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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @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"
#include "utils/ProgressBar.hpp"

namespace OpenMD {
  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) { 
    dt2 = 0.5 * dt;
  }
  
  VelocityVerletIntegrator::~VelocityVerletIntegrator() { 
  }
  
  void VelocityVerletIntegrator::initialize(){
    
    forceMan_->initialize();
    
    // remove center of mass drift velocity (in case we passed in a
    // configuration that was drifting)
    velocitizer_->removeComDrift();

    // find the initial fluctuating charges.
    flucQ_->initialize();
    
    // initialize the forces before the first step
    calcForce();
    
    // execute the constraint algorithm to make sure that the system is
    // constrained at the very beginning  
    if (info_->getNGlobalConstraints() > 0) {
      rattle_->constraintA();
      calcForce();
      rattle_->constraintB();      
      //copy the current snapshot to previous snapshot
      info_->getSnapshotManager()->advance();
    }
    
    if (needVelocityScaling) {
      velocitizer_->velocitize(targetScalingTemp);
    }
    
    dumpWriter = createDumpWriter();
    
    statWriter = createStatWriter();
 
    dumpWriter->writeDumpAndEor();

    progressBar = new ProgressBar();

    //save statistics, before writeStat,  we must save statistics
    saveConservedQuantity();
    stats->collectStats();

    if (simParams->getRNEMDParameters()->getUseRNEMD())
      rnemd_->getStarted();

    statWriter->writeStat();
    
    currSample = sampleTime + snap->getTime();
    currStatus =  statusTime + snap->getTime();
    currThermal = thermalTime + snap->getTime();
    if (needReset) {
      currReset = resetTime + snap->getTime();
    }
    if (simParams->getRNEMDParameters()->getUseRNEMD()){
      currRNEMD = RNEMD_exchangeTime + snap->getTime();
    }
    needPotential = false;
    needStress = false;       
    
  }
 
  void VelocityVerletIntegrator::doIntegrate() {
  
    initialize();
  
    while (snap->getTime() < runTime) {    
      preStep();    
      integrateStep();    
      postStep();      
    }  
    finalize();
  }


  void VelocityVerletIntegrator::preStep() {
    RealType difference = snap->getTime() + dt - currStatus;
  
    if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
      needPotential = true;
      needStress = true;   
    }
  }

  void VelocityVerletIntegrator::postStep() {

    //save snapshot
    info_->getSnapshotManager()->advance();
  
    //increase time
    snap->increaseTime(dt);        
   
    if (needVelocityScaling) {
      if (snap->getTime() >= currThermal) {
        velocitizer_->velocitize(targetScalingTemp);
        currThermal += thermalTime;
      }
    }
    if (useRNEMD) {
      if (snap->getTime() >= currRNEMD) {
        rnemd_->doRNEMD();
        currRNEMD += RNEMD_exchangeTime;
      }
      rnemd_->collectData();
    }
    
    if (snap->getTime() >= currSample) {
      dumpWriter->writeDumpAndEor();
      
      currSample += sampleTime;
    }
    
    if (snap->getTime() >= currStatus) {
      //save statistics, before writeStat,  we must save statistics
      stats->collectStats();
      saveConservedQuantity();

      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
        rnemd_->writeOutputFile();
      }

      statWriter->writeStat();

      progressBar->setStatus(snap->getTime(), runTime);
      progressBar->update();

      needPotential = false;
      needStress = false;
      currStatus += statusTime;
    }
    
    if (needReset && snap->getTime() >= currReset) {    
      resetIntegrator();
      currReset += resetTime;
    }        
  }


  void VelocityVerletIntegrator::finalize() {
    dumpWriter->writeEor();
    rnemd_->writeOutputFile();
  
    delete dumpWriter;
    delete statWriter;
  
    dumpWriter = NULL;
    statWriter = NULL;
  }

  void VelocityVerletIntegrator::integrateStep() { 
  
    moveA();
    calcForce();
    moveB();
  }


  void VelocityVerletIntegrator::calcForce() { 
    forceMan_->calcForces();
    flucQ_->applyConstraints();
  }

