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root/OpenMD/trunk/src/integrators/NPrT.cpp
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Comparing trunk/src/integrators/NPrT.cpp (file contents):
Revision 539 by tim, Fri May 20 16:01:38 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/NPrT.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    NPrT::NPrT(SimInfo* info) : NPT(info) {
52      Globals* simParams = info_->getSimParams();
53      if (!simParams->haveSurfaceTension()) {
54        sprintf(painCave.errMsg,
55                "If you use the NPT integrator, you must set tauBarostat.\n");
56 <      painCave.severity = OOPSE_ERROR;
56 >      painCave.severity = OPENMD_ERROR;
57        painCave.isFatal = 1;
58        simError();
59      } else {
60 <      surfaceTension= simParams->getSurfaceTension();
60 >      surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
61      }
62  
63    }
64    void NPrT::evolveEtaA() {
65      Mat3x3d hmat = currentSnapshot_->getHmat();
66 <    double hz = hmat(2, 2);
67 <    double Axy = hmat(0,0) * hmat(1, 1);
68 <    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
69 <    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
70 <    eta(0,0) -= Axy * (sx - surfaceTension) / (NkBT*tb2);
71 <    eta(1,1) -= Axy * (sy - surfaceTension) / (NkBT*tb2);
72 <    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
66 >    RealType hz = hmat(2, 2);
67 >    RealType Axy = hmat(0,0) * hmat(1, 1);
68 >    RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
69 >    RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
70 >    eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
71 >    eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
72 >    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
73      oldEta = eta;  
74    }
75  
76    void NPrT::evolveEtaB() {
77      Mat3x3d hmat = currentSnapshot_->getHmat();
78 <    double hz = hmat(2, 2);
79 <    double Axy = hmat(0,0) * hmat(1, 1);
78 >    RealType hz = hmat(2, 2);
79 >    RealType Axy = hmat(0,0) * hmat(1, 1);
80      prevEta = eta;
81 <    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
82 <    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
83 <    eta(0,0) = oldEta(0, 0) - Axy * (sx -surfaceTension) / (NkBT*tb2);
84 <    eta(1,1) = oldEta(1, 1) - Axy * (sy -surfaceTension) / (NkBT*tb2);
81 >    RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
82 >    RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
83 >    eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2);
84 >    eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2);
85      eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
86 <            (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
86 >            (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
87    }
88  
89    void NPrT::calcVelScale(){
# Line 110 | Line 110 | namespace oopse {
110    void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
111  
112      /**@todo */
113 <    Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
113 >    Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
114      sc = eta * rj;
115    }
116  
# Line 128 | Line 128 | namespace oopse {
128  
129    bool NPrT::etaConverged() {
130      int i;
131 <    double diffEta, sumEta;
131 >    RealType diffEta, sumEta;
132  
133      sumEta = 0;
134      for(i = 0; i < 3; i++) {
# Line 140 | Line 140 | namespace oopse {
140      return ( diffEta <= etaTolerance );
141    }
142  
143 <  double NPrT::calcConservedQuantity(){
143 >  RealType NPrT::calcConservedQuantity(){
144  
145      chi= currentSnapshot_->getChi();
146      integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
# Line 149 | Line 149 | namespace oopse {
149      // We need NkBT a lot, so just set it here: This is the RAW number
150      // of integrableObjects, so no subtraction or addition of constraints or
151      // orientational degrees of freedom:
152 <    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;
152 >    NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp;
153  
154      // fkBT is used because the thermostat operates on more degrees of freedom
155      // than the barostat (when there are particles with orientational degrees
156      // of freedom).  
157 <    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
157 >    fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp;    
158      
159  
160 <    double totalEnergy = thermo.getTotalE();
160 >    RealType totalEnergy = thermo.getTotalE();
161  
162 <    double thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
162 >    RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
163  
164 <    double thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
164 >    RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
165  
166 <    SquareMatrix<double, 3> tmp = eta.transpose() * eta;
167 <    double trEta = tmp.trace();
166 >    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
167 >    RealType trEta = tmp.trace();
168      
169 <    double barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
169 >    RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
170  
171 <    double barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
171 >    RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
172  
173      Mat3x3d hmat = currentSnapshot_->getHmat();
174 <    double hz = hmat(2, 2);
175 <    double area = hmat(0,0) * hmat(1, 1);
174 >    RealType hz = hmat(2, 2);
175 >    RealType area = hmat(0,0) * hmat(1, 1);
176  
177 <    double conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
178 <      barostat_kinetic + barostat_potential - surfaceTension * area;
177 >    RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
178 >      barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert;
179  
180      return conservedQuantity;
181  

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