src/integrators/VelocityVerletIntegrator.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @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:	1912
Committed:	Mon Jan 10 20:52:07 2005 UTC (19 years, 6 months ago) by tim
File size:	5127 byte(s)
Log Message:	zconstraint method is working now
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file VelocityVerletIntegrator.cpp
28	* @author tlin
29	* @date 11/09/2004
30	* @time 16:16am
31	* @version 1.0
32	*/
33
34	#include "integrators/VelocityVerletIntegrator.hpp"
35	#include "integrators/DLM.hpp"
36
37	namespace oopse {
38	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
39	dt2 = 0.5 * dt;
40	rotAlgo = new DLM();
41	rattle = new Rattle(info);
42	}
43
44	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
45	delete rotAlgo;
46	delete rattle;
47	}
48
49	void VelocityVerletIntegrator::initialize(){
50
51	forceMan_->init();
52
53	// remove center of mass drift velocity (in case we passed in a configuration
54	// that was drifting
55	velocitizer_->removeComDrift();
56
57	// initialize the forces before the first step
58	calcForce(true, true);
59
60	//execute constraint algorithm to make sure at the very beginning the system is constrained
61	if (info_->getNGlobalConstraints() > 0) {
62	rattle->constraintA();
63	calcForce(true, true);
64	rattle->constraintB();
65	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
66	}
67
68	if (needVelocityScaling) {
69	velocitizer_->velocitize(targetScalingTemp);
70	}
71
72	dumpWriter = createDumpWriter();
73	statWriter = createStatWriter();
74
75	dumpWriter->writeDump();
76
77	//save statistics, before writeStat, we must save statistics
78	thermo.saveStat();
79	saveConservedQuantity();
80	statWriter->writeStat(currentSnapshot_->statData);
81
82	currSample = sampleTime + currentSnapshot_->getTime();
83	currStatus = statusTime + currentSnapshot_->getTime();;
84	currThermal = thermalTime + + currentSnapshot_->getTime();
85	needPotential = false;
86	needStress = false;
87
88	}
89
90	void VelocityVerletIntegrator::doIntegrate() {
91
92
93	initialize();
94
95	while (currentSnapshot_->getTime() < runTime) {
96
97	preStep();
98
99	integrateStep();
100
101	postStep();
102
103	}
104
105	finalize();
106
107	}
108
109
110	void VelocityVerletIntegrator::preStep() {
111	double difference = currentSnapshot_->getTime() + dt - currStatus;
112
113	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
114	needPotential = true;
115	needStress = true;
116	}
117
118	}
119
120	void VelocityVerletIntegrator::postStep() {
121
122	//save snapshot
123	info_->getSnapshotManager()->advance();
124
125	//increase time
126	currentSnapshot_->increaseTime(dt);
127
128	if (needVelocityScaling) {
129	if (currentSnapshot_->getTime() >= currThermal) {
130	velocitizer_->velocitize(targetScalingTemp);
131	currThermal += thermalTime;
132	}
133	}
134
135	if (currentSnapshot_->getTime() >= currSample) {
136	dumpWriter->writeDump();
137	currSample += sampleTime;
138	}
139
140	if (currentSnapshot_->getTime() >= currStatus) {
141	//save statistics, before writeStat, we must save statistics
142	thermo.saveStat();
143	saveConservedQuantity();
144	statWriter->writeStat(currentSnapshot_->statData);
145
146	needPotential = false;
147	needStress = false;
148	currStatus += statusTime;
149	}
150
151
152	}
153
154
155	void VelocityVerletIntegrator::finalize() {
156
157	dumpWriter->writeDump();
158
159	delete dumpWriter;
160	delete statWriter;
161
162	dumpWriter = NULL;
163	statWriter = NULL;
164
165	}
166
167	void VelocityVerletIntegrator::integrateStep() {
168
169	moveA();
170	calcForce(needPotential, needStress);
171	moveB();
172	}
173
174
175	void VelocityVerletIntegrator::calcForce(bool needPotential,
176	bool needStress) {
177	forceMan_->calcForces(needPotential, needStress);
178	}
179
180	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
181	return new DumpWriter(info_, info_->getDumpFileName());
182	}
183
184	StatWriter* VelocityVerletIntegrator::createStatWriter() {
185	return new StatWriter(info_->getStatFileName());
186	}
187
188
189	} //end namespace oopse