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
#	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	rotAlgo = new DLM();
40	dt2 = 0.5 * dt;
41	}
42
43	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
44	delete rotAlgo;
45	}
46
47	void VelocityVerletIntegrator::initialize(){
48
49	currSample = 0.0;
50	currStatus = 0.0;
51	currThermal = 0.0;
52	needPotential = false;
53	needStress = false;
54
55	// remove center of mass drift velocity (in case we passed in a configuration
56	// that was drifting
57	velocitizer_->removeComDrift();
58
59	// initialize the forces before the first step
60	calcForce(true, true);
61
62	//execute constraint algorithm to make sure at the very beginning the system is constrained
63	//if (nConstrained) {
64	// constrainA();
65	// calcForce(true, true);
66	// constrainB();
67	//}
68
69	if (needVelocityScaling) {
70	velocitizer_->velocitize(targetScalingTemp);
71	}
72
73	dumpWriter = createDumpWriter();
74	statWriter = createStatWriter();
75
76	dumpWriter->writeDump();
77
78	//save statistics
79	thermo.saveStat();
80	saveConservedQuantity();
81
82	//before writeStat, we must save statistics
83	statWriter->writeStat(currentSnapshot_->statData);
84
85	}
86
87	void VelocityVerletIntegrator::doIntegrate() {
88
89
90	initialize();
91
92	while (currentSnapshot_->getTime() < runTime) {
93
94	preStep();
95
96	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	}
114
115	}
116
117	void VelocityVerletIntegrator::postStep() {
118
119	//save snapshot
120	info_->getSnapshotManager()->advance();
121
122	//increase time
123	currentSnapshot_->increaseTime(dt);
124
125	//save statistics
126	thermo.saveStat();
127	saveConservedQuantity();
128
129	if (needVelocityScaling) {
130	if (currentSnapshot_->getTime() >= currThermal) {
131	velocitizer_->velocitize(targetScalingTemp);
132	currThermal += thermalTime;
133	}
134	}
135
136	if (currentSnapshot_->getTime() >= currSample) {
137	dumpWriter->writeDump();
138	currSample += sampleTime;
139	}
140
141	if (currentSnapshot_->getTime() >= currStatus) {
142	statWriter->writeStat(currentSnapshot_->statData);
143	needPotential = false;
144	needStress = false;
145	currStatus += statusTime;
146	}
147
148
149	}
150
151
152	void VelocityVerletIntegrator::finalize() {
153
154	dumpWriter->writeDump();
155
156	delete dumpWriter;
157	delete statWriter;
158
159	dumpWriter = NULL;
160	statWriter = NULL;
161
162	}
163
164	void VelocityVerletIntegrator::integrateStep() {
165
166	moveA();
167	calcForce(needPotential, needStress);
168	moveB();
169	}
170
171
172	void VelocityVerletIntegrator::calcForce(bool needPotential,
173	bool needStress) {
174	forceMan_->calcForces(needPotential, needStress);
175	}
176
177	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
178	return new DumpWriter(info_, info_->getDumpFileName());
179	}
180
181	StatWriter* VelocityVerletIntegrator::createStatWriter() {
182	return new StatWriter(info_->getStatFileName());
183	}
184
185
186	} //end namespace oopse