src/integrators/VelocityVerletIntegrator.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file VelocityVerletIntegrator.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 16:16am
 * @version 1.0
 */

#include "integrators/VelocityVerletIntegrator.hpp"
#include "integrators/DLM.hpp"
#include "utils/StringUtils.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();
    
    if (simParams->getUseSolidThermInt()) {
      restWriter = createRestWriter();
      restWriter->writeZangle();
    }
    
    dumpWriter->writeDumpAndEor();
    
    
    //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->writeDumpAndEor();
    
    if (simParams->getUseSolidThermInt())
      restWriter->writeZangle();
    
    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->writeEor();
  
  if (simParams->getUseSolidThermInt()) {
    restWriter->writeZangle();
    delete restWriter;
    restWriter = NULL;
  }
  
  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_);
}

StatWriter* VelocityVerletIntegrator::createStatWriter() {
  // if solidThermInt is true, add extra information to the statfile
  if (simParams->getUseSolidThermInt()){
    StatsBitSet mask; 
    mask.set(Stats::TIME);
    mask.set(Stats::TOTAL_ENERGY);
    mask.set(Stats::POTENTIAL_ENERGY);
    mask.set(Stats::KINETIC_ENERGY);
    mask.set(Stats::TEMPERATURE);
    mask.set(Stats::PRESSURE);
    mask.set(Stats::CONSERVED_QUANTITY);
    mask.set(Stats::VRAW);
    mask.set(Stats::VHARM);
    return new StatWriter(info_->getStatFileName(), mask);
  }
  
  return new StatWriter(info_->getStatFileName());
}

RestWriter* VelocityVerletIntegrator::createRestWriter(){
  return new RestWriter(info_);
}


