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 (21 years, 4 months ago) by tim
File size:	5127 byte(s)
Log Message:	zconstraint method is working now
#	User	Rev	Content
1	tim	1722	/*
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	tim	1725	/**
27			* @file VelocityVerletIntegrator.cpp
28			* @author tlin
29			* @date 11/09/2004
30			* @time 16:16am
31			* @version 1.0
32			*/
33
34	tim	1722	#include "integrators/VelocityVerletIntegrator.hpp"
35	tim	1820	#include "integrators/DLM.hpp"
36	tim	1722
37			namespace oopse {
38	tim	1820	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
39	tim	1901	dt2 = 0.5 * dt;
40	tim	1820	rotAlgo = new DLM();
41	tim	1901	rattle = new Rattle(info);
42	tim	1819	}
43	tim	1722
44	tim	1820	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
45			delete rotAlgo;
46	tim	1901	delete rattle;
47	tim	1820	}
48	tim	1722
49	tim	1819	void VelocityVerletIntegrator::initialize(){
50	tim	1722
51	tim	1912	forceMan_->init();
52
53	tim	1725	// remove center of mass drift velocity (in case we passed in a configuration
54			// that was drifting
55	tim	1819	velocitizer_->removeComDrift();
56	tim	1722
57	tim	1725	// initialize the forces before the first step
58	tim	1819	calcForce(true, true);
59	tim	1722
60	tim	1725	//execute constraint algorithm to make sure at the very beginning the system is constrained
61	tim	1907	if (info_->getNGlobalConstraints() > 0) {
62			rattle->constraintA();
63			calcForce(true, true);
64	tim	1910	rattle->constraintB();
65			info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
66	tim	1907	}
67	tim	1725
68	tim	1819	if (needVelocityScaling) {
69			velocitizer_->velocitize(targetScalingTemp);
70	tim	1725	}
71	tim	1819
72			dumpWriter = createDumpWriter();
73			statWriter = createStatWriter();
74	tim	1725
75	tim	1820	dumpWriter->writeDump();
76	tim	1847
77	tim	1868	//save statistics, before writeStat, we must save statistics
78	tim	1847	thermo.saveStat();
79			saveConservedQuantity();
80	tim	1868	statWriter->writeStat(currentSnapshot_->statData);
81	tim	1847
82	tim	1868	currSample = sampleTime + currentSnapshot_->getTime();
83			currStatus = statusTime + currentSnapshot_->getTime();;
84			currThermal = thermalTime + + currentSnapshot_->getTime();
85			needPotential = false;
86			needStress = false;
87	tim	1820
88	tim	1819	}
89
90			void VelocityVerletIntegrator::doIntegrate() {
91	tim	1725
92
93	tim	1819	initialize();
94	tim	1725
95	tim	1819	while (currentSnapshot_->getTime() < runTime) {
96
97			preStep();
98	tim	1725
99	tim	1819	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	tim	1725	}
117
118	tim	1819	}
119
120			void VelocityVerletIntegrator::postStep() {
121	tim	1820
122			//save snapshot
123			info_->getSnapshotManager()->advance();
124
125			//increase time
126			currentSnapshot_->increaseTime(dt);
127	tim	1756
128	tim	1819	if (needVelocityScaling) {
129			if (currentSnapshot_->getTime() >= currThermal) {
130			velocitizer_->velocitize(targetScalingTemp);
131	tim	1725	currThermal += thermalTime;
132			}
133			}
134
135	tim	1819	if (currentSnapshot_->getTime() >= currSample) {
136	tim	1820	dumpWriter->writeDump();
137	tim	1725	currSample += sampleTime;
138			}
139
140	tim	1819	if (currentSnapshot_->getTime() >= currStatus) {
141	tim	1868	//save statistics, before writeStat, we must save statistics
142			thermo.saveStat();
143			saveConservedQuantity();
144	tim	1820	statWriter->writeStat(currentSnapshot_->statData);
145	tim	1868
146	tim	1819	needPotential = false;
147			needStress = false;
148	tim	1725	currStatus += statusTime;
149			}
150	tim	1820
151
152	tim	1819	}
153	tim	1725
154
155	tim	1819	void VelocityVerletIntegrator::finalize() {
156	tim	1725
157	tim	1820	dumpWriter->writeDump();
158	tim	1725
159	tim	1819	delete dumpWriter;
160			delete statWriter;
161	tim	1725
162	tim	1819	dumpWriter = NULL;
163			statWriter = NULL;
164
165	tim	1722	}
166
167	tim	1774	void VelocityVerletIntegrator::integrateStep() {
168	tim	1725
169	tim	1774	moveA();
170	tim	1819	calcForce(needPotential, needStress);
171	tim	1774	moveB();
172			}
173	tim	1725
174	tim	1774
175	tim	1819	void VelocityVerletIntegrator::calcForce(bool needPotential,
176			bool needStress) {
177	tim	1820	forceMan_->calcForces(needPotential, needStress);
178	tim	1722	}
179
180	tim	1820	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
181			return new DumpWriter(info_, info_->getDumpFileName());
182			}
183	tim	1722
184	tim	1820	StatWriter* VelocityVerletIntegrator::createStatWriter() {
185			return new StatWriter(info_->getStatFileName());
186			}
187
188
189	tim	1725	} //end namespace oopse