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root/OpenMD/trunk/src/integrators/Integrator.cpp

Comparing trunk/src/integrators/Integrator.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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"
45	–	namespace oopse {
46	–	Integrator::Integrator(SimInfo* info)
47	–	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), velocitizer_(NULL),
48	–	needVelocityScaling(false), dumpWriter(NULL), statWriter(NULL), thermo(info),
49	–	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
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), rotAlgo_(NULL), flucQ_(NULL),
55	+	rattle_(NULL), dumpWriter(NULL), statWriter(NULL), thermo(info),
56	+	snap(info->getSnapshotManager()->getCurrentSnapshot()) {
57	+
58		simParams = info->getSimParams();
59	<
59	>
60		if (simParams->haveDt()) {
61	<	dt = simParams->getDt();
61	>	dt = simParams->getDt();
62		} else {
63	<	sprintf(painCave.errMsg,
64	<	"Integrator Error: dt is not set\n");
65	<	painCave.isFatal = 1;
66	<	simError();
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();
70	>	runTime = simParams->getRunTime();
71		} else {
72	<	sprintf(painCave.errMsg,
73	<	"Integrator Error: runTime is not set\n");
74	<	painCave.isFatal = 1;
75	<	simError();
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;
80	>	sampleTime = simParams->getSampleTime();
81	>	statusTime = sampleTime;
82		} else{
83	<	sampleTime = simParams->getRunTime();
84	<	statusTime = sampleTime;
83	>	sampleTime = simParams->getRunTime();
84	>	statusTime = sampleTime;
85		}
86	<
86	>
87		if (simParams->haveStatusTime()){
88	<	statusTime = simParams->getStatusTime();
88	>	statusTime = simParams->getStatusTime();
89		}
90	<
90	>
91		if (simParams->haveThermalTime()){
92	<	thermalTime = simParams->getThermalTime();
92	>	thermalTime = simParams->getThermalTime();
93		} else {
94	<	thermalTime = simParams->getRunTime();
94	>	thermalTime = simParams->getRunTime();
95		}
96	<
97	<	if (!simParams->getUseInitTime()) {
98	<	currentSnapshot_->setTime(0.0);
96	>
97	>	if (!simParams->getUseInitalTime()) {
98	>	snap->setTime(0.0);
99		}
100
101	<	//create a default ForceManager
102	<	//if the subclass wants to use a different ForceManager, use setForceManager
103	<	forceMan_ = new ForceManager(info);
96	<
97	<	//set the force manager for thermodynamic integration if specified
98	<	if (simParams->getUseSolidThermInt() || simParams->getUseLiquidThermInt()){
99	<	ThermoIntegrationForceManager* thermoForce_
100	<	= new ThermoIntegrationForceManager(info);
101	<	setForceManager(thermoForce_);
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();
113	>	needVelocityScaling = simParams->getTempSet();
114	>	}
115
116	<	if (simParams->haveTargetTemp()) {
117	<	targetScalingTemp = simParams->getTargetTemp();
118	<	}
119	<	else {
120	<	sprintf(painCave.errMsg,
121	<	"Integrator Error: Target Temperature is not set\n");
122	<	painCave.isFatal = 1;
123	<	simError();
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
126	<	}
126	>	}
127		}
128
129	<	//create a default a velocitizer
130	<	//if the subclass want to using different velocitizer, use setVelocitizer
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	<	}
134	<
135	<	Integrator::~Integrator(){
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	>
144	>	rotAlgo_ = new DLM();
145	>	rattle_ = new Rattle(info);
146	>	if (simParams->getFluctuatingChargeParameters()->havePropagator()) {
147	>	std::string prop = toUpperCopy(simParams->getFluctuatingChargeParameters()->getPropagator());
148	>	if (prop.compare("NVT")==0){
149	>	flucQ_ = new FluctuatingChargeNVT(info);
150	>	} else if (prop.compare("LANGEVIN")==0) {
151	>	flucQ_ = new FluctuatingChargeLangevin(info);
152	>	} else {
153	>	sprintf(painCave.errMsg,
154	>	"Integrator Error: Unknown Fluctuating Charge propagator (%s) requested\n",
155	>	simParams->getFluctuatingChargeParameters()->getPropagator().c_str());
156	>	painCave.isFatal = 1;
157	>	}
158	>	}
159	>	flucQ_->setForceManager(forceMan_);
160	>	}
161	>
162	>	Integrator::~Integrator(){
163		delete forceMan_;
164		delete velocitizer_;
165	+	delete rnemd_;
166	+	delete flucQ_;
167	+	delete rotAlgo_;
168	+	delete rattle_;
169
170		delete dumpWriter;
171		delete statWriter;
172	<	delete restWriter;
172	>	}
173		}
174
135	–
136	–	}
137	–

Comparing trunk/src/integrators/Integrator.cpp (property svn:keywords):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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