src/integrators/VelocityVerletIntegrator.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file VelocityVerletIntegrator.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 16:16am
 * @version 1.0
 */

#include "integrators/VelocityVerletIntegrator.hpp"
#include "integrators/DLM.hpp"

namespace oopse {
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { 
    dt2 = 0.5 * dt;
    rotAlgo = new DLM();
    rattle = new Rattle(info);
}

VelocityVerletIntegrator::~VelocityVerletIntegrator() { 
    delete rotAlgo;
    delete rattle;
}

void VelocityVerletIntegrator::initialize(){

    forceMan_->init();

    // remove center of mass drift velocity (in case we passed in a configuration
    // that was drifting
    velocitizer_->removeComDrift();

    // initialize the forces before the first step
    calcForce(true, true);

    //execute constraint algorithm to make sure at the very beginning the system is constrained  
    if (info_->getNGlobalConstraints() > 0) {
        rattle->constraintA();
        calcForce(true, true);
        rattle->constraintB();        
        info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
    }

    if (needVelocityScaling) {
        velocitizer_->velocitize(targetScalingTemp);
    }
    
    dumpWriter = createDumpWriter();
    statWriter = createStatWriter();

    dumpWriter->writeDump();

    //save statistics, before writeStat,  we must save statistics
    thermo.saveStat();
    saveConservedQuantity();
    statWriter->writeStat(currentSnapshot_->statData);

    currSample = sampleTime + currentSnapshot_->getTime();
    currStatus =  statusTime + currentSnapshot_->getTime();;
    currThermal = thermalTime +  + currentSnapshot_->getTime();
    needPotential = false;
    needStress = false;       
   
}
        
void VelocityVerletIntegrator::doIntegrate() {


    initialize();

    while (currentSnapshot_->getTime() < runTime) {
        
        preStep();

        integrateStep();
        
        postStep();

    }

    finalize();
    
}


void VelocityVerletIntegrator::preStep() {
        double difference = currentSnapshot_->getTime() + dt - currStatus;

        if (difference > 0 || fabs(difference) < oopse::epsilon) {
            needPotential = true;
            needStress = true;   
        }

}

void VelocityVerletIntegrator::postStep() {

        //save snapshot
        info_->getSnapshotManager()->advance();

        //increase time
        currentSnapshot_->increaseTime(dt);        
        
        if (needVelocityScaling) {
            if (currentSnapshot_->getTime() >= currThermal) {
                velocitizer_->velocitize(targetScalingTemp);
                currThermal += thermalTime;
            }
        }

        if (currentSnapshot_->getTime() >= currSample) {
            dumpWriter->writeDump();
            currSample += sampleTime;
        }

        if (currentSnapshot_->getTime() >= currStatus) {
            //save statistics, before writeStat,  we must save statistics
            thermo.saveStat();
            saveConservedQuantity();
            statWriter->writeStat(currentSnapshot_->statData);

            needPotential = false;
            needStress = false;
            currStatus += statusTime;
        }

        
}


void VelocityVerletIntegrator::finalize() {

    dumpWriter->writeDump();

    delete dumpWriter;
    delete statWriter;

    dumpWriter = NULL;
    statWriter = NULL;
    
}

void VelocityVerletIntegrator::integrateStep() { 

    moveA();
    calcForce(needPotential, needStress);
    moveB();
}


void VelocityVerletIntegrator::calcForce(bool needPotential,
                                         bool needStress) { 
    forceMan_->calcForces(needPotential, needStress);
}

DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
    return new DumpWriter(info_, info_->getDumpFileName());
}

StatWriter* VelocityVerletIntegrator::createStatWriter() {
    return new StatWriter(info_->getStatFileName());
}


