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root/OpenMD/branches/development/src/integrators/NVE.cpp

Comparing:
trunk/src/integrators/NVE.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/integrators/NVE.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 49 | Line 50
50
51		#include "integrators/NVE.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54
55	<	namespace oopse {
55	>	namespace OpenMD {
56
57
58		NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
#	Line 68 | Line 69 | namespace oopse {
69		Vector3d frc;
70		Vector3d Tb;
71		Vector3d ji;
72	<	double mass;
72	>	RealType mass;
73
74		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
75		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 80 | Line 81 | namespace oopse {
81		mass = integrableObject->getMass();
82
83		// velocity half step
84	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
84	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
85
86		// position whole step
87		pos += dt * vel;
#	Line 98 | Line 99 | namespace oopse {
99
100		ji = integrableObject->getJ();
101
102	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
102	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
103
104		rotAlgo->rotate(integrableObject, ji, dt);
105
#	Line 122 | Line 123 | namespace oopse {
123		Vector3d frc;
124		Vector3d Tb;
125		Vector3d ji;
126	<	double mass;
126	>	RealType mass;
127
128		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
129		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 133 | Line 134 | namespace oopse {
134		mass = integrableObject->getMass();
135
136		// velocity half step
137	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
137	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
138
139		integrableObject->setVel(vel);
140
#	Line 147 | Line 148 | namespace oopse {
148
149		ji = integrableObject->getJ();
150
151	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
151	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
152
153		integrableObject->setJ(ji);
154		}
#	Line 162 | Line 163 | namespace oopse {
163		}
164
165
166	<	double NVE::calcConservedQuantity() {
167	<	return thermo.getTotalE();
166	>	RealType NVE::calcConservedQuantity() {
167	>	return thermo.getTotalE() ;
168		}
169
170	<	} //end namespace oopse
170	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/NVE.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/integrators/NVE.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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