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root/OpenMD/trunk/src/integrators/NVT.cpp
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Comparing trunk/src/integrators/NVT.cpp (file contents):
Revision 271 by tim, Mon Jan 17 16:58:32 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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) {
49 >  NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
50  
51      Globals* simParams = info_->getSimParams();
52  
53 <    if (!simParams->getUseInitXSstate()) {
54 <        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55 <        currSnapshot->setChi(0.0);
56 <        currSnapshot->setIntegralOfChiDt(0.0);
53 >    if (!simParams->getUseIntialExtendedSystemState()) {
54 >      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55 >      currSnapshot->setChi(0.0);
56 >      currSnapshot->setIntegralOfChiDt(0.0);
57      }
58      
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();
60 >      sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
61 >      painCave.isFatal = 1;
62 >      painCave.severity = OPENMD_ERROR;
63 >      simError();
64      } else {
65 <        targetTemp_ = simParams->getTargetTemp();
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");
71 >      sprintf(painCave.errMsg, "If you use the constant temperature\n"
72 >              "\tintegrator, you must set tauThermostat.\n");
73  
74 <        painCave.severity = OOPSE_ERROR;
75 <        painCave.isFatal = 1;
76 <        simError();
74 >      painCave.severity = OPENMD_ERROR;
75 >      painCave.isFatal = 1;
76 >      simError();
77      } else {
78 <        tauThermostat_ = simParams->getTauThermostat();
78 >      tauThermostat_ = simParams->getTauThermostat();
79      }
80  
81      update();
82 < }
82 >  }
83  
84 < void NVT::doUpdate() {
84 >  void NVT::doUpdate() {
85      oldVel_.resize(info_->getNIntegrableObjects());
86      oldJi_.resize(info_->getNIntegrableObjects());    
87 < }
88 < void NVT::moveA() {
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 <    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;
109 <               integrableObject = mol->nextIntegrableObject(j)) {
108 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
109 >           integrableObject = mol->nextIntegrableObject(j)) {
110  
111          vel = integrableObject->getVel();
112          pos = integrableObject->getPos();
# Line 115 | Line 115 | void NVT::moveA() {
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 127 | Line 127 | void NVT::moveA() {
127  
128          if (integrableObject->isDirectional()) {
129  
130 <            //convert the torque to body frame
131 <            Tb = integrableObject->lab2Body(integrableObject->getTrq());
130 >          //convert the torque to body frame
131 >          Tb = integrableObject->lab2Body(integrableObject->getTrq());
132  
133 <            // get the angular momentum, and propagate a half step
133 >          // get the angular momentum, and propagate a half step
134  
135 <            ji = integrableObject->getJ();
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;
139 <            rotAlgo->rotate(integrableObject, ji, dt);
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);
141 >          integrableObject->setJ(ji);
142          }
143 <    }
143 >      }
144  
145      }
146      
# Line 155 | Line 155 | void NVT::moveA() {
155  
156      currentSnapshot_->setChi(chi);
157      currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
158 < }
158 >  }
159  
160 < void NVT::moveB() {
160 >  void NVT::moveB() {
161      SimInfo::MoleculeIterator i;
162      Molecule::IntegrableObjectIterator  j;
163      Molecule* mol;
# Line 167 | Line 167 | void NVT::moveB() {
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)) {
182 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
183 <               integrableObject = mol->nextIntegrableObject(j)) {
184 <                oldVel_[index] = integrableObject->getVel();
185 <                oldJi_[index] = integrableObject->getJ();                
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 <                ++index;    
188 <        }
187 >        ++index;    
188 >      }
189            
190      }
191  
192      // do the iteration:
193  
194      for(int k = 0; k < maxIterNum_; k++) {
195 <        index = 0;
196 <        instTemp = thermo.getTemperature();
195 >      index = 0;
196 >      instTemp = thermo.getTemperature();
197  
198 <        // evolve chi another half step using the temperature at t + dt/2
198 >      // evolve chi another half step using the temperature at t + dt/2
199  
200 <        prevChi = chi;
201 <        chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
200 >      prevChi = chi;
201 >      chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
202  
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)) {
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 <                frc = integrableObject->getFrc();
208 <                vel = integrableObject->getVel();
207 >          frc = integrableObject->getFrc();
208 >          vel = integrableObject->getVel();
209  
210 <                mass = integrableObject->getMass();
210 >          mass = integrableObject->getMass();
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];
212 >          // velocity half step
213 >          //for(j = 0; j < 3; j++)
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);
217 >          integrableObject->setVel(vel);
218  
219 <                if (integrableObject->isDirectional()) {
219 >          if (integrableObject->isDirectional()) {
220  
221 <                    // get and convert the torque to body frame
221 >            // get and convert the torque to body frame
222  
223 <                    Tb =  integrableObject->lab2Body(integrableObject->getTrq());
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];
225 >            //for(j = 0; j < 3; j++)
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 <                }
229 >            integrableObject->setJ(ji);
230 >          }
231  
232  
233 <                ++index;
234 <            }
235 <        }
233 >          ++index;
234 >        }
235 >      }
236      
237  
238 <        rattle->constraintB();
238 >      rattle->constraintB();
239  
240 <        if (fabs(prevChi - chi) <= chiTolerance_)
241 <            break;
240 >      if (fabs(prevChi - chi) <= chiTolerance_)
241 >        break;
242  
243      }
244  
# Line 246 | Line 246 | void NVT::moveB() {
246  
247      currentSnapshot_->setChi(chi);
248      currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
249 < }
249 >  }
250  
251 +  void NVT::resetIntegrator() {
252 +      currentSnapshot_->setChi(0.0);
253 +      currentSnapshot_->setIntegralOfChiDt(0.0);
254 +  }
255 +  
256 +  RealType NVT::calcConservedQuantity() {
257  
258 < double NVT::calcConservedQuantity() {
259 <
260 <    double chi = currentSnapshot_->getChi();
261 <    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
262 <    double conservedQuantity;
263 <    double fkBT;
264 <    double Energy;
259 <    double thermostat_kinetic;
260 <    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  
276      return conservedQuantity;
277 < }
277 >  }
278  
279  
280 < }//end namespace oopse
280 > }//end namespace OpenMD

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