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 the constraint algorithm to make sure that the system is
    // constrained at the very beginning  
    if (info_->getNGlobalConstraints() > 0) {
      rattle->constraintA();
      calcForce(true, true);
      rattle->constraintB();      
      //copy the current snapshot to previous snapshot
      info_->getSnapshotManager()->advance();
    }
    
    if (needVelocityScaling) {
      velocitizer_->velocitize(targetScalingTemp);
    }
    
    dumpWriter = createDumpWriter();
    
    statWriter = createStatWriter();
 
    dumpWriter->writeDumpAndEor();

    if (simParams->getUseSolidThermInt()) {
      restWriter = createRestWriter();
      restWriter->writeZAngFile();
    }
    
    //save statistics, before writeStat,  we must save statistics
    thermo.saveStat();
    saveConservedQuantity();
    if (simParams->getUseRNEMD())
      rnemd_->getStatus();

    statWriter->writeStat(currentSnapshot_->statData);
    
    currSample = sampleTime + currentSnapshot_->getTime();
    currStatus =  statusTime + currentSnapshot_->getTime();
    currThermal = thermalTime + currentSnapshot_->getTime();
    if (needReset) {
      currReset = resetTime + currentSnapshot_->getTime();
    }
    if (simParams->getUseRNEMD()){
      currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
    }
    needPotential = false;
    needStress = false;       
    
  }

  void VelocityVerletIntegrator::doIntegrate() {
  
  
    initialize();
  
    while (currentSnapshot_->getTime() < runTime) {
    
      preStep();
    
      integrateStep();
    
      postStep();
    
    }
  
    finalize();
  
  }


  void VelocityVerletIntegrator::preStep() {
    RealType 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 (useRNEMD) {
      if (currentSnapshot_->getTime() >= currRNEMD) {
        rnemd_->doSwap();
        currRNEMD += RNEMD_swapTime;
      }
    }
    
    if (currentSnapshot_->getTime() >= currSample) {
      dumpWriter->writeDumpAndEor();
      
      if (simParams->getUseSolidThermInt())
        restWriter->writeZAngFile();
      
      currSample += sampleTime;
    }
    
    if (currentSnapshot_->getTime() >= currStatus) {
      //save statistics, before writeStat,  we must save statistics
      thermo.saveStat();
      saveConservedQuantity();

      if (simParams->getUseRNEMD())
        rnemd_->getStatus();

      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->writeZAngFile();
      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_XX);
      mask.set(Stats::PRESSURE_TENSOR_XY);
      mask.set(Stats::PRESSURE_TENSOR_XZ);
      mask.set(Stats::PRESSURE_TENSOR_YX);
      mask.set(Stats::PRESSURE_TENSOR_YY);
      mask.set(Stats::PRESSURE_TENSOR_YZ);
      mask.set(Stats::PRESSURE_TENSOR_ZX);
      mask.set(Stats::PRESSURE_TENSOR_ZY);
      mask.set(Stats::PRESSURE_TENSOR_ZZ);
    }
    
    if (simParams->getAccumulateBoxDipole()) {
      mask.set(Stats::BOX_DIPOLE_X);
      mask.set(Stats::BOX_DIPOLE_Y);
      mask.set(Stats::BOX_DIPOLE_Z);
    }
   
    if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
      if (simParams->getPrintTaggedPairDistance()) {
        mask.set(Stats::TAGGED_PAIR_DISTANCE);
      }
    }

