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root/OpenMD/trunk/src/integrators/NPTsz.cpp
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Comparing trunk/src/integrators/NPTsz.cpp (file contents):
Revision 1519 by gezelter, Tue Oct 26 14:27:28 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 56 | Line 57 | namespace OpenMD {
57     */  
58    RealType NPTsz::calcConservedQuantity(){
59  
60 <    chi= currentSnapshot_->getChi();
60 <    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
60 >    thermostat = snap->getThermostat();
61      loadEta();
62      
63      // We need NkBT a lot, so just set it here: This is the RAW number
# Line 79 | Line 79 | namespace OpenMD {
79      RealType barostat_potential;
80      RealType trEta;
81  
82 <    totalEnergy = thermo.getTotalE();
82 >    totalEnergy = thermo.getTotalEnergy();
83  
84 <    thermostat_kinetic = fkBT * tt2 * chi * chi /
84 >    thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /
85        (2.0 * PhysicalConstants::energyConvert);
86  
87 <    thermostat_potential = fkBT* integralOfChidt /
87 >    thermostat_potential = fkBT* thermostat.second /
88        PhysicalConstants::energyConvert;
89  
90      SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
# Line 106 | Line 106 | namespace OpenMD {
106      
107    void NPTsz::scaleSimBox(){
108  
109 <    int i,j,k;
109 >    int i, j;
110      Mat3x3d scaleMat;
111 <    RealType eta2ij, scaleFactor;
112 <    RealType bigScale, smallScale, offDiagMax;
111 >    RealType scaleFactor;
112 >    RealType bigScale, smallScale;
113      Mat3x3d hm;
114      Mat3x3d hmnew;
115  
# Line 121 | Line 121 | namespace OpenMD {
121  
122      bigScale = 1.0;
123      smallScale = 1.0;
124 –    offDiagMax = 0.0;
124  
125      for(i=0; i<3; i++){
126        for(j=0; j<3; j++){
# Line 161 | Line 160 | namespace OpenMD {
160        simError();
161      } else {
162  
163 <      Mat3x3d hmat = currentSnapshot_->getHmat();
163 >      Mat3x3d hmat = snap->getHmat();
164        hmat = hmat *scaleMat;
165 <      currentSnapshot_->setHmat(hmat);
165 >      snap->setHmat(hmat);
166      }
167    }
168  
169    void NPTsz::loadEta() {
170 <    eta= currentSnapshot_->getEta();
170 >    eta= snap->getBarostat();
171    }
172   }

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