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

Comparing trunk/src/integrators/Integrator.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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"
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	<	simParams = info->getSimParams();
51	<
52	<	if (simParams->haveDt()) {
53	<	dt = simParams->getDt();
54	<	} else {
55	<	sprintf(painCave.errMsg,
56	<	"Integrator Error: dt is not set\n");
57	<	painCave.isFatal = 1;
59	<	simError();
60	<	}
50	>	namespace OpenMD {
51	>	Integrator::Integrator(SimInfo* info)
52	>	: info_(info), forceMan_(NULL), rotAlgo_(NULL), flucQ_(NULL),
53	>	rattle_(NULL), velocitizer_(NULL), rnemd_(NULL),
54	>	needPotential(false), needStress(false),
55	>	needReset(false),  needVelocityScaling(false),
56	>	useRNEMD(false), dumpWriter(NULL), statWriter(NULL), thermo(info_),
57	>	snap(info_->getSnapshotManager()->getCurrentSnapshot()) {
58
59	<	if (simParams->haveRunTime()) {
60	<	runTime = simParams->getRunTime();
61	<	} else {
62	<	sprintf(painCave.errMsg,
63	<	"Integrator Error: runTime is not set\n");
64	<	painCave.isFatal = 1;
65	<	simError();
66	<	}
67	<	// set the status, sample, and thermal kick times
68	<	if (simParams->haveSampleTime()){
69	<	sampleTime = simParams->getSampleTime();
70	<	statusTime = sampleTime;
71	<	} else{
72	<	sampleTime = simParams->getRunTime();
73	<	statusTime = sampleTime;
74	<	}
59	>	simParams = info->getSimParams();
60	>
61	>	if (simParams->haveDt()) {
62	>	dt = simParams->getDt();
63	>	} else {
64	>	sprintf(painCave.errMsg,
65	>	"Integrator Error: dt is not set\n");
66	>	painCave.isFatal = 1;
67	>	simError();
68	>	}
69	>
70	>	if (simParams->haveRunTime()) {
71	>	runTime = simParams->getRunTime();
72	>	} else {
73	>	sprintf(painCave.errMsg,
74	>	"Integrator Error: runTime is not set\n");
75	>	painCave.isFatal = 1;
76	>	simError();
77	>	}
78	>
79	>	// set the status, sample, and thermal kick times
80	>	if (simParams->haveSampleTime()){
81	>	sampleTime = simParams->getSampleTime();
82	>	statusTime = sampleTime;
83	>	} else{
84	>	sampleTime = simParams->getRunTime();
85	>	statusTime = sampleTime;
86	>	}
87	>
88	>	if (simParams->haveStatusTime()){
89	>	statusTime = simParams->getStatusTime();
90	>	}
91	>
92	>	if (simParams->haveThermalTime()){
93	>	thermalTime = simParams->getThermalTime();
94	>	} else {
95	>	thermalTime = simParams->getRunTime();
96	>	}
97	>
98	>	if (!simParams->getUseInitalTime()) {
99	>	snap->setTime(0.0);
100	>	}
101	>
102	>	if (simParams->haveResetTime()) {
103	>	needReset = true;
104	>	resetTime = simParams->getResetTime();
105	>	}
106	>
107	>	// Create a default ForceManager: If the subclass wants to use
108	>	// a different ForceManager, use setForceManager
109	>	forceMan_ = new ForceManager(info);
110	>
111	>	// check for the temperature set flag (velocity scaling)
112	>	needVelocityScaling = false;
113	>	if (simParams->haveTempSet()) {
114	>	needVelocityScaling = simParams->getTempSet();
115	>	}
116
117	<	if (simParams->haveStatusTime()){
118	<	statusTime = simParams->getStatusTime();
117	>	if (needVelocityScaling) {
118	>	if (simParams->haveTargetTemp()) {
119	>	targetScalingTemp = simParams->getTargetTemp();
120		}
121	+	else {
122	+	sprintf(painCave.errMsg,
123	+	"Integrator Error: Target Temperature must be set to turn on tempSet\n");
124	+	painCave.isFatal = 1;
125	+	simError();
126
83	–	if (simParams->haveThermalTime()){
84	–	thermalTime = simParams->getThermalTime();
85	–	} else {
86	–	thermalTime = simParams->getRunTime();
127		}
128	<
89	<	if (!simParams->getUseInitTime()) {
90	<	currentSnapshot_->setTime(0.0);
91	<	}
128	>	}
129
130	<	//create a default ForceManager
131	<	//if the subclass wants to use a different ForceManager, use setForceManager
132	<	forceMan_ = new ForceManager(info);
130	>	// Create a default a velocitizer: If the subclass wants to use
131	>	// a different velocitizer, use setVelocitizer
132	>	velocitizer_ = new Velocitizer(info);
133
134	<	//set the force manager for thermodynamic integration if specified
135	<	if (simParams->getUseSolidThermInt() || simParams->getUseLiquidThermInt()){
136	<	ThermoIntegrationForceManager* thermoForce_
137	<	= new ThermoIntegrationForceManager(info);
138	<	setForceManager(thermoForce_);
134	>	if (simParams->getRNEMDParameters()->haveUseRNEMD()) {
135	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
136	>	// Create a default a RNEMD.
137	>	rnemd_ = new RNEMD(info);
138	>	useRNEMD = simParams->getRNEMDParameters()->getUseRNEMD();
139	>	if (simParams->getRNEMDParameters()->haveExchangeTime()) {
140	>	RNEMD_exchangeTime = simParams->getRNEMDParameters()->getExchangeTime();
141	>	}
142		}
143	+	}
144
145	<	// check for the temperature set flag (velocity scaling)
146	<	if (simParams->haveTempSet()) {
147	<	needVelocityScaling = simParams->getTempSet();
148	<
149	<	if (simParams->haveTargetTemp()) {
150	<	targetScalingTemp = simParams->getTargetTemp();
151	<	}
152	<	else {
153	<	sprintf(painCave.errMsg,
154	<	"Integrator Error: Target Temperature is not set\n");
155	<	painCave.isFatal = 1;
156	<	simError();
157	<
117	<	}
145	>	rotAlgo_ = new DLM();
146	>	rattle_ = new Rattle(info);
147	>	if (simParams->getFluctuatingChargeParameters()->havePropagator()) {
148	>	std::string prop = toUpperCopy(simParams->getFluctuatingChargeParameters()->getPropagator());
149	>	if (prop.compare("NVT")==0){
150	>	flucQ_ = new FluctuatingChargeNVT(info);
151	>	} else if (prop.compare("LANGEVIN")==0) {
152	>	flucQ_ = new FluctuatingChargeLangevin(info);
153	>	} else {
154	>	sprintf(painCave.errMsg,
155	>	"Integrator Error: Unknown Fluctuating Charge propagator (%s) requested\n",
156	>	simParams->getFluctuatingChargeParameters()->getPropagator().c_str());
157	>	painCave.isFatal = 1;
158		}
119	–
120	–	//create a default a velocitizer
121	–	//if the subclass want to using different velocitizer, use setVelocitizer
122	–	velocitizer_ = new Velocitizer(info);
123	–
159		}
160	<
160	>	flucQ_->setForceManager(forceMan_);
161	>	}
162	>
163		Integrator::~Integrator(){
164		delete forceMan_;
165		delete velocitizer_;
166	+	delete rnemd_;
167	+	delete flucQ_;
168	+	delete rotAlgo_;
169	+	delete rattle_;
170
171		delete dumpWriter;
172		delete statWriter;
173		}
133	–
134	–
174		}
175

Comparing trunk/src/integrators/Integrator.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
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