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root/OpenMD/trunk/src/integrators/NPAT.cpp
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Comparing trunk/src/integrators/NPAT.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
42  
43   #include "brains/SimInfo.hpp"
# Line 69 | Line 70 | namespace OpenMD {
70          vScale(i, j) = eta(i, j);
71  
72          if (i == j) {
73 <          vScale(i, j) += chi;
73 >          vScale(i, j) += thermostat.first;
74          }
75        }
76      }
# Line 103 | Line 104 | namespace OpenMD {
104      }
105      
106      scaleMat(2, 2) = exp(dt*eta(2, 2));
107 <    Mat3x3d hmat = currentSnapshot_->getHmat();
107 >    Mat3x3d hmat = snap->getHmat();
108      hmat = hmat *scaleMat;
109 <    currentSnapshot_->setHmat(hmat);
109 >    snap->setHmat(hmat);
110    }
111  
112    bool NPAT::etaConverged() {
# Line 124 | Line 125 | namespace OpenMD {
125  
126    RealType NPAT::calcConservedQuantity(){
127  
128 <    chi= currentSnapshot_->getChi();
128 <    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
128 >    thermostat = snap->getThermostat();
129      loadEta();
130      
131      // We need NkBT a lot, so just set it here: This is the RAW number
# Line 146 | Line 146 | namespace OpenMD {
146      RealType barostat_potential;
147      RealType trEta;
148  
149 <    totalEnergy = thermo.getTotalE();
149 >    totalEnergy = thermo.getTotalEnergy();
150  
151 <    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
151 >    thermostat_kinetic = fkBT * tt2 * thermostat.first *
152 >      thermostat.first /(2.0 * PhysicalConstants::energyConvert);
153  
154 <    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
154 >    thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
155  
156      SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
157      trEta = tmp.trace();
# Line 167 | Line 168 | namespace OpenMD {
168    }
169  
170    void NPAT::loadEta() {
171 <    eta= currentSnapshot_->getEta();
171 >    eta= snap->getBarostat();
172  
173      //if (!eta.isDiagonal()) {
174      //    sprintf( painCave.errMsg,
# Line 178 | Line 179 | namespace OpenMD {
179    }
180  
181    void NPAT::saveEta() {
182 <    currentSnapshot_->setEta(eta);
182 >    snap->setBarostat(eta);
183    }
184  
185   }

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