  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
    return new DumpWriter(info_);
  }

  StatWriter* VelocityVerletIntegrator::createStatWriter() {
    
    stats = new Stats(info_);
    statWriter = new StatWriter(info_->getStatFileName(), stats);
    
    return statWriter;
  }

} //end namespace OpenMD
Revision:	1773
Committed:	Tue Aug 7 18:26:40 2012 UTC (12 years, 8 months ago) by gezelter
File size:	6735 byte(s)
Log Message:	Adding new RNEMD options and output file format
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			/**
44			* @file VelocityVerletIntegrator.cpp
45			* @author tlin
46			* @date 11/09/2004
47			* @time 16:16am
48			* @version 1.0
49			*/
50
51			#include "integrators/VelocityVerletIntegrator.hpp"
52			#include "integrators/DLM.hpp"
53	tim	276	#include "utils/StringUtils.hpp"
54	gezelter	1413	#include "utils/ProgressBar.hpp"
55	gezelter	246
56	gezelter	1390	namespace OpenMD {
57	gezelter	1715	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
58	gezelter	246	dt2 = 0.5 * dt;
59	chrisfen	417	}
60
61			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62			}
63
64			void VelocityVerletIntegrator::initialize(){
65
66	gezelter	1576	forceMan_->initialize();
67	chrisfen	417
68	chrisfen	993	// remove center of mass drift velocity (in case we passed in a
69			// configuration that was drifting)
70	gezelter	246	velocitizer_->removeComDrift();
71	gezelter	1715
72			// find the initial fluctuating charges.
73			flucQ_->initialize();
74	chrisfen	417
75	gezelter	246	// initialize the forces before the first step
76	gezelter	1464	calcForce();
77	chrisfen	417
78	chrisfen	993	// execute the constraint algorithm to make sure that the system is
79			// constrained at the very beginning
80	gezelter	246	if (info_->getNGlobalConstraints() > 0) {
81	gezelter	1715	rattle_->constraintA();
82	gezelter	1464	calcForce();
83	gezelter	1715	rattle_->constraintB();
84	chrisfen	993	//copy the current snapshot to previous snapshot
85			info_->getSnapshotManager()->advance();
86	gezelter	246	}
87	chrisfen	417
88	gezelter	246	if (needVelocityScaling) {
89	chrisfen	417	velocitizer_->velocitize(targetScalingTemp);
90	gezelter	246	}
91
92			dumpWriter = createDumpWriter();
93	chrisfen	417
94	gezelter	246	statWriter = createStatWriter();
95	chrisfen	993
96			dumpWriter->writeDumpAndEor();
97
98	gezelter	1413	progressBar = new ProgressBar();
99
100	gezelter	246	//save statistics, before writeStat, we must save statistics
101			saveConservedQuantity();
102	gezelter	1764	stats->collectStats();
103
104	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD())
105	skuang	1368	rnemd_->getStarted();
106	skuang	1341
107	gezelter	1764	statWriter->writeStat();
108	chrisfen	417
109	gezelter	1764	currSample = sampleTime + snap->getTime();
110			currStatus = statusTime + snap->getTime();
111			currThermal = thermalTime + snap->getTime();
112	tim	546	if (needReset) {
113	gezelter	1764	currReset = resetTime + snap->getTime();
114	tim	546	}
115	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD()){
116	gezelter	1764	currRNEMD = RNEMD_exchangeTime + snap->getTime();
117	gezelter	1329	}
118	gezelter	246	needPotential = false;
119			needStress = false;
120	chrisfen	417
121	gezelter	507	}
122	gezelter	1413
123	gezelter	507	void VelocityVerletIntegrator::doIntegrate() {
124	chrisfen	417
125	gezelter	507	initialize();
126	chrisfen	417
