->setPos( pos ); |
| 125 |
> |
integrableObject->setVel(vel); |
| 126 |
> |
integrableObject->setPos(pos); |
| 127 |
|
|
| 128 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 128 |
> |
if (integrableObject->isDirectional()) { |
| 129 |
|
|
| 130 |
< |
// get and convert the torque to body frame |
| 130 |
> |
//convert the torque to body frame |
| 131 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 132 |
|
|
| 133 |
< |
integrableObjects[i]->getTrq( Tb ); |
| 99 |
< |
integrableObjects[i]->lab2Body( Tb ); |
| 133 |
> |
// get the angular momentum, and propagate a half step |
| 134 |
|
|
| 135 |
< |
// get the angular momentum, and propagate a half step |
| 135 |
> |
ji = integrableObject->getJ(); |
| 136 |
|
|
| 137 |
< |
integrableObjects[i]->getJ( ji ); |
| 137 |
> |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
| 138 |
> |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
| 139 |
> |
rotAlgo->rotate(integrableObject, ji, dt); |
| 140 |
|
|
| 141 |
< |
for (j=0; j < 3; j++) |
| 142 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 141 |
> |
integrableObject->setJ(ji); |
| 142 |
> |
} |
| 143 |
> |
} |
| 144 |
|
|
| 108 |
– |
this->rotationPropagation( integrableObjects[i], ji ); |
| 109 |
– |
|
| 110 |
– |
integrableObjects[i]->setJ( ji ); |
| 145 |
|
} |
| 146 |
< |
} |
| 147 |
< |
|
| 114 |
< |
if(nConstrained) |
| 115 |
< |
constrainA(); |
| 146 |
> |
|
| 147 |
> |
rattle->constraintA(); |
| 148 |
|
|
| 149 |
< |
// Finally, evolve chi a half step (just like a velocity) using |
| 150 |
< |
// temperature at time t, not time t+dt/2 |
| 149 |
> |
// Finally, evolve chi a half step (just like a velocity) using |
| 150 |
> |
// temperature at time t, not time t+dt/2 |
| 151 |
|
|
| 152 |
< |
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
| 153 |
< |
|
| 154 |
< |
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
| 123 |
< |
integralOfChidt += chi*dt2; |
| 152 |
> |
|
| 153 |
> |
chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 154 |
> |
integralOfChidt += chi * dt2; |
| 155 |
|
|
| 156 |
< |
} |
| 157 |
< |
|
| 127 |
< |
template<typename T> void NVT<T>::moveB( void ){ |
| 128 |
< |
int i, j, k; |
| 129 |
< |
double Tb[3], ji[3]; |
| 130 |
< |
double vel[3], frc[3]; |
| 131 |
< |
double mass; |
| 132 |
< |
double instTemp; |
| 133 |
< |
double oldChi, prevChi; |
| 134 |
< |
|
| 135 |
< |
// Set things up for the iteration: |
| 136 |
< |
|
| 137 |
< |
oldChi = chi; |
| 138 |
< |
|
| 139 |
< |
for( i=0; i < integrableObjects.size(); i++ ){ |
| 140 |
< |
|
| 141 |
< |
integrableObjects[i]->getVel( vel ); |
| 142 |
< |
|
| 143 |
< |
for (j=0; j < 3; j++) |
| 144 |
< |
oldVel[3*i + j] = vel[j]; |
| 145 |
< |
|
| 146 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 147 |
< |
|
| 148 |
< |
integrableObjects[i]->getJ( ji ); |
| 149 |
< |
|
| 150 |
< |
for (j=0; j < 3; j++) |
| 151 |
< |
oldJi[3*i + j] = ji[j]; |
| 152 |
< |
|
| 153 |
< |
} |
| 156 |
> |
currentSnapshot_->setChi(chi); |
| 157 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 158 |
|
} |
| 159 |
|
|
| 160 |
< |
// do the iteration: |
| 160 |
> |
void NVT::moveB() { |
| 161 |
> |
SimInfo::MoleculeIterator i; |
| 162 |
> |
Molecule::IntegrableObjectIterator j; |
| 163 |
> |
Molecule* mol; |
| 164 |
> |
StuntDouble* integrableObject; |
| 165 |
> |
|
| 166 |
> |
Vector3d Tb; |
| 167 |
> |
Vector3d ji; |
| 168 |
> |
Vector3d vel; |
| 169 |
> |
Vector3d frc; |
| 170 |
> |
RealType mass; |
| 171 |
> |
RealType instTemp; |
| 172 |
> |
int index; |
| 173 |
> |
// Set things up for the iteration: |
| 174 |
|
|
| 175 |
< |
for (k=0; k < 4; k++) { |
| 175 |
> |
RealType chi = currentSnapshot_->getChi(); |
