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

Comparing:
trunk/src/integrators/Integrator.cpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/integrators/Integrator.cpp (file contents), Revision 1755 by gezelter, Thu Jun 14 01:58:35 2012 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		#include "brains/Snapshot.hpp"
44		#include "integrators/Integrator.hpp"
45	+	#include "integrators/DLM.hpp"
46	+	#include "flucq/FluctuatingChargeNVT.hpp"
47		#include "utils/simError.h"
48	<	namespace oopse {
48	>
49	>	namespace OpenMD {
50		Integrator::Integrator(SimInfo* info)
51		: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
52		needReset(false), velocitizer_(NULL), needVelocityScaling(false),
53	<	rnemd_(NULL), useRNEMD(false),
54	<	dumpWriter(NULL), statWriter(NULL), thermo(info),
53	>	rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
54	>	rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
55		currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
52	–
53	–	simParams = info->getSimParams();
54	–
55	–	if (simParams->haveDt()) {
56	–	dt = simParams->getDt();
57	–	} else {
58	–	sprintf(painCave.errMsg,
59	–	"Integrator Error: dt is not set\n");
60	–	painCave.isFatal = 1;
61	–	simError();
62	–	}
56
57	<	if (simParams->haveRunTime()) {
58	<	runTime = simParams->getRunTime();
59	<	} else {
60	<	sprintf(painCave.errMsg,
61	<	"Integrator Error: runTime is not set\n");
62	<	painCave.isFatal = 1;
63	<	simError();
64	<	}
65	<	// set the status, sample, and thermal kick times
66	<	if (simParams->haveSampleTime()){
67	<	sampleTime = simParams->getSampleTime();
68	<	statusTime = sampleTime;
69	<	} else{
70	<	sampleTime = simParams->getRunTime();
71	<	statusTime = sampleTime;
72	<	}
57	>	simParams = info->getSimParams();
58	>
59	>	if (simParams->haveDt()) {
60	>	dt = simParams->getDt();
61	>	} else {
62	>	sprintf(painCave.errMsg,
63	>	"Integrator Error: dt is not set\n");
64	>	painCave.isFatal = 1;
65	>	simError();
66	>	}
67	>
68	>	if (simParams->haveRunTime()) {
69	>	runTime = simParams->getRunTime();
70	>	} else {
71	>	sprintf(painCave.errMsg,
72	>	"Integrator Error: runTime is not set\n");
73	>	painCave.isFatal = 1;
74	>	simError();
75	>	}
76	>
77	>	// set the status, sample, and thermal kick times
78	>	if (simParams->haveSampleTime()){
79	>	sampleTime = simParams->getSampleTime();
80	>	statusTime = sampleTime;
81	>	} else{
82	>	sampleTime = simParams->getRunTime();
83	>	statusTime = sampleTime;
84	>	}
85	>
86	>	if (simParams->haveStatusTime()){
87	>	statusTime = simParams->getStatusTime();
88	>	}
89	>
90	>	if (simParams->haveThermalTime()){
91	>	thermalTime = simParams->getThermalTime();
92	>	} else {
93	>	thermalTime = simParams->getRunTime();
94	>	}
95	>
96	>	if (!simParams->getUseInitalTime()) {
97	>	currentSnapshot_->setTime(0.0);
98	>	}
99	>
100	>	if (simParams->haveResetTime()) {
101	>	needReset = true;
102	>	resetTime = simParams->getResetTime();
103	>	}
104	>
105	>	// Create a default ForceManager: If the subclass wants to use
106	>	// a different ForceManager, use setForceManager
107	>	forceMan_ = new ForceManager(info);
108	>
109	>	// check for the temperature set flag (velocity scaling)
110	>	if (simParams->haveTempSet()) {
111	>	needVelocityScaling = simParams->getTempSet();
112
113	<	if (simParams->haveStatusTime()){
114	<	statusTime = simParams->getStatusTime();
113	>	if (simParams->haveTargetTemp()) {
114	>	targetScalingTemp = simParams->getTargetTemp();
115		}
116	+	else {
117	+	sprintf(painCave.errMsg,
118	+	"Integrator Error: Target Temperature is not set\n");
119	+	painCave.isFatal = 1;
120	+	simError();
121
85	–	if (simParams->haveThermalTime()){
86	–	thermalTime = simParams->getThermalTime();
87	–	} else {
88	–	thermalTime = simParams->getRunTime();
122		}
123	<
91	<	if (!simParams->getUseInitalTime()) {
92	<	currentSnapshot_->setTime(0.0);
93	<	}
94	<
95	<	if (simParams->haveResetTime()) {
96	<	needReset = true;
97	<	resetTime = simParams->getResetTime();
98	<	}
99	<
100	<
101	<	if (simParams->haveUseRNEMD()) {
102	<	if (simParams->getUseRNEMD()) {
103	<	useRNEMD = simParams->getUseRNEMD();
104	<	if (simParams->haveRNEMD_swapTime()) {
105	<	RNEMD_swapTime = simParams->getRNEMD_swapTime();
106	<	}
107	<	}
108	<	}
109	<
110	<	// Create a default ForceManager: If the subclass wants to use
111	<	// a different ForceManager, use setForceManager
112	<	forceMan_ = new ForceManager(info);
123	>	}
124
125	<	// check for the temperature set flag (velocity scaling)
126	<	if (simParams->haveTempSet()) {
127	<	needVelocityScaling = simParams->getTempSet();
117	<
118	<	if (simParams->haveTargetTemp()) {
119	<	targetScalingTemp = simParams->getTargetTemp();
120	<	}
121	<	else {
122	<	sprintf(painCave.errMsg,
123	<	"Integrator Error: Target Temperature is not set\n");
124	<	painCave.isFatal = 1;
125	<	simError();
126	<
127	<	}
128	<	}
125	>	// Create a default a velocitizer: If the subclass wants to use
126	>	// a different velocitizer, use setVelocitizer
127	>	velocitizer_ = new Velocitizer(info);
128
129	<	// Create a default a velocitizer: If the subclass wants to use
130	<	// a different velocitizer, use setVelocitizer
131	<	velocitizer_ = new Velocitizer(info);
132	<	// Create a default a RNEMD.
133	<	rnemd_ = new RNEMD(info);
134	<
129	>	if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
130	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
131	>	// Create a default a RNEMD.
132	>	rnemd_ = new RNEMD(info);
133	>	useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
134	>	if (simParams->getRNEMDParameters()->haveExchangeTime()) {
135	>	RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
136	>	}
137	>	}
138		}
139	<
139	>
140	>	rotAlgo_ = new DLM();
141	>	rattle_ = new Rattle(info);
142	>	//forceMan_->initialize();
143	>	flucQ_ = new FluctuatingChargeNVT(info, forceMan_);
144	>	}
145	>
146		Integrator::~Integrator(){
147		delete forceMan_;
148		delete velocitizer_;
149		delete rnemd_;
150	+	delete flucQ_;
151	+	delete rotAlgo_;
152	+	delete rattle_;
153
154		delete dumpWriter;
155		delete statWriter;
156		}
146	–
147	–
157		}
158

Comparing:
trunk/src/integrators/Integrator.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/integrators/Integrator.cpp (property svn:keywords), Revision 1755 by gezelter, Thu Jun 14 01:58:35 2012 UTC

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