127	gezelter	1764	while (snap->getTime() < runTime) {
128	gezelter	1715	preStep();
129			integrateStep();
130			postStep();
131			}
132	gezelter	507	finalize();
133			}
134	gezelter	246
135
136	gezelter	507	void VelocityVerletIntegrator::preStep() {
137	gezelter	1764	RealType difference = snap->getTime() + dt - currStatus;
138	chrisfen	417
139	gezelter	1390	if (difference > 0 \|\| fabs(difference) < OpenMD::epsilon) {
140	gezelter	507	needPotential = true;
141			needStress = true;
142			}
143	chrisfen	417	}
144	gezelter	246
145	gezelter	507	void VelocityVerletIntegrator::postStep() {
146	tim	749
147	gezelter	507	//save snapshot
148			info_->getSnapshotManager()->advance();
149	chrisfen	417
150	gezelter	507	//increase time
151	gezelter	1764	snap->increaseTime(dt);
152	chrisfen	993
153	gezelter	507	if (needVelocityScaling) {
154	gezelter	1764	if (snap->getTime() >= currThermal) {
155	gezelter	507	velocitizer_->velocitize(targetScalingTemp);
156			currThermal += thermalTime;
157			}
158	chrisfen	417	}
159	gezelter	1329	if (useRNEMD) {
160	gezelter	1764	if (snap->getTime() >= currRNEMD) {
161	skuang	1368	rnemd_->doRNEMD();
162			currRNEMD += RNEMD_exchangeTime;
163	gezelter	1329	}
164	gezelter	1396	rnemd_->collectData();
165	gezelter	1329	}
166
167	gezelter	1764	if (snap->getTime() >= currSample) {
168	gezelter	507	dumpWriter->writeDumpAndEor();
169	gezelter	1329
170	gezelter	507	currSample += sampleTime;
171			}
172	gezelter	1329
173	gezelter	1764	if (snap->getTime() >= currStatus) {
174	gezelter	507	//save statistics, before writeStat, we must save statistics
175	gezelter	1764	stats->collectStats();
176	gezelter	507	saveConservedQuantity();
177	skuang	1341
178	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
179	gezelter	1773	rnemd_->writeOutputFile();
180	skuang	1368	}
181	skuang	1341
182	gezelter	1764	statWriter->writeStat();
183	gezelter	1413
184	gezelter	1764	progressBar->setStatus(snap->getTime(), runTime);
185	gezelter	1413	progressBar->update();
186
187	gezelter	507	needPotential = false;
188			needStress = false;
189			currStatus += statusTime;
190			}
191	gezelter	1329
192	gezelter	1764	if (needReset && snap->getTime() >= currReset) {
193	gezelter	1329	resetIntegrator();
194			currReset += resetTime;
195			}
196	gezelter	507	}
197	gezelter	246
198
199	gezelter	507	void VelocityVerletIntegrator::finalize() {
200			dumpWriter->writeEor();
201	gezelter	1773	rnemd_->writeOutputFile();
202	chrisfen	417
203	gezelter	507	delete dumpWriter;
204			delete statWriter;
205	chrisfen	417
206	gezelter	507	dumpWriter = NULL;
207			statWriter = NULL;
208			}
209	gezelter	246
210	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
211	chrisfen	417
212	gezelter	507	moveA();
213	gezelter	1464	calcForce();
214	gezelter	507	moveB();
215			}
216	gezelter	246
217
218	gezelter	1464	void VelocityVerletIntegrator::calcForce() {
219			forceMan_->calcForces();
220	gezelter	1718	flucQ_->applyConstraints();
221	gezelter	507	}
222	gezelter	246
223	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224			return new DumpWriter(info_);
225			}
226	gezelter	246
227	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
228	tim	541
229	gezelter	1764	stats = new Stats(info_);
230			statWriter = new StatWriter(info_->getStatFileName(), stats);
231	skuang	1368
232	gezelter	1764	return statWriter;
233	chrisfen	417	}
234	gezelter	246
235	gezelter	1390	} //end namespace OpenMD