    if (simParams->getUseRNEMD()) {
      mask.set(Stats::RNEMD_SWAP_TOTAL);
    }
      

     return new StatWriter(info_->getStatFileName(), mask);
  }

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


} //end namespace oopse
Revision:	1341
Committed:	Fri May 8 19:47:05 2009 UTC (16 years, 5 months ago) by skuang
File size:	8292 byte(s)
Log Message:	Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
#	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	chrisfen	993	// remove center of mass drift velocity (in case we passed in a
71			// configuration that was drifting)
72	gezelter	246	velocitizer_->removeComDrift();
73	chrisfen	417
74	gezelter	246	// initialize the forces before the first step
75			calcForce(true, true);
76	chrisfen	417
77	chrisfen	993	// execute the constraint algorithm to make sure that the system is
78			// constrained at the very beginning
79	gezelter	246	if (info_->getNGlobalConstraints() > 0) {
80	chrisfen	417	rattle->constraintA();
81			calcForce(true, true);
82	chrisfen	993	rattle->constraintB();
83			//copy the current snapshot to previous snapshot
84			info_->getSnapshotManager()->advance();
85	gezelter	246	}
86	chrisfen	417
87	gezelter	246	if (needVelocityScaling) {
88	chrisfen	417	velocitizer_->velocitize(targetScalingTemp);
89	gezelter	246	}
90
91			dumpWriter = createDumpWriter();
92	chrisfen	417
93	gezelter	246	statWriter = createStatWriter();
94	chrisfen	993
95			dumpWriter->writeDumpAndEor();
96
97	chrisfen	417	if (simParams->getUseSolidThermInt()) {
98			restWriter = createRestWriter();
99	chrisfen	993	restWriter->writeZAngFile();
100	chrisfen	417	}
101
102	gezelter	246	//save statistics, before writeStat, we must save statistics
103			thermo.saveStat();
104			saveConservedQuantity();
105	skuang	1341	if (simParams->getUseRNEMD())
106			rnemd_->getStatus();
107
108	gezelter	246	statWriter->writeStat(currentSnapshot_->statData);
109	chrisfen	417
110	gezelter	246	currSample = sampleTime + currentSnapshot_->getTime();
111	gezelter	1329	currStatus = statusTime + currentSnapshot_->getTime();
112	tim	546	currThermal = thermalTime + currentSnapshot_->getTime();
113			if (needReset) {
114			currReset = resetTime + currentSnapshot_->getTime();
115			}
116	gezelter	1329	if (simParams->getUseRNEMD()){
117			currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
118			}
119	gezelter	246	needPotential = false;
120			needStress = false;
121	chrisfen	417
122	gezelter	507	}
123	chrisfen	417
124	gezelter	507	void VelocityVerletIntegrator::doIntegrate() {
125	chrisfen	417
126
127	gezelter	507	initialize();
128	chrisfen	417
129	gezelter	507	while (currentSnapshot_->getTime() < runTime) {
130	gezelter	246
131	gezelter	507	preStep();
132	chrisfen	417
133	gezelter	507	integrateStep();
134	chrisfen	417
135	gezelter	507	postStep();
136	chrisfen	417
137	gezelter	507	}
138	chrisfen	417
139	gezelter	507	finalize();
140	chrisfen	417
141	gezelter	507	}
142	gezelter	246
143
144	gezelter	507	void VelocityVerletIntegrator::preStep() {
145	tim	963	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
146	chrisfen	417
147	gezelter	507	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
148			needPotential = true;
149			needStress = true;
150			}
151	chrisfen	417	}
152	gezelter	246
153	gezelter	507	void VelocityVerletIntegrator::postStep() {
154	tim	749
155	gezelter	507	//save snapshot
156			info_->getSnapshotManager()->advance();
157	chrisfen	417
158	gezelter	507	//increase time
159			currentSnapshot_->increaseTime(dt);
160	chrisfen	993
161	gezelter	507	if (needVelocityScaling) {
162			if (currentSnapshot_->getTime() >= currThermal) {
163			velocitizer_->velocitize(targetScalingTemp);
164			currThermal += thermalTime;
165			}
166	chrisfen	417	}
167	gezelter	1329	if (useRNEMD) {
168			if (currentSnapshot_->getTime() >= currRNEMD) {
