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root/OpenMD/trunk/src/integrators/NVT.cpp
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Comparing trunk/src/integrators/NVT.cpp (file contents):
Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include "integrators/NVT.hpp"
43   #include "primitives/Molecule.hpp"
44   #include "utils/simError.h"
45 < #include "utils/OOPSEConstant.hpp"
45 > #include "utils/PhysicalConstants.hpp"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
50  
51      Globals* simParams = info_->getSimParams();
52  
53 <    if (!simParams->getUseInitXSstate()) {
53 >    if (!simParams->getUseIntialExtendedSystemState()) {
54        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55        currSnapshot->setChi(0.0);
56        currSnapshot->setIntegralOfChiDt(0.0);
# Line 59 | Line 59 | namespace oopse {
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;
62 >      painCave.severity = OPENMD_ERROR;
63        simError();
64      } else {
65        targetTemp_ = simParams->getTargetTemp();
66      }
67  
68 <    // We must set tauThermostat_.
68 >    // We must set tauThermostat.
69  
70      if (!simParams->haveTauThermostat()) {
71        sprintf(painCave.errMsg, "If you use the constant temperature\n"
72 <              "\tintegrator, you must set tauThermostat_.\n");
72 >              "\tintegrator, you must set tauThermostat.\n");
73  
74 <      painCave.severity = OOPSE_ERROR;
74 >      painCave.severity = OPENMD_ERROR;
75        painCave.isFatal = 1;
76        simError();
77      } else {
# Line 92 | Line 92 | namespace oopse {
92      StuntDouble* integrableObject;
93      Vector3d Tb;
94      Vector3d ji;
95 <    double mass;
95 >    RealType mass;
96      Vector3d vel;
97      Vector3d pos;
98      Vector3d frc;
99  
100 <    double chi = currentSnapshot_->getChi();
101 <    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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 <    double instTemp = thermo.getTemperature();
105 >    RealType instTemp = thermo.getTemperature();
106  
107      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
108        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 115 | Line 115 | namespace oopse {
115          mass = integrableObject->getMass();
116  
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;
118 >        //vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi);
119 >        vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel;
120          
121          // position whole step
122          //pos[j] += dt * vel[j];
# Line 134 | Line 134 | namespace oopse {
134  
135            ji = integrableObject->getJ();
136  
137 <          //ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
138 <          ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji;
137 >          //ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
138 >          ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji;
139            rotAlgo->rotate(integrableObject, ji, dt);
140  
141            integrableObject->setJ(ji);
# Line 167 | Line 167 | namespace oopse {
167      Vector3d ji;    
168      Vector3d vel;
169      Vector3d frc;
170 <    double mass;
171 <    double instTemp;
170 >    RealType mass;
171 >    RealType instTemp;
172      int index;
173      // Set things up for the iteration:
174  
175 <    double chi = currentSnapshot_->getChi();
176 <    double oldChi = chi;
177 <    double  prevChi;
178 <    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
175 >    RealType chi = currentSnapshot_->getChi();
176 >    RealType oldChi = chi;
177 >    RealType  prevChi;
178 >    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
179  
180      index = 0;
181      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
# Line 211 | Line 211 | namespace oopse {
211  
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];
214 >          //    vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi);
215 >          vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index];
216              
217            integrableObject->setVel(vel);
218  
# Line 223 | Line 223 | namespace oopse {
223              Tb =  integrableObject->lab2Body(integrableObject->getTrq());
224  
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];
226 >            //    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi);
227 >            ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index];
228  
229              integrableObject->setJ(ji);
230            }
# Line 253 | Line 253 | namespace oopse {
253        currentSnapshot_->setIntegralOfChiDt(0.0);
254    }
255    
256 <  double NVT::calcConservedQuantity() {
256 >  RealType NVT::calcConservedQuantity() {
257  
258 <    double chi = currentSnapshot_->getChi();
259 <    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
260 <    double conservedQuantity;
261 <    double fkBT;
262 <    double Energy;
263 <    double thermostat_kinetic;
264 <    double thermostat_potential;
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_;
266 >    fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_;
267  
268      Energy = thermo.getTotalE();
269  
270 <    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
270 >    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert);
271  
272 <    thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
272 >    thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert;
273  
274      conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
275  
# Line 277 | Line 277 | namespace oopse {
277    }
278  
279  
280 < }//end namespace oopse
280 > }//end namespace OpenMD

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