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root/OpenMD/trunk/src/integrators/NPAT.cpp
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Comparing trunk/src/integrators/NPAT.cpp (file contents):
Revision 538 by tim, Thu May 19 21:31:23 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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 "brains/SimInfo.hpp"
# Line 44 | Line 44
44   #include "integrators/IntegratorCreator.hpp"
45   #include "integrators/NPAT.hpp"
46   #include "primitives/Molecule.hpp"
47 < #include "utils/OOPSEConstant.hpp"
47 > #include "utils/PhysicalConstants.hpp"
48   #include "utils/simError.h"
49  
50 < namespace oopse {
50 > namespace OpenMD {
51    
52    void NPAT::evolveEtaA() {
53  
54 <    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
54 >    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
55      oldEta = eta;  
56    }
57  
# Line 59 | Line 59 | namespace oopse {
59  
60      prevEta = eta;
61      eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
62 <            (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
62 >            (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
63    }
64  
65    void NPAT::calcVelScale(){
# Line 86 | Line 86 | namespace oopse {
86    void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
87  
88      /**@todo */
89 <    Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
89 >    Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
90      sc = eta * rj;
91    }
92  
# Line 110 | Line 110 | namespace oopse {
110  
111    bool NPAT::etaConverged() {
112      int i;
113 <    double diffEta, sumEta;
113 >    RealType diffEta, sumEta;
114  
115      sumEta = 0;
116      for(i = 0; i < 3; i++) {
# Line 122 | Line 122 | namespace oopse {
122      return ( diffEta <= etaTolerance );
123    }
124  
125 <  double NPAT::calcConservedQuantity(){
125 >  RealType NPAT::calcConservedQuantity(){
126  
127      chi= currentSnapshot_->getChi();
128      integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
# Line 131 | Line 131 | namespace oopse {
131      // We need NkBT a lot, so just set it here: This is the RAW number
132      // of integrableObjects, so no subtraction or addition of constraints or
133      // orientational degrees of freedom:
134 <    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;
134 >    NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp;
135  
136      // fkBT is used because the thermostat operates on more degrees of freedom
137      // than the barostat (when there are particles with orientational degrees
138      // of freedom).  
139 <    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
139 >    fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp;    
140      
141 <    double conservedQuantity;
142 <    double totalEnergy;
143 <    double thermostat_kinetic;
144 <    double thermostat_potential;
145 <    double barostat_kinetic;
146 <    double barostat_potential;
147 <    double trEta;
141 >    RealType conservedQuantity;
142 >    RealType totalEnergy;
143 >    RealType thermostat_kinetic;
144 >    RealType thermostat_potential;
145 >    RealType barostat_kinetic;
146 >    RealType barostat_potential;
147 >    RealType trEta;
148  
149      totalEnergy = thermo.getTotalE();
150  
151 <    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
151 >    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
152  
153 <    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
153 >    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
154  
155 <    SquareMatrix<double, 3> tmp = eta.transpose() * eta;
155 >    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
156      trEta = tmp.trace();
157      
158 <    barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
158 >    barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
159  
160 <    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
160 >    barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
161  
162      conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
163        barostat_kinetic + barostat_potential;

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