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root/OpenMD/trunk/src/flucq/FluctuatingChargeNVT.cpp
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Comparing:
branches/development/src/flucq/FluctuatingChargeNVT.cpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC vs.
trunk/src/flucq/FluctuatingChargeNVT.cpp (file contents), Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 45 | Line 45
45   #include "utils/simError.h"
46   #include "utils/PhysicalConstants.hpp"
47  
48 +
49   namespace OpenMD {
50  
51    FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
52 <    FluctuatingChargePropagator(info), chiTolerance_ (1e-6),
53 <    maxIterNum_(4), thermo(info),
54 <    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
55 <    
56 <    if (hasFlucQ_) {    
52 >    FluctuatingChargePropagator(info), maxIterNum_(4), chiTolerance_ (1e-6),
53 >    snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {  
54 >  }
55 >
56 >  void FluctuatingChargeNVT::initialize() {
57 >    FluctuatingChargePropagator::initialize();  
58 >    if (hasFlucQ_) {
59        if (info_->getSimParams()->haveDt()) {
60          dt_ = info_->getSimParams()->getDt();
61          dt2_ = dt_ * 0.5;
# Line 64 | Line 67 | namespace OpenMD {
67        }
68        
69        if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
70 <        currentSnapshot_->setChiElectronic(0.0);
68 <        currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
70 >        snap->setElectronicThermostat(make_pair(0.0, 0.0));
71        }
72        
73        if (!fqParams_->haveTargetTemp()) {
# Line 90 | Line 92 | namespace OpenMD {
92        } else {
93          tauThermostat_ = fqParams_->getTauThermostat();
94        }
95 <      updateSizes();
95 >      updateSizes();
96      }
97    }
98  
97 –  void FluctuatingChargeNVT::initialize() {
98 –    FluctuatingChargePropagator::initialize();
99 –  }
99  
101 –
100    void FluctuatingChargeNVT::moveA() {
101  
102      if (!hasFlucQ_) return;
# Line 109 | Line 107 | namespace OpenMD {
107      Atom* atom;
108      RealType cvel, cpos, cfrc, cmass;
109  
110 <    RealType chi = currentSnapshot_->getChiElectronic();
111 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
110 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
111 >    RealType chi = thermostat.first;
112 >    RealType integralOfChidt = thermostat.second;
113      RealType instTemp = thermo.getElectronicTemperature();
114  
116 –
115      for (mol = info_->beginMolecule(i); mol != NULL;
116           mol = info_->nextMolecule(i)) {
117        for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
# Line 122 | Line 120 | namespace OpenMD {
120          cvel = atom->getFlucQVel();
121          cpos = atom->getFlucQPos();
122          cfrc = atom->getFlucQFrc();
123 <        cmass = atom->getChargeMass();
124 <        
127 <        cerr << atom->getType() << "\n";
128 <        cerr << "Before\n";
129 <        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\tcfrc: " << cfrc << "\tcmass: " << cmass << "\n";
130 <        
123 >        cmass = atom->getChargeMass();      
124 >
125          // velocity half step
126          cvel += dt2_ * cfrc / cmass - dt2_*chi*cvel;                    
127          // position whole step
128          cpos += dt_ * cvel;
129          
136 –        cerr << "After\n";
137 –        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\n\n";        
138 –
130          atom->setFlucQVel(cvel);
131          atom->setFlucQPos(cpos);
132        }
# Line 145 | Line 136 | namespace OpenMD {
136        (tauThermostat_ * tauThermostat_);
137  
138      integralOfChidt += chi * dt2_;
139 <    cerr << "Move A instTemp: " << instTemp << "\n";
149 <    currentSnapshot_->setChiElectronic(chi);
150 <    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
151 <      
139 >    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
140    }
141  
142    void FluctuatingChargeNVT::updateSizes() {
155 –    if (!hasFlucQ_) return;
143      oldVel_.resize(info_->getNFluctuatingCharges());
144    }
145  
# Line 163 | Line 150 | namespace OpenMD {
150      Molecule* mol;
151      Atom* atom;
152      RealType instTemp;
153 <    RealType chi = currentSnapshot_->getChiElectronic();
153 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
154 >    RealType chi = thermostat.first;
155      RealType oldChi = chi;
156      RealType prevChi;
157 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
157 >    RealType integralOfChidt = thermostat.second;
158      int index;
159      RealType cfrc, cvel, cmass;
160  
# Line 186 | Line 174 | namespace OpenMD {
174      for(int k = 0; k < maxIterNum_; k++) {
175        index = 0;
176        instTemp = thermo.getElectronicTemperature();
189 –      cerr << "MoveB instTemp: " << instTemp << "\n";
177        // evolve chi another half step using the temperature at t + dt/2
178        prevChi = chi;
179        chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
# Line 198 | Line 185 | namespace OpenMD {
185               atom = mol->nextFluctuatingCharge(j)) {
186  
187            cfrc = atom->getFlucQFrc();
201 –          cvel =atom->getFlucQVel();
188            cmass = atom->getChargeMass();
189            
190            // velocity half step
191            cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_*chi*oldVel_[index];
206 –          
192            atom->setFlucQVel(cvel);      
193            ++index;          
194          }
# Line 212 | Line 197 | namespace OpenMD {
197          break;
198      }
199      integralOfChidt += dt2_ * chi;
200 <    currentSnapshot_->setChiElectronic(chi);
216 <    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
200 >    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
201    }
202    
203    void FluctuatingChargeNVT::resetPropagator() {
204      if (!hasFlucQ_) return;
205 <    currentSnapshot_->setChiElectronic(0.0);
222 <    currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
205 >    snap->setElectronicThermostat(make_pair(0.0, 0.0));
206    }
207    
208    RealType FluctuatingChargeNVT::calcConservedQuantity() {
209      if (!hasFlucQ_) return 0.0;
210 <    RealType chi = currentSnapshot_->getChiElectronic();
211 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
210 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
211 >    RealType chi = thermostat.first;
212 >    RealType integralOfChidt = thermostat.second;
213      RealType fkBT = info_->getNFluctuatingCharges() *
214        PhysicalConstants::kB *targetTemp_;
215  

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