} //end namespace oopse
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	6057 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file VelocityVerletIntegrator.cpp
44	* @author tlin
45	* @date 11/09/2004
46	* @time 16:16am
47	* @version 1.0
48	*/
49
50	#include "integrators/VelocityVerletIntegrator.hpp"
51	#include "integrators/DLM.hpp"
52
53	namespace oopse {
54	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
55	dt2 = 0.5 * dt;
56	rotAlgo = new DLM();
57	rattle = new Rattle(info);
58	}
59
60	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61	delete rotAlgo;
62	delete rattle;
63	}
64
65	void VelocityVerletIntegrator::initialize(){
66
67	forceMan_->init();
68
69	// remove center of mass drift velocity (in case we passed in a configuration
70	// that was drifting
71	velocitizer_->removeComDrift();
72
73	// initialize the forces before the first step
74	calcForce(true, true);
75
76	//execute constraint algorithm to make sure at the very beginning the system is constrained
77	if (info_->getNGlobalConstraints() > 0) {
78	rattle->constraintA();
79	calcForce(true, true);
80	rattle->constraintB();
81	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
82	}
83
84	if (needVelocityScaling) {
85	velocitizer_->velocitize(targetScalingTemp);
86	}
87
88	dumpWriter = createDumpWriter();
89	statWriter = createStatWriter();
90
91	dumpWriter->writeDump();
92
93	//save statistics, before writeStat, we must save statistics
94	thermo.saveStat();
95	saveConservedQuantity();
96	statWriter->writeStat(currentSnapshot_->statData);
97
98	currSample = sampleTime + currentSnapshot_->getTime();
99	currStatus = statusTime + currentSnapshot_->getTime();;
100	currThermal = thermalTime + + currentSnapshot_->getTime();
101	needPotential = false;
102	needStress = false;
103
104	}
105
106	void VelocityVerletIntegrator::doIntegrate() {
107
108
109	initialize();
110
111	while (currentSnapshot_->getTime() < runTime) {
112
113	preStep();
114
115	integrateStep();
116
117	postStep();
118
119	}
120
121	finalize();
122
123	}
124
125
126	void VelocityVerletIntegrator::preStep() {
127	double difference = currentSnapshot_->getTime() + dt - currStatus;
128
129	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
130	needPotential = true;
131	needStress = true;
132	}
133
134	}
135
136	void VelocityVerletIntegrator::postStep() {
137
138	//save snapshot
139	info_->getSnapshotManager()->advance();
140
141	//increase time
142	currentSnapshot_->increaseTime(dt);
143
144	if (needVelocityScaling) {
145	if (currentSnapshot_->getTime() >= currThermal) {
146	velocitizer_->velocitize(targetScalingTemp);
147	currThermal += thermalTime;
148	}
149	}
150
151	if (currentSnapshot_->getTime() >= currSample) {
152	dumpWriter->writeDump();
153	currSample += sampleTime;
154	}
155
156	if (currentSnapshot_->getTime() >= currStatus) {
157	//save statistics, before writeStat, we must save statistics
158	thermo.saveStat();
159	saveConservedQuantity();
160	statWriter->writeStat(currentSnapshot_->statData);
161
162	needPotential = false;
163	needStress = false;
164	currStatus += statusTime;
165	}
166
167
168	}
169
170
171	void VelocityVerletIntegrator::finalize() {
172
173	dumpWriter->writeDump();
174
175	delete dumpWriter;
176	delete statWriter;
177
178	dumpWriter = NULL;
179	statWriter = NULL;
180
181	}
182
183	void VelocityVerletIntegrator::integrateStep() {
184
185	moveA();
186	calcForce(needPotential, needStress);
187	moveB();
188	}
189
190
191	void VelocityVerletIntegrator::calcForce(bool needPotential,
192	bool needStress) {
193	forceMan_->calcForces(needPotential, needStress);
194	}
195
196	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
197	return new DumpWriter(info_, info_->getDumpFileName());
198	}
199
200	StatWriter* VelocityVerletIntegrator::createStatWriter() {
201	return new StatWriter(info_->getStatFileName());
202	}
203
204
205	} //end namespace oopse