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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1389 by gezelter, Wed Oct 22 20:01:49 2008 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 <math.h>
# Line 49 | Line 49
49   #include "brains/Thermo.hpp"
50   #include "primitives/Molecule.hpp"
51   #include "utils/simError.h"
52 < #include "utils/OOPSEConstant.hpp"
52 > #include "utils/PhysicalConstants.hpp"
53  
54 < namespace oopse {
54 > namespace OpenMD {
55  
56    RealType Thermo::getKinetic() {
57      SimInfo::MoleculeIterator miter;
# Line 103 | Line 103 | namespace oopse {
103  
104   #endif //is_mpi
105  
106 <    kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
106 >    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107  
108      return kinetic;
109    }
# Line 139 | Line 139 | namespace oopse {
139  
140    RealType Thermo::getTemperature() {
141      
142 <    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142 >    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143      return temperature;
144    }
145  
# Line 158 | Line 158 | namespace oopse {
158  
159      tensor = getPressureTensor();
160  
161 <    pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161 >    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162  
163      return pressure;
164    }
# Line 173 | Line 173 | namespace oopse {
173  
174      tensor = getPressureTensor();
175  
176 <    pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
176 >    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177  
178      return pressure;
179    }
# Line 210 | Line 210 | namespace oopse {
210      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211      Mat3x3d tau = curSnapshot->statData.getTau();
212  
213 <    pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
213 >    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
214      
215      return pressureTensor;
216    }
# Line 304 | Line 304 | namespace oopse {
304      
305    }
306  
307 < } //end namespace oopse
307 > } //end namespace OpenMD

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