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Comparing branches/development/src/flucq/FluctuatingChargeNVT.cpp (file contents):
Revision 1739 by gezelter, Tue Jun 5 17:58:55 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 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, ForceManager* fm) :
52 <    FluctuatingChargePropagator(info, fm), chiTolerance_ (1e-6),
53 <    maxIterNum_(4), thermo(info),
54 <    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
55 <    
56 <    if (hasFlucQ_) {    
51 >  FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
52 >    FluctuatingChargePropagator(info), chiTolerance_ (1e-6),
53 >    maxIterNum_(4), thermo(info),
54 >    snap(info->getSnapshotManager()->getCurrentSnapshot()) {  
55 >  }
56 >
57 >  void FluctuatingChargeNVT::initialize() {
58 >    FluctuatingChargePropagator::initialize();  
59 >    if (hasFlucQ_) {
60        if (info_->getSimParams()->haveDt()) {
61          dt_ = info_->getSimParams()->getDt();
62          dt2_ = dt_ * 0.5;
# Line 64 | Line 68 | namespace OpenMD {
68        }
69        
70        if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
71 <        currentSnapshot_->setChiElectronic(0.0);
68 <        currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
71 >        snap->setElectronicThermostat(make_pair(0.0, 0.0));
72        }
73        
74        if (!fqParams_->haveTargetTemp()) {
# Line 90 | Line 93 | namespace OpenMD {
93        } else {
94          tauThermostat_ = fqParams_->getTauThermostat();
95        }
96 <      updateSizes();
96 >      updateSizes();
97      }
98    }
99  
97 –  void FluctuatingChargeNVT::initialize() {
98 –    FluctuatingChargePropagator::initialize();
99 –  }
100  
101 –
101    void FluctuatingChargeNVT::moveA() {
102  
103      if (!hasFlucQ_) return;
# Line 109 | Line 108 | namespace OpenMD {
108      Atom* atom;
109      RealType cvel, cpos, cfrc, cmass;
110  
111 <    RealType chi = currentSnapshot_->getChiElectronic();
112 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
111 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
112 >    RealType chi = thermostat.first;
113 >    RealType integralOfChidt = thermostat.second;
114      RealType instTemp = thermo.getElectronicTemperature();
115  
116 –
116      for (mol = info_->beginMolecule(i); mol != NULL;
117           mol = info_->nextMolecule(i)) {
118        for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
# Line 122 | Line 121 | namespace OpenMD {
121          cvel = atom->getFlucQVel();
122          cpos = atom->getFlucQPos();
123          cfrc = atom->getFlucQFrc();
124 <        cmass = atom->getChargeMass();
125 <        
127 <        cerr << atom->getType() << "\n";
128 <        cerr << "Before\n";
129 <        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\tcfrc: " << cfrc << "\tcmass: " << cmass << "\n";
130 <        
124 >        cmass = atom->getChargeMass();      
125 >
126          // velocity half step
127          cvel += dt2_ * cfrc / cmass - dt2_*chi*cvel;                    
128          // position whole step
129          cpos += dt_ * cvel;
130          
136 –        cerr << "After\n";
137 –        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\n\n";        
138 –
131          atom->setFlucQVel(cvel);
132          atom->setFlucQPos(cpos);
133        }
# Line 145 | Line 137 | namespace OpenMD {
137        (tauThermostat_ * tauThermostat_);
138  
139      integralOfChidt += chi * dt2_;
140 <    cerr << "Move A instTemp: " << instTemp << "\n";
149 <    currentSnapshot_->setChiElectronic(chi);
150 <    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
151 <      
140 >    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
141    }
142  
143    void FluctuatingChargeNVT::updateSizes() {
155 –    if (!hasFlucQ_) return;
144      oldVel_.resize(info_->getNFluctuatingCharges());
145    }
146  
# Line 163 | Line 151 | namespace OpenMD {
151      Molecule* mol;
152      Atom* atom;
153      RealType instTemp;
154 <    RealType chi = currentSnapshot_->getChiElectronic();
154 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
155 >    RealType chi = thermostat.first;
156      RealType oldChi = chi;
157      RealType prevChi;
158 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
158 >    RealType integralOfChidt = thermostat.second;
159      int index;
160      RealType cfrc, cvel, cmass;
161  
# Line 186 | Line 175 | namespace OpenMD {
175      for(int k = 0; k < maxIterNum_; k++) {
176        index = 0;
177        instTemp = thermo.getElectronicTemperature();
189 –      cerr << "MoveB instTemp: " << instTemp << "\n";
178        // evolve chi another half step using the temperature at t + dt/2
179        prevChi = chi;
180        chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
# Line 198 | Line 186 | namespace OpenMD {
186               atom = mol->nextFluctuatingCharge(j)) {
187  
188            cfrc = atom->getFlucQFrc();
201 –          cvel =atom->getFlucQVel();
189            cmass = atom->getChargeMass();
190            
191            // velocity half step
192            cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_*chi*oldVel_[index];
206 –          
193            atom->setFlucQVel(cvel);      
194            ++index;          
195          }
# Line 212 | Line 198 | namespace OpenMD {
198          break;
199      }
200      integralOfChidt += dt2_ * chi;
201 <    currentSnapshot_->setChiElectronic(chi);
216 <    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
201 >    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
202    }
203    
204    void FluctuatingChargeNVT::resetPropagator() {
205      if (!hasFlucQ_) return;
206 <    currentSnapshot_->setChiElectronic(0.0);
222 <    currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
206 >    snap->setElectronicThermostat(make_pair(0.0, 0.0));
207    }
208    
209    RealType FluctuatingChargeNVT::calcConservedQuantity() {
210      if (!hasFlucQ_) return 0.0;
211 <    RealType chi = currentSnapshot_->getChiElectronic();
212 <    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
211 >    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
212 >    RealType chi = thermostat.first;
213 >    RealType integralOfChidt = thermostat.second;
214      RealType fkBT = info_->getNFluctuatingCharges() *
215        PhysicalConstants::kB *targetTemp_;
216  

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