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:	2101
Committed:	Thu Mar 10 15:10:24 2005 UTC (19 years, 4 months ago) by chrisfen
File size:	6814 byte(s)
Log Message:	First commit of the new restraints code
#	Content
1	/*
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	#include "utils/StringUtils.hpp"
53
54	namespace oopse {
55	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56	dt2 = 0.5 * dt;
57	rotAlgo = new DLM();
58	rattle = new Rattle(info);
59	}
60
61	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	delete rotAlgo;
63	delete rattle;
64	}
65
66	void VelocityVerletIntegrator::initialize(){
67
68	forceMan_->init();
69
70	// remove center of mass drift velocity (in case we passed in a configuration
71	// that was drifting
72	velocitizer_->removeComDrift();
73
74	// initialize the forces before the first step
75	calcForce(true, true);
76
77	//execute constraint algorithm to make sure at the very beginning the system is constrained
78	if (info_->getNGlobalConstraints() > 0) {
79	rattle->constraintA();
80	calcForce(true, true);
81	rattle->constraintB();
82	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
83	}
84
85	if (needVelocityScaling) {
86	velocitizer_->velocitize(targetScalingTemp);
87	}
88
89	dumpWriter = createDumpWriter();
90
91	statWriter = createStatWriter();
92
93	if (simParams->getUseSolidThermInt()) {
94	restWriter = createRestWriter();
95	restWriter->writeZangle();
96	}
97
98	dumpWriter->writeDumpAndEor();
99
100
101	//save statistics, before writeStat, we must save statistics
102	thermo.saveStat();
103	saveConservedQuantity();
104	statWriter->writeStat(currentSnapshot_->statData);
105
106	currSample = sampleTime + currentSnapshot_->getTime();
107	currStatus = statusTime + currentSnapshot_->getTime();;
108	currThermal = thermalTime + + currentSnapshot_->getTime();
109	needPotential = false;
110	needStress = false;
111
112	}
113
114	void VelocityVerletIntegrator::doIntegrate() {
115
116
117	initialize();
118
119	while (currentSnapshot_->getTime() < runTime) {
120
121	preStep();
122
123	integrateStep();
124
125	postStep();
126
127	}
128
129	finalize();
130
131	}
132
133
134	void VelocityVerletIntegrator::preStep() {
135	double difference = currentSnapshot_->getTime() + dt - currStatus;
136
137	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
138	needPotential = true;
139	needStress = true;
140	}
141
142	}
143
144	void VelocityVerletIntegrator::postStep() {
145
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	}
181
182
183	void VelocityVerletIntegrator::finalize() {
184	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	}
199
200	void VelocityVerletIntegrator::integrateStep() {
201
202	moveA();
203	calcForce(needPotential, needStress);
204	moveB();
205	}
206
207
208	void VelocityVerletIntegrator::calcForce(bool needPotential,
209	bool needStress) {
210	forceMan_->calcForces(needPotential, needStress);
211	}
212
213	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
214	return new DumpWriter(info_);
215	}
216
217	StatWriter* VelocityVerletIntegrator::createStatWriter() {
218	// 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	}
235
236	RestWriter* VelocityVerletIntegrator::createRestWriter(){
237	return new RestWriter(info_);
238	}
239
240
241	} //end namespace oopse