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();

    //save statistics, before writeStat,  we must save statistics
    thermo.saveStat();
    saveConservedQuantity();
    if (simParams->getUseRNEMD())
      rnemd_->getStarted();

    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_exchangeTime + 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) {
      rnemd_->collectData();
      if (currentSnapshot_->getTime() >= currRNEMD) {
        rnemd_->doRNEMD();
        currRNEMD += RNEMD_exchangeTime;
      }
    }
    
    if (currentSnapshot_->getTime() >= currSample) {
      dumpWriter->writeDumpAndEor();
      
      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();
  
    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 we're doing a thermodynamic integration, we'll want the raw
    // potential as well as the full potential:

 
    if (simParams->getUseThermodynamicIntegration()) 
      mask.set(Stats::VRAW);

    // if we've got restraints turned on, we'll also want a report of the
    // total harmonic restraints
    if (simParams->getUseRestraints()){
      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_EXCHANGE_TOTAL);
    }
    

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


} //end namespace oopse
Revision:	3541
Committed:	Mon Oct 19 13:39:04 2009 UTC (15 years, 7 months ago) by skuang
File size:	8103 byte(s)
Log Message:	added RNEMD scaling
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	1960	#include "utils/StringUtils.hpp"
53	gezelter	1930
54			namespace oopse {
55	chrisfen	2101	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56	gezelter	1930	dt2 = 0.5 * dt;
57			rotAlgo = new DLM();
58			rattle = new Rattle(info);
59	chrisfen	2101	}
60
61			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	gezelter	1930	delete rotAlgo;
63			delete rattle;
64	chrisfen	2101	}
65
66			void VelocityVerletIntegrator::initialize(){
67
68	gezelter	1930	forceMan_->init();
69	chrisfen	2101
70	chrisfen	2879	// remove center of mass drift velocity (in case we passed in a
71			// configuration that was drifting)
72	gezelter	1930	velocitizer_->removeComDrift();
73	chrisfen	2101
74	gezelter	1930	// initialize the forces before the first step
75			calcForce(true, true);
76	chrisfen	2101
77	chrisfen	2879	// execute the constraint algorithm to make sure that the system is
78			// constrained at the very beginning
79	gezelter	1930	if (info_->getNGlobalConstraints() > 0) {
80	chrisfen	2101	rattle->constraintA();
81			calcForce(true, true);
82	chrisfen	2879	rattle->constraintB();
83			//copy the current snapshot to previous snapshot
84			info_->getSnapshotManager()->advance();
85	gezelter	1930	}
86	chrisfen	2101
87	gezelter	1930	if (needVelocityScaling) {
88	chrisfen	2101	velocitizer_->velocitize(targetScalingTemp);
89	gezelter	1930	}
90
91			dumpWriter = createDumpWriter();
92	chrisfen	2101
93	gezelter	1930	statWriter = createStatWriter();
94	chrisfen	2879
95			dumpWriter->writeDumpAndEor();
96
97	gezelter	1930	//save statistics, before writeStat, we must save statistics
98			thermo.saveStat();
99			saveConservedQuantity();
100	skuang	3501	if (simParams->getUseRNEMD())
101	skuang	3541	rnemd_->getStarted();
102	skuang	3501
103	gezelter	1930	statWriter->writeStat(currentSnapshot_->statData);
104	chrisfen	2101
105	gezelter	1930	currSample = sampleTime + currentSnapshot_->getTime();
106	gezelter	3488	currStatus = statusTime + currentSnapshot_->getTime();
107	tim	2243	currThermal = thermalTime + currentSnapshot_->getTime();
108			if (needReset) {
109			currReset = resetTime + currentSnapshot_->getTime();
110			}
111	gezelter	3488	if (simParams->getUseRNEMD()){
112	skuang	3541	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
113	gezelter	3488	}
114	gezelter	1930	needPotential = false;
115			needStress = false;
116	chrisfen	2101
117	gezelter	2204	}
118	chrisfen	2101
119	gezelter	2204	void VelocityVerletIntegrator::doIntegrate() {
120	chrisfen	2101
121
122	gezelter	2204	initialize();
123	chrisfen	2101
124	gezelter	2204	while (currentSnapshot_->getTime() < runTime) {
125	gezelter	1930
126	gezelter	2204	preStep();
127	chrisfen	2101
128	gezelter	2204	integrateStep();
129	chrisfen	2101
130	gezelter	2204	postStep();
131	chrisfen	2101
132	gezelter	2204	}
133	chrisfen	2101
134	gezelter	2204	finalize();
135	chrisfen	2101
136	gezelter	2204	}
137	gezelter	1930
138
139	gezelter	2204	void VelocityVerletIntegrator::preStep() {
140	tim	2759	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141	chrisfen	2101