169			rnemd_->doSwap();
170			currRNEMD += RNEMD_swapTime;
171			}
172			}
173
174	gezelter	507	if (currentSnapshot_->getTime() >= currSample) {
175			dumpWriter->writeDumpAndEor();
176	gezelter	1329
177	gezelter	507	if (simParams->getUseSolidThermInt())
178	chrisfen	993	restWriter->writeZAngFile();
179	gezelter	1329
180	gezelter	507	currSample += sampleTime;
181			}
182	gezelter	1329
183	gezelter	507	if (currentSnapshot_->getTime() >= currStatus) {
184			//save statistics, before writeStat, we must save statistics
185			thermo.saveStat();
186			saveConservedQuantity();
187	skuang	1341
188	skuang	1338	if (simParams->getUseRNEMD())
189			rnemd_->getStatus();
190	skuang	1341
191			statWriter->writeStat(currentSnapshot_->statData);
192	gezelter	1329
193	gezelter	507	needPotential = false;
194			needStress = false;
195			currStatus += statusTime;
196			}
197	gezelter	1329
198			if (needReset && currentSnapshot_->getTime() >= currReset) {
199			resetIntegrator();
200			currReset += resetTime;
201			}
202	gezelter	507	}
203	gezelter	246
204
205	gezelter	507	void VelocityVerletIntegrator::finalize() {
206			dumpWriter->writeEor();
207	chrisfen	417
208	gezelter	507	if (simParams->getUseSolidThermInt()) {
209	chrisfen	1029	restWriter->writeZAngFile();
210	gezelter	507	delete restWriter;
211			restWriter = NULL;
212			}
213	chrisfen	417
214	gezelter	507	delete dumpWriter;
215			delete statWriter;
216	chrisfen	417
217	gezelter	507	dumpWriter = NULL;
218			statWriter = NULL;
219	chrisfen	417
220	gezelter	507	}
221	gezelter	246
222	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
223	chrisfen	417
224	gezelter	507	moveA();
225			calcForce(needPotential, needStress);
226			moveB();
227			}
228	gezelter	246
229
230	gezelter	507	void VelocityVerletIntegrator::calcForce(bool needPotential,
231			bool needStress) {
232			forceMan_->calcForces(needPotential, needStress);
233			}
234	gezelter	246
235	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
236			return new DumpWriter(info_);
237			}
238	gezelter	246
239	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
240	tim	681
241			std::string statFileFormatString = simParams->getStatFileFormat();
242			StatsBitSet mask = parseStatFileFormat(statFileFormatString);
243
244	gezelter	507	// if solidThermInt is true, add extra information to the statfile
245			if (simParams->getUseSolidThermInt()){
246			mask.set(Stats::VRAW);
247			mask.set(Stats::VHARM);
248			}
249	tim	541
250	chrisfen	993	if (simParams->havePrintPressureTensor() &&
251			simParams->getPrintPressureTensor()){
252	gezelter	1291	mask.set(Stats::PRESSURE_TENSOR_XX);
253			mask.set(Stats::PRESSURE_TENSOR_XY);
254			mask.set(Stats::PRESSURE_TENSOR_XZ);
255			mask.set(Stats::PRESSURE_TENSOR_YX);
256			mask.set(Stats::PRESSURE_TENSOR_YY);
257			mask.set(Stats::PRESSURE_TENSOR_YZ);
258			mask.set(Stats::PRESSURE_TENSOR_ZX);
259			mask.set(Stats::PRESSURE_TENSOR_ZY);
260			mask.set(Stats::PRESSURE_TENSOR_ZZ);
261	tim	541	}
262
263	chrisfen	998	if (simParams->getAccumulateBoxDipole()) {
264			mask.set(Stats::BOX_DIPOLE_X);
265			mask.set(Stats::BOX_DIPOLE_Y);
266			mask.set(Stats::BOX_DIPOLE_Z);
267			}
268	gezelter	1329
269	gezelter	1291	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
270			if (simParams->getPrintTaggedPairDistance()) {
271			mask.set(Stats::TAGGED_PAIR_DISTANCE);
272			}
273			}
274	gezelter	1329
275			if (simParams->getUseRNEMD()) {
276			mask.set(Stats::RNEMD_SWAP_TOTAL);
277			}
278	gezelter	1291
279	chrisfen	998
280	tim	681	return new StatWriter(info_->getStatFileName(), mask);
281	chrisfen	417	}
282	gezelter	246
283	gezelter	507	RestWriter* VelocityVerletIntegrator::createRestWriter(){
284			return new RestWriter(info_);
285			}
286	gezelter	246
287	chrisfen	417
288	gezelter	246	} //end namespace oopse