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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 1850 by gezelter, Wed Feb 20 15:39:39 2013 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, 234107 (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/FluctuatingChargeLangevin.hpp"
47	+	#include "flucq/FluctuatingChargeNVT.hpp"
48		#include "utils/simError.h"
49	<	namespace oopse {
49	>
50	>	namespace OpenMD {
51		Integrator::Integrator(SimInfo* info)
52		: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
53		needReset(false), velocitizer_(NULL), needVelocityScaling(false),
54	<	rnemd_(NULL), useRNEMD(false),
55	<	dumpWriter(NULL), statWriter(NULL), thermo(info),
56	<	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	<	}
54	>	rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
55	>	rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
56	>	snap(info->getSnapshotManager()->getCurrentSnapshot()) {
57
58	<	if (simParams->haveRunTime()) {
59	<	runTime = simParams->getRunTime();
60	<	} else {
61	<	sprintf(painCave.errMsg,
62	<	"Integrator Error: runTime is not set\n");
63	<	painCave.isFatal = 1;
64	<	simError();
65	<	}
66	<	// set the status, sample, and thermal kick times
67	<	if (simParams->haveSampleTime()){
68	<	sampleTime = simParams->getSampleTime();
69	<	statusTime = sampleTime;
70	<	} else{
71	<	sampleTime = simParams->getRunTime();
72	<	statusTime = sampleTime;
73	<	}
58	>	simParams = info->getSimParams();
59	>
60	>	if (simParams->haveDt()) {
61	>	dt = simParams->getDt();
62	>	} else {
63	>	sprintf(painCave.errMsg,
64	>	"Integrator Error: dt is not set\n");
65	>	painCave.isFatal = 1;
66	>	simError();
67	>	}
68	>
69	>	if (simParams->haveRunTime()) {
70	>	runTime = simParams->getRunTime();
71	>	} else {
72	>	sprintf(painCave.errMsg,
73	>	"Integrator Error: runTime is not set\n");
74	>	painCave.isFatal = 1;
75	>	simError();
76	>	}
77	>
78	>	// set the status, sample, and thermal kick times
79	>	if (simParams->haveSampleTime()){
80	>	sampleTime = simParams->getSampleTime();
81	>	statusTime = sampleTime;
82	>	} else{
83	>	sampleTime = simParams->getRunTime();
84	>	statusTime = sampleTime;
85	>	}
86	>
87	>	if (simParams->haveStatusTime()){
88	>	statusTime = simParams->getStatusTime();
89	>	}
90	>
91	>	if (simParams->haveThermalTime()){
92	>	thermalTime = simParams->getThermalTime();
93	>	} else {
94	>	thermalTime = simParams->getRunTime();
95	>	}
96	>
97	>	if (!simParams->getUseInitalTime()) {
98	>	snap->setTime(0.0);
99	>	}
100	>
101	>	if (simParams->haveResetTime()) {
102	>	needReset = true;
103	>	resetTime = simParams->getResetTime();
104	>	}
105	>
106	>	// Create a default ForceManager: If the subclass wants to use
107	>	// a different ForceManager, use setForceManager
108	>	forceMan_ = new ForceManager(info);
109	>
110	>	// check for the temperature set flag (velocity scaling)
111	>	needVelocityScaling = false;
112	>	if (simParams->haveTempSet()) {
113	>	needVelocityScaling = simParams->getTempSet();
114	>	}
115
116	<	if (simParams->haveStatusTime()){
117	<	statusTime = simParams->getStatusTime();
116	>	if (needVelocityScaling) {
117	>	if (simParams->haveTargetTemp()) {
118	>	targetScalingTemp = simParams->getTargetTemp();
119		}
120	+	else {
121	+	sprintf(painCave.errMsg,
122	+	"Integrator Error: Target Temperature must be set to turn on tempSet\n");
123	+	painCave.isFatal = 1;
124	+	simError();
125
85	–	if (simParams->haveThermalTime()){
86	–	thermalTime = simParams->getThermalTime();
87	–	} else {
88	–	thermalTime = simParams->getRunTime();
126		}
127	<
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);
127	>	}
128
129	<	// check for the temperature set flag (velocity scaling)
130	<	if (simParams->haveTempSet()) {
131	<	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	<	}
129	>	// Create a default a velocitizer: If the subclass wants to use
130	>	// a different velocitizer, use setVelocitizer
131	>	velocitizer_ = new Velocitizer(info);
132
133	<	// Create a default a velocitizer: If the subclass wants to use
134	<	// a different velocitizer, use setVelocitizer
135	<	velocitizer_ = new Velocitizer(info);
136	<	// Create a default a RNEMD.
137	<	rnemd_ = new RNEMD(info);
138	<
133	>	if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
134	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
135	>	// Create a default a RNEMD.
136	>	rnemd_ = new RNEMD(info);
137	>	useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
138	>	if (simParams->getRNEMDParameters()->haveExchangeTime()) {
139	>	RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
140	>	}
141	>	}
142		}
143	<
143	>
144	>	rotAlgo_ = new DLM();
145	>	rattle_ = new Rattle(info);
146	>	flucQ_ = new FluctuatingChargeLangevin(info);
147	>	flucQ_->setForceManager(forceMan_);
148	>	}
149	>
150		Integrator::~Integrator(){
151		delete forceMan_;
152		delete velocitizer_;
153		delete rnemd_;
154	+	delete flucQ_;
155	+	delete rotAlgo_;
156	+	delete rattle_;
157
158		delete dumpWriter;
159		delete statWriter;
160		}
146	–
147	–
161		}
162

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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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