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root/OpenMD/trunk/src/integrators/NPTi.cpp
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Comparing trunk/src/integrators/NPTi.cpp (file contents):
Revision 546 by tim, Sun May 29 00:06:14 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 "NPTi.hpp"
# Line 44 | Line 44
44   #include "brains/Thermo.hpp"
45   #include "integrators/NPT.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    // Basic isotropic thermostating and barostating via the Melchionna
53    // modification of the Hoover algorithm:
# Line 65 | Line 65 | namespace oopse {
65  
66    void NPTi::evolveEtaA() {
67      eta += dt2 * ( instaVol * (instaPress - targetPressure) /
68 <                   (OOPSEConstant::pressureConvert*NkBT*tb2));
68 >                   (PhysicalConstants::pressureConvert*NkBT*tb2));
69      oldEta = eta;
70    }
71  
# Line 73 | Line 73 | namespace oopse {
73  
74      prevEta = eta;
75      eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
76 <                           (OOPSEConstant::pressureConvert*NkBT*tb2));
76 >                           (PhysicalConstants::pressureConvert*NkBT*tb2));
77    }
78  
79    void NPTi::calcVelScale() {
# Line 92 | Line 92 | namespace oopse {
92    void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
93                           int index, Vector3d& sc){
94      /**@todo*/
95 <    sc  = (oldPos[index] + pos)/2.0 -COM;
95 >    sc  = (oldPos[index] + pos)/(RealType)2.0 -COM;
96      sc *= eta;
97    }
98  
99    void NPTi::scaleSimBox(){
100  
101 <    double scaleFactor;
101 >    RealType scaleFactor;
102  
103      scaleFactor = exp(dt*eta);
104  
# Line 123 | Line 123 | namespace oopse {
123      return ( fabs(prevEta - eta) <= etaTolerance );
124    }
125  
126 <  double NPTi::calcConservedQuantity(){
126 >  RealType NPTi::calcConservedQuantity(){
127  
128      chi= currentSnapshot_->getChi();
129      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 Energy;
143 <    double thermostat_kinetic;
144 <    double thermostat_potential;
145 <    double barostat_kinetic;
146 <    double barostat_potential;
141 >    RealType conservedQuantity;
142 >    RealType Energy;
143 >    RealType thermostat_kinetic;
144 >    RealType thermostat_potential;
145 >    RealType barostat_kinetic;
146 >    RealType barostat_potential;
147  
148      Energy =thermo.getTotalE();
149  
150 <    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
150 >    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * PhysicalConstants::energyConvert);
151  
152 <    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
152 >    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
153  
154  
155 <    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
155 >    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert);
156  
157 <    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
158 <      OOPSEConstant::energyConvert;
157 >    barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /
158 >      PhysicalConstants::energyConvert;
159  
160      conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
161        barostat_kinetic + barostat_potential;
# Line 166 | Line 166 | namespace oopse {
166    void NPTi::loadEta() {
167      Mat3x3d etaMat = currentSnapshot_->getEta();
168      eta = etaMat(0,0);
169 <    //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) {
169 >    //if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) {
170      //    sprintf( painCave.errMsg,
171      //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
172      //    painCave.isFatal = 1;

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