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"
#include "utils/StringUtils.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();
            //eorWriter->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() {

    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:	2019
Committed:	Mon Feb 14 18:12:43 2005 UTC (19 years, 4 months ago) by tim
File size:	6103 byte(s)
Log Message:	fix a bug in VelocityVerletIntegrator : last frame is written twice
#	User	Rev	Content
1	gezelter	1930	/*
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	tim	1960	#include "utils/StringUtils.hpp"
53	gezelter	1930
54			namespace oopse {
55			VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56			dt2 = 0.5 * dt;
57			rotAlgo = new DLM();
58			rattle = new Rattle(info);
59			}
60
61			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62			delete rotAlgo;
63			delete rattle;
64			}
65
66			void VelocityVerletIntegrator::initialize(){
67
68			forceMan_->init();
69
70			// remove center of mass drift velocity (in case we passed in a configuration
71			// that was drifting
72			velocitizer_->removeComDrift();
73
74			// initialize the forces before the first step
75			calcForce(true, true);
76
77			//execute constraint algorithm to make sure at the very beginning the system is constrained
78			if (info_->getNGlobalConstraints() > 0) {
79			rattle->constraintA();
80			calcForce(true, true);
81			rattle->constraintB();
82			info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
83			}
84
85			if (needVelocityScaling) {
86			velocitizer_->velocitize(targetScalingTemp);
87			}
88
89			dumpWriter = createDumpWriter();
90	tim	2008
91	gezelter	1930	statWriter = createStatWriter();
92
93			dumpWriter->writeDump();
94	tim	1960
95	gezelter	1930	//save statistics, before writeStat, we must save statistics
96			thermo.saveStat();
97			saveConservedQuantity();
98			statWriter->writeStat(currentSnapshot_->statData);
99
100			currSample = sampleTime + currentSnapshot_->getTime();
101			currStatus = statusTime + currentSnapshot_->getTime();;
102			currThermal = thermalTime + + currentSnapshot_->getTime();
103			needPotential = false;
104			needStress = false;
105
106			}
107
108			void VelocityVerletIntegrator::doIntegrate() {
109
110
111			initialize();
112
113			while (currentSnapshot_->getTime() < runTime) {
114
115			preStep();
116
117			integrateStep();
118
119			postStep();
120
121			}
122
123			finalize();
124
125			}
126
127
128			void VelocityVerletIntegrator::preStep() {
129			double difference = currentSnapshot_->getTime() + dt - currStatus;
130
131			if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
132			needPotential = true;
133			needStress = true;
134			}
135
136			}
137
138			void VelocityVerletIntegrator::postStep() {
139
140			//save snapshot
141			info_->getSnapshotManager()->advance();
142
143			//increase time
144			currentSnapshot_->increaseTime(dt);
145
146			if (needVelocityScaling) {
147			if (currentSnapshot_->getTime() >= currThermal) {
148			velocitizer_->velocitize(targetScalingTemp);
149			currThermal += thermalTime;
150			}
151			}
152
153			if (currentSnapshot_->getTime() >= currSample) {
154			dumpWriter->writeDump();
155	tim	2008	//eorWriter->writeDump();
156	gezelter	1930	currSample += sampleTime;
157			}
158
159			if (currentSnapshot_->getTime() >= currStatus) {
160			//save statistics, before writeStat, we must save statistics
161			thermo.saveStat();
162			saveConservedQuantity();
163			statWriter->writeStat(currentSnapshot_->statData);
164
165			needPotential = false;
166			needStress = false;
167			currStatus += statusTime;
168			}
169
170
171			}
172
173
174			void VelocityVerletIntegrator::finalize() {
175
176			delete dumpWriter;
177			delete statWriter;
178
179			dumpWriter = NULL;
180			statWriter = NULL;
181
182			}
183
184			void VelocityVerletIntegrator::integrateStep() {
185
186			moveA();
187			calcForce(needPotential, needStress);
188			moveB();
189			}
190
191
192			void VelocityVerletIntegrator::calcForce(bool needPotential,
193			bool needStress) {
194			forceMan_->calcForces(needPotential, needStress);
195			}
196
197			DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
198			return new DumpWriter(info_, info_->getDumpFileName());
199			}
200
201			StatWriter* VelocityVerletIntegrator::createStatWriter() {
202			return new StatWriter(info_->getStatFileName());
203			}
204
205
206			} //end namespace oopse