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) { 
    rotAlgo = new DLM();
    dt2 = 0.5 * dt;
}

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

void VelocityVerletIntegrator::initialize(){

    currSample = 0.0;
    currStatus = 0.0;
    currThermal = 0.0;
    needPotential = false;
    needStress = false;       

    // 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 (nConstrained) {
    //    constrainA();
    //    calcForce(true, true);
    //    constrainB();
    //}

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

    dumpWriter->writeDump();
    statWriter->writeStat(currentSnapshot_->statData);
   
}
        
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);        

        //save statistics
        thermo.saveStat();
        calcConservedQuantity();
        
        if (needVelocityScaling) {
            if (currentSnapshot_->getTime() >= currThermal) {
                velocitizer_->velocitize(targetScalingTemp);
                currThermal += thermalTime;
            }
        }

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

        if (currentSnapshot_->getTime() >= currStatus) {
            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:	1846
Committed:	Sat Dec 4 00:01:32 2004 UTC (19 years, 7 months ago) by tim
File size:	4627 byte(s)
Log Message:	Dump2Xyz is also working, energy of NVE is not conserved
#	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			rotAlgo = new DLM();
40	tim	1819	dt2 = 0.5 * dt;
41			}
42	tim	1722
43	tim	1820	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
44			delete rotAlgo;
45			}
46	tim	1722
47	tim	1819	void VelocityVerletIntegrator::initialize(){
48	tim	1722
49	tim	1819	currSample = 0.0;
50			currStatus = 0.0;
51			currThermal = 0.0;
52			needPotential = false;
53			needStress = false;
54	tim	1722
55	tim	1725	// remove center of mass drift velocity (in case we passed in a configuration
56			// that was drifting
57	tim	1819	velocitizer_->removeComDrift();
58	tim	1722
59	tim	1725	// initialize the forces before the first step
60	tim	1819	calcForce(true, true);
61	tim	1722
62	tim	1725	//execute constraint algorithm to make sure at the very beginning the system is constrained
63	tim	1819	//if (nConstrained) {
64			// constrainA();
65			// calcForce(true, true);
66			// constrainB();
67			//}
68	tim	1725
69	tim	1819	if (needVelocityScaling) {
70			velocitizer_->velocitize(targetScalingTemp);
71	tim	1725	}
72	tim	1819
73			dumpWriter = createDumpWriter();
74			statWriter = createStatWriter();
75	tim	1725
76	tim	1820	dumpWriter->writeDump();
77			statWriter->writeStat(currentSnapshot_->statData);
78
79	tim	1819	}
80
81			void VelocityVerletIntegrator::doIntegrate() {
82	tim	1725
83
84	tim	1819	initialize();
85	tim	1725
86	tim	1819	while (currentSnapshot_->getTime() < runTime) {
87
88			preStep();
89	tim	1725
90	tim	1819	integrateStep();
91
92			postStep();
93
94			}
95
96			finalize();
97
98			}
99
100
101			void VelocityVerletIntegrator::preStep() {
102			double difference = currentSnapshot_->getTime() + dt - currStatus;
103
104			if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
105			needPotential = true;
106			needStress = true;
107	tim	1725	}
108
109	tim	1819	}
110
111			void VelocityVerletIntegrator::postStep() {
112	tim	1820
113			//save snapshot
114			info_->getSnapshotManager()->advance();
115
116			//increase time
117			currentSnapshot_->increaseTime(dt);
118
119			//save statistics
120			thermo.saveStat();
121	tim	1846	calcConservedQuantity();
122	tim	1756
123	tim	1819	if (needVelocityScaling) {
124			if (currentSnapshot_->getTime() >= currThermal) {
125			velocitizer_->velocitize(targetScalingTemp);
126	tim	1725	currThermal += thermalTime;
127			}
128			}
129
130	tim	1819	if (currentSnapshot_->getTime() >= currSample) {
131	tim	1820	dumpWriter->writeDump();
132	tim	1725	currSample += sampleTime;
133			}
134
135	tim	1819	if (currentSnapshot_->getTime() >= currStatus) {
136	tim	1820	statWriter->writeStat(currentSnapshot_->statData);
137	tim	1819	needPotential = false;
138			needStress = false;
139	tim	1725	currStatus += statusTime;
140			}
141	tim	1820
142
143	tim	1819	}
144	tim	1725
145
146	tim	1819	void VelocityVerletIntegrator::finalize() {
147	tim	1725
148	tim	1820	dumpWriter->writeDump();
149	tim	1725
150	tim	1819	delete dumpWriter;
151			delete statWriter;
152	tim	1725
153	tim	1819	dumpWriter = NULL;
154			statWriter = NULL;
155
156	tim	1722	}
157
158	tim	1774	void VelocityVerletIntegrator::integrateStep() {
159	tim	1725
160	tim	1774	moveA();
161	tim	1819	calcForce(needPotential, needStress);
162	tim	1774	moveB();
163			}
164	tim	1725
165	tim	1774
166	tim	1819	void VelocityVerletIntegrator::calcForce(bool needPotential,
167			bool needStress) {
168	tim	1820	forceMan_->calcForces(needPotential, needStress);
169	tim	1722	}
170
171	tim	1820	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
172			return new DumpWriter(info_, info_->getDumpFileName());
173			}
174	tim	1722
175	tim	1820	StatWriter* VelocityVerletIntegrator::createStatWriter() {
176			return new StatWriter(info_->getStatFileName());
177			}
178
179
180	tim	1725	} //end namespace oopse