| 176 |
> |
RealType oldChi = chi; |
| 177 |
> |
RealType prevChi; |
| 178 |
> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 179 |
|
|
| 180 |
< |
instTemp = tStats->getTemperature(); |
| 180 |
> |
index = 0; |
| 181 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 182 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 183 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 184 |
> |
oldVel_[index] = integrableObject->getVel(); |
| 185 |
> |
oldJi_[index] = integrableObject->getJ(); |
| 186 |
|
|
| 187 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
| 187 |
> |
++index; |
| 188 |
> |
} |
| 189 |
> |
|
| 190 |
> |
} |
| 191 |
|
|
| 192 |
< |
prevChi = chi; |
| 165 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 166 |
< |
(tauThermostat*tauThermostat); |
| 192 |
> |
// do the iteration: |
| 193 |
|
|
| 194 |
< |
for( i=0; i < integrableObjects.size(); i++ ){ |
| 194 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
| 195 |
> |
index = 0; |
| 196 |
> |
instTemp = thermo.getTemperature(); |
| 197 |
|
|
| 198 |
< |
integrableObjects[i]->getFrc( frc ); |
| 171 |
< |
integrableObjects[i]->getVel(vel); |
| 198 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 199 |
|
|
| 200 |
< |
mass = integrableObjects[i]->getMass(); |
| 200 |
> |
prevChi = chi; |
| 201 |
> |
chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 202 |
|
|
| 203 |
< |
// velocity half step |
| 204 |
< |
for (j=0; j < 3; j++) |
| 205 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
| 203 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 204 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 205 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 206 |
|
|
| 207 |
< |
integrableObjects[i]->setVel( vel ); |
| 207 |
> |
frc = integrableObject->getFrc(); |
| 208 |
> |
vel = integrableObject->getVel(); |
| 209 |
|
|
| 210 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 210 |
> |
mass = integrableObject->getMass(); |
| 211 |
|
|
| 212 |
< |
// get and convert the torque to body frame |
| 212 |
> |
// velocity half step |
| 213 |
> |
//for(j = 0; j < 3; j++) |
| 214 |
> |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
| 215 |
> |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 216 |
> |
|
| 217 |
> |
integrableObject->setVel(vel); |
| 218 |
|
|
| 219 |
< |
integrableObjects[i]->getTrq( Tb ); |
| 186 |
< |
integrableObjects[i]->lab2Body( Tb ); |
| 219 |
> |
if (integrableObject->isDirectional()) { |
| 220 |
|
|
| 221 |
< |
for (j=0; j < 3; j++) |
| 189 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 221 |
> |
// get and convert the torque to body frame |
| 222 |
|
|
| 223 |
< |
integrableObjects[i]->setJ( ji ); |
| 192 |
< |
} |
| 193 |
< |
} |
| 194 |
< |
|
| 195 |
< |
if(nConstrained) |
| 196 |
< |
constrainB(); |
| 223 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 224 |
|
|
| 225 |
< |
if (fabs(prevChi - chi) <= chiTolerance) break; |
| 226 |
< |
} |
| 225 |
> |
//for(j = 0; j < 3; j++) |
| 226 |
> |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
| 227 |
> |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 228 |
|
|
| 229 |
< |
integralOfChidt += dt2*chi; |
| 230 |
< |
} |
| 229 |
> |
integrableObject->setJ(ji); |
| 230 |
> |
} |
| 231 |
|
|
| 204 |
– |
template<typename T> void NVT<T>::resetIntegrator( void ){ |
| 232 |
|
|
| 233 |
< |
chi = 0.0; |
| 234 |
< |
integralOfChidt = 0.0; |
| 235 |
< |
} |
| 233 |
> |
++index; |
| 234 |
> |
} |
| 235 |
> |
} |
| 236 |
> |
|
| 237 |
|
|
| 238 |
< |
template<typename T> int NVT<T>::readyCheck() { |
| 238 |
> |
rattle->constraintB(); |
| 239 |
|
|
| 240 |
< |
//check parent's readyCheck() first |