} //end namespace oopse
Revision:	417
Committed:	Thu Mar 10 15:10:24 2005 UTC (20 years, 7 months ago) by chrisfen
File size:	6814 byte(s)
Log Message:	First commit of the new restraints code
#	User	Rev	Content
1	gezelter	246	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file VelocityVerletIntegrator.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 16:16am
47			* @version 1.0
48			*/
49
50			#include "integrators/VelocityVerletIntegrator.hpp"
51			#include "integrators/DLM.hpp"
52	tim	276	#include "utils/StringUtils.hpp"
53	gezelter	246
54			namespace oopse {
55	chrisfen	417	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56	gezelter	246	dt2 = 0.5 * dt;
57			rotAlgo = new DLM();
58			rattle = new Rattle(info);
59	chrisfen	417	}
60
61			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	gezelter	246	delete rotAlgo;
63			delete rattle;
64	chrisfen	417	}
65
66			void VelocityVerletIntegrator::initialize(){
67
68	gezelter	246	forceMan_->init();
69	chrisfen	417
70	gezelter	246	// remove center of mass drift velocity (in case we passed in a configuration
71			// that was drifting
72			velocitizer_->removeComDrift();
73	chrisfen	417
74	gezelter	246	// initialize the forces before the first step
75			calcForce(true, true);
76	chrisfen	417
77	gezelter	246	//execute constraint algorithm to make sure at the very beginning the system is constrained
78			if (info_->getNGlobalConstraints() > 0) {
79	chrisfen	417	rattle->constraintA();
80			calcForce(true, true);
81			rattle->constraintB();
82			info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
83	gezelter	246	}
84	chrisfen	417
85	gezelter	246	if (needVelocityScaling) {
86	chrisfen	417	velocitizer_->velocitize(targetScalingTemp);
87	gezelter	246	}
88
89			dumpWriter = createDumpWriter();
90	chrisfen	417
91	gezelter	246	statWriter = createStatWriter();
92	chrisfen	417
93			if (simParams->getUseSolidThermInt()) {
94			restWriter = createRestWriter();
95			restWriter->writeZangle();
96			}
97
98	tim	376	dumpWriter->writeDumpAndEor();
99	tim	276
100	chrisfen	417
101	gezelter	246	//save statistics, before writeStat, we must save statistics
102			thermo.saveStat();
103			saveConservedQuantity();
104			statWriter->writeStat(currentSnapshot_->statData);
105	chrisfen	417
106	gezelter	246	currSample = sampleTime + currentSnapshot_->getTime();
107			currStatus = statusTime + currentSnapshot_->getTime();;
108			currThermal = thermalTime + + currentSnapshot_->getTime();
109			needPotential = false;
110			needStress = false;
111	chrisfen	417
112	gezelter	246	}
113	chrisfen	417
114	gezelter	246	void VelocityVerletIntegrator::doIntegrate() {
115	chrisfen	417
116
117			initialize();
118
119			while (currentSnapshot_->getTime() < runTime) {
120	gezelter	246
121	chrisfen	417	preStep();
122
123			integrateStep();
124
125			postStep();
126
127			}
128
129			finalize();
130
131	gezelter	246	}
132
133
134			void VelocityVerletIntegrator::preStep() {
135	chrisfen	417	double difference = currentSnapshot_->getTime() + dt - currStatus;
136
137			if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
138			needPotential = true;
139			needStress = true;
140			}
141
142	gezelter	246	}
143
144			void VelocityVerletIntegrator::postStep() {
145	chrisfen	417
146			//save snapshot
147			info_->getSnapshotManager()->advance();
148
149			//increase time
150			currentSnapshot_->increaseTime(dt);
151
152			if (needVelocityScaling) {
153			if (currentSnapshot_->getTime() >= currThermal) {
154			velocitizer_->velocitize(targetScalingTemp);
155			currThermal += thermalTime;
156			}
157			}
158
159			if (currentSnapshot_->getTime() >= currSample) {
160			dumpWriter->writeDumpAndEor();
161
162			if (simParams->getUseSolidThermInt())
163			restWriter->writeZangle();
164
165			currSample += sampleTime;
166			}
167
168			if (currentSnapshot_->getTime() >= currStatus) {
169			//save statistics, before writeStat, we must save statistics
170			thermo.saveStat();
171			saveConservedQuantity();
172			statWriter->writeStat(currentSnapshot_->statData);
173
174			needPotential = false;
175			needStress = false;
176			currStatus += statusTime;
177			}
178
179
180	gezelter	246	}
181
182
183			void VelocityVerletIntegrator::finalize() {
184	chrisfen	417	dumpWriter->writeEor();
185
186			if (simParams->getUseSolidThermInt()) {
187			restWriter->writeZangle();
188			delete restWriter;
189			restWriter = NULL;
190			}
191
192			delete dumpWriter;
193			delete statWriter;
194
195			dumpWriter = NULL;
196			statWriter = NULL;
197
198	gezelter	246	}
199
200			void VelocityVerletIntegrator::integrateStep() {
201	chrisfen	417
202			moveA();
203			calcForce(needPotential, needStress);
204			moveB();
205	gezelter	246	}
206
207
208			void VelocityVerletIntegrator::calcForce(bool needPotential,
209			bool needStress) {
210	chrisfen	417	forceMan_->calcForces(needPotential, needStress);
211	gezelter	246	}
212
213			DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
214	chrisfen	417	return new DumpWriter(info_);
215	gezelter	246	}
216
217			StatWriter* VelocityVerletIntegrator::createStatWriter() {
218	chrisfen	417	// if solidThermInt is true, add extra information to the statfile
219			if (simParams->getUseSolidThermInt()){
220			StatsBitSet mask;
221			mask.set(Stats::TIME);
222			mask.set(Stats::TOTAL_ENERGY);
223			mask.set(Stats::POTENTIAL_ENERGY);
224			mask.set(Stats::KINETIC_ENERGY);
225			mask.set(Stats::TEMPERATURE);
226			mask.set(Stats::PRESSURE);
227			mask.set(Stats::CONSERVED_QUANTITY);
228			mask.set(Stats::VRAW);
229			mask.set(Stats::VHARM);
230			return new StatWriter(info_->getStatFileName(), mask);
231			}
232
233			return new StatWriter(info_->getStatFileName());
234	gezelter	246	}
235
236	chrisfen	417	RestWriter* VelocityVerletIntegrator::createRestWriter(){
237			return new RestWriter(info_);
238			}
239	gezelter	246
240	chrisfen	417
241	gezelter	246	} //end namespace oopse