142	gezelter	2204	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
143			needPotential = true;
144			needStress = true;
145			}
146	chrisfen	2101	}
147	gezelter	1930
148	gezelter	2204	void VelocityVerletIntegrator::postStep() {
149	tim	2448
150	gezelter	2204	//save snapshot
151			info_->getSnapshotManager()->advance();
152	chrisfen	2101
153	gezelter	2204	//increase time
154			currentSnapshot_->increaseTime(dt);
155	chrisfen	2879
156	gezelter	2204	if (needVelocityScaling) {
157			if (currentSnapshot_->getTime() >= currThermal) {
158			velocitizer_->velocitize(targetScalingTemp);
159			currThermal += thermalTime;
160			}
161	chrisfen	2101	}
162	gezelter	3488	if (useRNEMD) {
163	skuang	3541	rnemd_->collectData();
164	gezelter	3488	if (currentSnapshot_->getTime() >= currRNEMD) {
165	skuang	3541	rnemd_->doRNEMD();
166			currRNEMD += RNEMD_exchangeTime;
167	gezelter	3488	}
168			}
169
170	gezelter	2204	if (currentSnapshot_->getTime() >= currSample) {
171			dumpWriter->writeDumpAndEor();
172	gezelter	3488
173	gezelter	2204	currSample += sampleTime;
174			}
175	gezelter	3488
176	gezelter	2204	if (currentSnapshot_->getTime() >= currStatus) {
177			//save statistics, before writeStat, we must save statistics
178			thermo.saveStat();
179			saveConservedQuantity();
180	skuang	3501
181	skuang	3541	if (simParams->getUseRNEMD()) {
182	skuang	3498	rnemd_->getStatus();
183	skuang	3541	}
184	skuang	3501
185			statWriter->writeStat(currentSnapshot_->statData);
186	gezelter	3488
187	gezelter	2204	needPotential = false;
188			needStress = false;
189			currStatus += statusTime;
190			}
191	gezelter	3488
192			if (needReset && currentSnapshot_->getTime() >= currReset) {
193			resetIntegrator();
194			currReset += resetTime;
195			}
196	gezelter	2204	}
197	gezelter	1930
198
199	gezelter	2204	void VelocityVerletIntegrator::finalize() {
200			dumpWriter->writeEor();
201	chrisfen	2101
202	gezelter	2204	delete dumpWriter;
203			delete statWriter;
204	chrisfen	2101
205	gezelter	2204	dumpWriter = NULL;
206			statWriter = NULL;
207	chrisfen	2101
208	gezelter	2204	}
209	gezelter	1930
210	gezelter	2204	void VelocityVerletIntegrator::integrateStep() {
211	chrisfen	2101
212	gezelter	2204	moveA();
213			calcForce(needPotential, needStress);
214			moveB();
215			}
216	gezelter	1930
217
218	gezelter	2204	void VelocityVerletIntegrator::calcForce(bool needPotential,
219			bool needStress) {
220			forceMan_->calcForces(needPotential, needStress);
221			}
222	gezelter	1930
223	gezelter	2204	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224			return new DumpWriter(info_);
225			}
226	gezelter	1930
227	gezelter	2204	StatWriter* VelocityVerletIntegrator::createStatWriter() {
228	tim	2380
229			std::string statFileFormatString = simParams->getStatFileFormat();
230			StatsBitSet mask = parseStatFileFormat(statFileFormatString);
231	cli2	3520
232			// if we're doing a thermodynamic integration, we'll want the raw
233			// potential as well as the full potential:
234
235
236			if (simParams->getUseThermodynamicIntegration())
237	gezelter	2204	mask.set(Stats::VRAW);
238	cli2	3520
239			// if we've got restraints turned on, we'll also want a report of the
240			// total harmonic restraints
241			if (simParams->getUseRestraints()){
242	gezelter	2204	mask.set(Stats::VHARM);
243			}
244	tim	2238
245	chrisfen	2879	if (simParams->havePrintPressureTensor() &&
246			simParams->getPrintPressureTensor()){
247	gezelter	3448	mask.set(Stats::PRESSURE_TENSOR_XX);
248			mask.set(Stats::PRESSURE_TENSOR_XY);
249			mask.set(Stats::PRESSURE_TENSOR_XZ);
250			mask.set(Stats::PRESSURE_TENSOR_YX);
251			mask.set(Stats::PRESSURE_TENSOR_YY);
252			mask.set(Stats::PRESSURE_TENSOR_YZ);
253			mask.set(Stats::PRESSURE_TENSOR_ZX);
254			mask.set(Stats::PRESSURE_TENSOR_ZY);
255			mask.set(Stats::PRESSURE_TENSOR_ZZ);
256	tim	2238	}
257
258	chrisfen	2917	if (simParams->getAccumulateBoxDipole()) {
259			mask.set(Stats::BOX_DIPOLE_X);
260			mask.set(Stats::BOX_DIPOLE_Y);
261			mask.set(Stats::BOX_DIPOLE_Z);
262			}
263	gezelter	3488
264	gezelter	3448	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
265			if (simParams->getPrintTaggedPairDistance()) {
266			mask.set(Stats::TAGGED_PAIR_DISTANCE);
267			}
268			}
269	gezelter	3488
270			if (simParams->getUseRNEMD()) {
271	skuang	3541	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272	gezelter	3488	}
273	skuang	3541
274	chrisfen	2917
275	skuang	3541	return new StatWriter(info_->getStatFileName(), mask);
276	chrisfen	2101	}
277	gezelter	1930
278
279			} //end namespace oopse