| 241 |
< |
if (T::readyCheck() == -1) |
| 214 |
< |
return -1; |
| 240 |
> |
if (fabs(prevChi - chi) <= chiTolerance_) |
| 241 |
> |
break; |
| 242 |
|
|
| 243 |
< |
// First check to see if we have a target temperature. |
| 217 |
< |
// Not having one is fatal. |
| 243 |
> |
} |
| 244 |
|
|
| 245 |
< |
if (!have_target_temp) { |
| 220 |
< |
sprintf( painCave.errMsg, |
| 221 |
< |
"You can't use the NVT integrator without a targetTemp!\n" |
| 222 |
< |
); |
| 223 |
< |
painCave.isFatal = 1; |
| 224 |
< |
painCave.severity = OOPSE_ERROR; |
| 225 |
< |
simError(); |
| 226 |
< |
return -1; |
| 227 |
< |
} |
| 245 |
> |
integralOfChidt += dt2 * chi; |
| 246 |
|
|
| 247 |
< |
// We must set tauThermostat. |
| 248 |
< |
|
| 231 |
< |
if (!have_tau_thermostat) { |
| 232 |
< |
sprintf( painCave.errMsg, |
| 233 |
< |
"If you use the constant temperature\n" |
| 234 |
< |
"\tintegrator, you must set tauThermostat.\n"); |
| 235 |
< |
painCave.severity = OOPSE_ERROR; |
| 236 |
< |
painCave.isFatal = 1; |
| 237 |
< |
simError(); |
| 238 |
< |
return -1; |
| 247 |
> |
currentSnapshot_->setChi(chi); |
| 248 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 249 |
|
} |
| 250 |
|
|
| 251 |
< |
if (!have_chi_tolerance) { |
| 252 |
< |
sprintf( painCave.errMsg, |
| 253 |
< |
"In NVT integrator: setting chi tolerance to 1e-6\n"); |
| 244 |
< |
chiTolerance = 1e-6; |
| 245 |
< |
have_chi_tolerance = 1; |
| 246 |
< |
painCave.severity = OOPSE_INFO; |
| 247 |
< |
painCave.isFatal = 0; |
| 248 |
< |
simError(); |
| 251 |
> |
void NVT::resetIntegrator() { |
| 252 |
> |
currentSnapshot_->setChi(0.0); |
| 253 |
> |
currentSnapshot_->setIntegralOfChiDt(0.0); |
| 254 |
|
} |
| 255 |
+ |
|
| 256 |
+ |
RealType NVT::calcConservedQuantity() { |
| 257 |
|
|
| 258 |
< |
return 1; |
| 258 |
> |
RealType chi = currentSnapshot_->getChi(); |
| 259 |
> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 260 |
> |
RealType conservedQuantity; |
| 261 |
> |
RealType fkBT; |
| 262 |
> |
RealType Energy; |
| 263 |
> |
RealType thermostat_kinetic; |
| 264 |
> |
RealType thermostat_potential; |
| 265 |
> |
|
| 266 |
> |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
| 267 |
|
|
| 268 |
< |
} |
| 268 |
> |
Energy = thermo.getTotalE(); |
| 269 |
|
|
| 270 |
< |
template<typename T> double NVT<T>::getConservedQuantity(void){ |
| 270 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 271 |
|
|
| 272 |
< |
double conservedQuantity; |
| 258 |
< |
double fkBT; |
| 259 |
< |
double Energy; |
| 260 |
< |
double thermostat_kinetic; |
| 261 |
< |
double thermostat_potential; |
| 272 |
> |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 273 |
|
|
| 274 |
< |
fkBT = (double)(info->ndf) * kB * targetTemp; |
| 274 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 275 |
|
|
| 276 |
< |
Energy = tStats->getTotalE(); |
| 276 |
> |
return conservedQuantity; |
| 277 |
> |
} |
| 278 |
|
|
| 267 |
– |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 268 |
– |
(2.0 * eConvert); |
| 279 |
|
|
| 280 |
< |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 271 |
< |
|
| 272 |
< |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 273 |
< |
|
| 274 |
< |
return conservedQuantity; |
| 275 |
< |
} |
| 276 |
< |
|
| 277 |
< |
template<typename T> string NVT<T>::getAdditionalParameters(void){ |
| 278 |
< |
string parameters; |
| 279 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 280 |
< |
char buffer[BUFFERSIZE]; |
| 281 |
< |
|
| 282 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 283 |
< |
parameters += buffer; |
| 284 |
< |
|
| 285 |
< |
return parameters; |
| 286 |
< |
} |
| 280 |
> |
}//end namespace oopse |
