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();

    //save statistics
    thermo.saveStat();
    saveConservedQuantity();

    //before writeStat,  we must save statistics
    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();
        saveConservedQuantity();
        
        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:	1847
Committed:	Sat Dec 4 05:24:07 2004 UTC (19 years, 7 months ago) by tim
File size:	4752 byte(s)
Log Message:	NVE conserved energy, however, potential is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step 4 EAM Step 5 Shape Step 6 Constraint & Restraint
#	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	tim	1847
78			//save statistics
79			thermo.saveStat();
80			saveConservedQuantity();
81
82			//before writeStat, we must save statistics
83	tim	1820	statWriter->writeStat(currentSnapshot_->statData);
84
85	tim	1819	}
86
87			void VelocityVerletIntegrator::doIntegrate() {
88	tim	1725
89
90	tim	1819	initialize();
91	tim	1725
92	tim	1819	while (currentSnapshot_->getTime() < runTime) {
93
94			preStep();
95	tim	1725
96	tim	1819	integrateStep();
97
98			postStep();
99
100			}
101
102			finalize();
103
104			}
105
106
107			void VelocityVerletIntegrator::preStep() {
108			double difference = currentSnapshot_->getTime() + dt - currStatus;
109
110			if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
111			needPotential = true;
112			needStress = true;
113	tim	1725	}
114
115	tim	1819	}
116
117			void VelocityVerletIntegrator::postStep() {
118	tim	1820
119			//save snapshot
120			info_->getSnapshotManager()->advance();
121
122			//increase time
123			currentSnapshot_->increaseTime(dt);
124
125			//save statistics
126			thermo.saveStat();
127	tim	1847	saveConservedQuantity();
128	tim	1756
129	tim	1819	if (needVelocityScaling) {
130			if (currentSnapshot_->getTime() >= currThermal) {
131			velocitizer_->velocitize(targetScalingTemp);
132	tim	1725	currThermal += thermalTime;
133			}
134			}
135
136	tim	1819	if (currentSnapshot_->getTime() >= currSample) {
137	tim	1820	dumpWriter->writeDump();
138	tim	1725	currSample += sampleTime;
139			}
140
141	tim	1819	if (currentSnapshot_->getTime() >= currStatus) {
142	tim	1820	statWriter->writeStat(currentSnapshot_->statData);
143	tim	1819	needPotential = false;
144			needStress = false;
145	tim	1725	currStatus += statusTime;
146			}
147	tim	1820
148
149	tim	1819	}
150	tim	1725
151
152	tim	1819	void VelocityVerletIntegrator::finalize() {
153	tim	1725
154	tim	1820	dumpWriter->writeDump();
155	tim	1725
156	tim	1819	delete dumpWriter;
157			delete statWriter;
158	tim	1725
159	tim	1819	dumpWriter = NULL;
160			statWriter = NULL;
161
162	tim	1722	}
163
164	tim	1774	void VelocityVerletIntegrator::integrateStep() {
165	tim	1725
166	tim	1774	moveA();
167	tim	1819	calcForce(needPotential, needStress);
168	tim	1774	moveB();
169			}
170	tim	1725
171	tim	1774
172	tim	1819	void VelocityVerletIntegrator::calcForce(bool needPotential,
173			bool needStress) {
174	tim	1820	forceMan_->calcForces(needPotential, needStress);
175	tim	1722	}
176
177	tim	1820	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
178			return new DumpWriter(info_, info_->getDumpFileName());
179			}
180	tim	1722
181	tim	1820	StatWriter* VelocityVerletIntegrator::createStatWriter() {
182			return new StatWriter(info_->getStatFileName());
183			}
184
185
186	tim	1725	} //end namespace oopse