ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1737 by jmichalk, Tue Jun 5 17:54:42 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()) {
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();
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	<	}
108	>	forceMan_ = new ForceManager(info);
109
110	<	if (simParams->haveRunTime()) {
111	<	runTime = simParams->getRunTime();
112	<	} 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{
77	<	sampleTime = simParams->getRunTime();
78	<	statusTime = sampleTime;
79	<	}
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
85	–	if (simParams->haveThermalTime()){
86	–	thermalTime = simParams->getThermalTime();
87	–	} else {
88	–	thermalTime = simParams->getRunTime();
123		}
124	<
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);
124	>	}
125
126	<	// check for the temperature set flag (velocity scaling)
127	<	if (simParams->haveTempSet()) {
128	<	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	<	}
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	<	// Create a default a velocitizer: If the subclass wants to use
131	<	// a different velocitizer, use setVelocitizer
132	<	velocitizer_ = new Velocitizer(info);
133	<	// Create a default a RNEMD.
134	<	rnemd_ = new RNEMD(info);
135	<
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	>	}
139		}
140	<
140	>
141	>	rotAlgo_ = new DLM();
142	>	rattle_ = new Rattle(info);
143	>	forceMan_->initialize();
144	>	flucQ_ = new FluctuatingChargeNVT(info);
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		}
146	–
147	–
158		}
159

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 1737 by jmichalk, Tue Jun 5 17:54:42 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines