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

Comparing:
trunk/src/integrators/Integrator.cpp (file contents), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/integrators/Integrator.cpp (file contents), Revision 1738 by gezelter, Tue Jun 5 17:58:01 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), needReset(false), velocitizer_(NULL),
52	<	needVelocityScaling(false), dumpWriter(NULL), statWriter(NULL), thermo(info),
51	>	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
52	>	needReset(false), velocitizer_(NULL), needVelocityScaling(false),
53	>	rnemd_(NULL), useRNEMD(false), rotAlgo_(NULL), flucQ_(NULL),
54	>	rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
55		currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
56	+
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
108	<	simParams = info->getSimParams();
52	<
53	<	if (simParams->haveDt()) {
54	<	dt = simParams->getDt();
55	<	} else {
56	<	sprintf(painCave.errMsg,
57	<	"Integrator Error: dt is not set\n");
58	<	painCave.isFatal = 1;
59	<	simError();
60	<	}
108	>	forceMan_ = new ForceManager(info);
109
110	<	if (simParams->haveRunTime()) {
111	<	runTime = simParams->getRunTime();
112	<	} else {
65	<	sprintf(painCave.errMsg,
66	<	"Integrator Error: runTime is not set\n");
67	<	painCave.isFatal = 1;
68	<	simError();
69	<	}
70	<	// set the status, sample, and thermal kick times
71	<	if (simParams->haveSampleTime()){
72	<	sampleTime = simParams->getSampleTime();
73	<	statusTime = sampleTime;
74	<	} else{
75	<	sampleTime = simParams->getRunTime();
76	<	statusTime = sampleTime;
77	<	}
110	>	// check for the temperature set flag (velocity scaling)
111	>	if (simParams->haveTempSet()) {
112	>	needVelocityScaling = simParams->getTempSet();
113
114	<	if (simParams->haveStatusTime()){
115	<	statusTime = simParams->getStatusTime();
114	>	if (simParams->haveTargetTemp()) {
115	>	targetScalingTemp = simParams->getTargetTemp();
116		}
117	+	else {
118	+	sprintf(painCave.errMsg,
119	+	"Integrator Error: Target Temperature is not set\n");
120	+	painCave.isFatal = 1;
121	+	simError();
122
83	–	if (simParams->haveThermalTime()){
84	–	thermalTime = simParams->getThermalTime();
85	–	} else {
86	–	thermalTime = simParams->getRunTime();
123		}
124	<
89	<	if (!simParams->getUseInitalTime()) {
90	<	currentSnapshot_->setTime(0.0);
91	<	}
92	<
93	<	if (simParams->haveResetTime()) {
94	<	needReset = true;
95	<	resetTime = simParams->getResetTime();
96	<	}
97	<
98	<	//create a default ForceManager
99	<	//if the subclass wants to use a different ForceManager, use setForceManager
100	<	forceMan_ = new ForceManager(info);
124	>	}
125
126	<	//set the force manager for thermodynamic integration if specified
127	<	if (simParams->getUseSolidThermInt() || simParams->getUseLiquidThermInt()){
128	<	ThermoIntegrationForceManager* thermoForce_
105	<	= new ThermoIntegrationForceManager(info);
106	<	setForceManager(thermoForce_);
107	<	}
126	>	// Create a default a velocitizer: If the subclass wants to use
127	>	// a different velocitizer, use setVelocitizer
128	>	velocitizer_ = new Velocitizer(info);
129
130	<	// check for the temperature set flag (velocity scaling)
131	<	if (simParams->haveTempSet()) {
132	<	needVelocityScaling = simParams->getTempSet();
133	<
134	<	if (simParams->haveTargetTemp()) {
135	<	targetScalingTemp = simParams->getTargetTemp();
136	<	}
137	<	else {
117	<	sprintf(painCave.errMsg,
118	<	"Integrator Error: Target Temperature is not set\n");
119	<	painCave.isFatal = 1;
120	<	simError();
121	<
122	<	}
130	>	if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
131	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
132	>	// Create a default a RNEMD.
133	>	rnemd_ = new RNEMD(info);
134	>	useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
135	>	if (simParams->getRNEMDParameters()->haveExchangeTime()) {
136	>	RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
137	>	}
138		}
124	–
125	–	//create a default a velocitizer
126	–	//if the subclass want to using different velocitizer, use setVelocitizer
127	–	velocitizer_ = new Velocitizer(info);
128	–
139		}
140	<
140	>
141	>	rotAlgo_ = new DLM();
142	>	rattle_ = new Rattle(info);
143	>	forceMan_->initialize();
144	>	flucQ_ = new FluctuatingChargeNVT(info, forceMan_);
145	>	}
146	>
147		Integrator::~Integrator(){
148		delete forceMan_;
149		delete velocitizer_;
150	+	delete rnemd_;
151	+	delete flucQ_;
152	+	delete rotAlgo_;
153	+	delete rattle_;
154
155		delete dumpWriter;
156		delete statWriter;
157		}
138	–
139	–
158		}
159

Comparing:
trunk/src/integrators/Integrator.cpp (property svn:keywords), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/integrators/Integrator.cpp (property svn:keywords), Revision 1738 by gezelter, Tue Jun 5 17:58:01 2012 UTC

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