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();
    if (needReset) {
      currReset = resetTime + 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;
    }

      if (needReset && currentSnapshot_->getTime() >= currReset) {    
        resetIntegrator();
        currReset += resetTime;
      }
  
  }


  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() {

    std::string statFileFormatString = simParams->getStatFileFormat();
    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
    
    // if solidThermInt is true, add extra information to the statfile
    if (simParams->getUseSolidThermInt()){
      mask.set(Stats::VRAW);
      mask.set(Stats::VHARM);
    }

    if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
        mask.set(Stats::PRESSURE_TENSOR_X);
        mask.set(Stats::PRESSURE_TENSOR_Y);
        mask.set(Stats::PRESSURE_TENSOR_Z);
    }
    
     return new StatWriter(info_->getStatFileName(), mask);
  }

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


} //end namespace oopse
Revision:	770
Committed:	Fri Dec 2 15:38:03 2005 UTC (19 years, 5 months ago) by tim
Original Path:	*trunk/src/integrators/VelocityVerletIntegrator.cpp*
File size:	7181 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	tim	546	currThermal = thermalTime + currentSnapshot_->getTime();
109			if (needReset) {
110			currReset = resetTime + currentSnapshot_->getTime();
111			}
112	gezelter	246	needPotential = false;
113			needStress = false;
114	chrisfen	417
115	gezelter	507	}
116	chrisfen	417
117	gezelter	507	void VelocityVerletIntegrator::doIntegrate() {
118	chrisfen	417
119
120	gezelter	507	initialize();
121	chrisfen	417
122	gezelter	507	while (currentSnapshot_->getTime() < runTime) {
123	gezelter	246
124	gezelter	507	preStep();
125	chrisfen	417
126	gezelter	507	integrateStep();
127	chrisfen	417
128	gezelter	507	postStep();
129	chrisfen	417
130	gezelter	507	}
131	chrisfen	417
132	gezelter	507	finalize();
133	chrisfen	417
134	gezelter	507	}
135	gezelter	246
136
137	gezelter	507	void VelocityVerletIntegrator::preStep() {
138			double difference = currentSnapshot_->getTime() + dt - currStatus;
139	chrisfen	417
140	gezelter	507	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
141			needPotential = true;
142			needStress = true;
143			}
144	tim	749
145	chrisfen	417	}
146	gezelter	246
147	gezelter	507	void VelocityVerletIntegrator::postStep() {
148	tim	749
149	gezelter	507	//save snapshot
150			info_->getSnapshotManager()->advance();
151	chrisfen	417
152	gezelter	507	//increase time
153			currentSnapshot_->increaseTime(dt);
154	chrisfen	417
155	gezelter	507	if (needVelocityScaling) {
156			if (currentSnapshot_->getTime() >= currThermal) {
157			velocitizer_->velocitize(targetScalingTemp);
158			currThermal += thermalTime;
159			}
160	chrisfen	417	}
161
162	gezelter	507	if (currentSnapshot_->getTime() >= currSample) {
163			dumpWriter->writeDumpAndEor();
164	chrisfen	417
165	gezelter	507	if (simParams->getUseSolidThermInt())
166			restWriter->writeZangle();
167	chrisfen	417
168	gezelter	507	currSample += sampleTime;
169			}
170	chrisfen	417
171	gezelter	507	if (currentSnapshot_->getTime() >= currStatus) {
172			//save statistics, before writeStat, we must save statistics
173			thermo.saveStat();
174			saveConservedQuantity();
175			statWriter->writeStat(currentSnapshot_->statData);
176	chrisfen	417
177	gezelter	507	needPotential = false;
178			needStress = false;
179			currStatus += statusTime;
180			}
181	tim	546
182			if (needReset && currentSnapshot_->getTime() >= currReset) {
183			resetIntegrator();
184			currReset += resetTime;
185			}
186	chrisfen	417
187	gezelter	507	}
188	gezelter	246
189
190	gezelter	507	void VelocityVerletIntegrator::finalize() {
191			dumpWriter->writeEor();
192	chrisfen	417
193	gezelter	507	if (simParams->getUseSolidThermInt()) {
194			restWriter->writeZangle();
195			delete restWriter;
196			restWriter = NULL;
197			}
198	chrisfen	417
199	gezelter	507	delete dumpWriter;
200			delete statWriter;
201	chrisfen	417
202	gezelter	507	dumpWriter = NULL;
203			statWriter = NULL;
204	chrisfen	417
205	gezelter	507	}
206	gezelter	246
207	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
208	chrisfen	417
209	gezelter	507	moveA();
210			calcForce(needPotential, needStress);
211			moveB();
212			}
213	gezelter	246
214
215	gezelter	507	void VelocityVerletIntegrator::calcForce(bool needPotential,
216			bool needStress) {
217			forceMan_->calcForces(needPotential, needStress);
218			}
219	gezelter	246
220	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
221			return new DumpWriter(info_);
222			}
223	gezelter	246
224	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
225	tim	681
226			std::string statFileFormatString = simParams->getStatFileFormat();
227			StatsBitSet mask = parseStatFileFormat(statFileFormatString);
228
229	gezelter	507	// if solidThermInt is true, add extra information to the statfile
230			if (simParams->getUseSolidThermInt()){
231			mask.set(Stats::VRAW);
232			mask.set(Stats::VHARM);
233			}
234	tim	541
235	chuckv	542	if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
236	tim	541	mask.set(Stats::PRESSURE_TENSOR_X);
237			mask.set(Stats::PRESSURE_TENSOR_Y);
238			mask.set(Stats::PRESSURE_TENSOR_Z);
239			}
240
241	tim	681	return new StatWriter(info_->getStatFileName(), mask);
242	chrisfen	417	}
243	gezelter	246
244	gezelter	507	RestWriter* VelocityVerletIntegrator::createRestWriter(){
245			return new RestWriter(info_);
246			}
247	gezelter	246
248	chrisfen	417
249	gezelter	246	} //end namespace oopse