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

Comparing:
trunk/src/integrators/Integrator.cpp (file contents), Revision 441 by gezelter, Tue Mar 15 14:21:31 2005 UTC vs.
branches/development/src/integrators/Integrator.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "brains/Snapshot.hpp"
43		#include "integrators/Integrator.hpp"
44		#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),
45	>	namespace OpenMD {
46	>	Integrator::Integrator(SimInfo* info)
47	>	: info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
48	>	needReset(false), velocitizer_(NULL), needVelocityScaling(false),
49	>	rnemd_(NULL), useRNEMD(false),
50	>	dumpWriter(NULL), statWriter(NULL), thermo(info),
51		currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
52
53	<	simParams = info->getSimParams();
53	>	simParams = info->getSimParams();
54
55	<	if (simParams->haveDt()) {
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	<	}
57	>	} else {
58	>	sprintf(painCave.errMsg,
59	>	"Integrator Error: dt is not set\n");
60	>	painCave.isFatal = 1;
61	>	simError();
62	>	}
63
64	<	if (simParams->haveRunTime()) {
64	>	if (simParams->haveRunTime()) {
65		runTime = simParams->getRunTime();
66	<	} else {
67	<	sprintf(painCave.errMsg,
68	<	"Integrator Error: runTime is not set\n");
69	<	painCave.isFatal = 1;
70	<	simError();
71	<	}
72	<	// set the status, sample, and thermal kick times
73	<	if (simParams->haveSampleTime()){
66	>	} else {
67	>	sprintf(painCave.errMsg,
68	>	"Integrator Error: runTime is not set\n");
69	>	painCave.isFatal = 1;
70	>	simError();
71	>	}
72	>	// set the status, sample, and thermal kick times
73	>	if (simParams->haveSampleTime()){
74		sampleTime = simParams->getSampleTime();
75		statusTime = sampleTime;
76	<	} else{
76	>	} else{
77		sampleTime = simParams->getRunTime();
78		statusTime = sampleTime;
79	<	}
79	>	}
80
81	<	if (simParams->haveStatusTime()){
81	>	if (simParams->haveStatusTime()){
82		statusTime = simParams->getStatusTime();
83	<	}
83	>	}
84
85	<	if (simParams->haveThermalTime()){
85	>	if (simParams->haveThermalTime()){
86		thermalTime = simParams->getThermalTime();
87	<	} else {
87	>	} else {
88		thermalTime = simParams->getRunTime();
89	<	}
89	>	}
90
91	<	if (!simParams->getUseInitTime()) {
91	>	if (!simParams->getUseInitalTime()) {
92		currentSnapshot_->setTime(0.0);
93	<	}
93	>	}
94	>
95	>	if (simParams->haveResetTime()) {
96	>	needReset = true;
97	>	resetTime = simParams->getResetTime();
98	>	}
99	>
100	>	// Create a default ForceManager: If the subclass wants to use
101	>	// a different ForceManager, use setForceManager
102	>	forceMan_ = new ForceManager(info);
103
104	<	//create a default ForceManager
105	<	//if the subclass wants to use a different ForceManager, use setForceManager
95	<	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_);
102	<	}
103	<
104	<	// check for the temperature set flag (velocity scaling)
105	<	if (simParams->haveTempSet()) {
104	>	// check for the temperature set flag (velocity scaling)
105	>	if (simParams->haveTempSet()) {
106		needVelocityScaling = simParams->getTempSet();
107
108		if (simParams->haveTargetTemp()) {
109	<	targetScalingTemp = simParams->getTargetTemp();
109	>	targetScalingTemp = simParams->getTargetTemp();
110		}
111		else {
112	<	sprintf(painCave.errMsg,
113	<	"Integrator Error: Target Temperature is not set\n");
114	<	painCave.isFatal = 1;
115	<	simError();
112	>	sprintf(painCave.errMsg,
113	>	"Integrator Error: Target Temperature is not set\n");
114	>	painCave.isFatal = 1;
115	>	simError();
116
117		}
118	<	}
119	<
120	<	//create a default a velocitizer
121	<	//if the subclass want to using different velocitizer, use setVelocitizer
122	<	velocitizer_ = new Velocitizer(info);
123	<
124	<	}
118	>	}
119	>
120	>	// Create a default a velocitizer: If the subclass wants to use
121	>	// a different velocitizer, use setVelocitizer
122	>	velocitizer_ = new Velocitizer(info);
123
124	<	Integrator::~Integrator(){
124	>	if (simParams->haveUseRNEMD()) {
125	>	if (simParams->getUseRNEMD()) {
126	>	// Create a default a RNEMD.
127	>	rnemd_ = new RNEMD(info);
128	>	useRNEMD = simParams->getUseRNEMD();
129	>	if (simParams->haveRNEMD_exchangeTime()) {
130	>	RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime();
131	>	}
132	>	}
133	>	}
134	>	}
135	>
136	>	Integrator::~Integrator(){
137		delete forceMan_;
138		delete velocitizer_;
139	+	delete rnemd_;
140
141		delete dumpWriter;
142		delete statWriter;
143	<	}
143	>	}
144
145
146		}

Comparing:
trunk/src/integrators/Integrator.cpp (property svn:keywords), Revision 441 by gezelter, Tue Mar 15 14:21:31 2005 UTC vs.
branches/development/src/integrators/Integrator.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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