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, 234107 (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
 * @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() {

   
    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
      saveConservedQuantity();
      stats->collectStats();

      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;
    }        
    //save snapshot
    info_->getSnapshotManager()->advance();
  
    //increase time
    snap->increaseTime(dt);        

  }


  void VelocityVerletIntegrator::finalize() {
    dumpWriter->writeEor();
    if (simParams->getRNEMDParameters()->getUseRNEMD()) {
      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:	1856
Committed:	Tue Apr 2 21:30:34 2013 UTC (12 years, 7 months ago) by gezelter
File size:	6785 byte(s)
Log Message:	Bug fixes to get new parallel decomposition methods working without periodic boundary conditions. Updated volume in stats file correctly. LangevinHull fixes for low viscosity values.
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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			* @version 1.0
48			*/
49
50			#include "integrators/VelocityVerletIntegrator.hpp"
51			#include "integrators/DLM.hpp"
52	tim	276	#include "utils/StringUtils.hpp"
53	gezelter	1413	#include "utils/ProgressBar.hpp"
54	gezelter	246
55	gezelter	1390	namespace OpenMD {
56	gezelter	1715	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
57	gezelter	246	dt2 = 0.5 * dt;
58	chrisfen	417	}
59
60			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61			}
62
63			void VelocityVerletIntegrator::initialize(){
64
65	gezelter	1576	forceMan_->initialize();
66	chrisfen	417
67	chrisfen	993	// remove center of mass drift velocity (in case we passed in a
68			// configuration that was drifting)
69	gezelter	246	velocitizer_->removeComDrift();
70	gezelter	1715
71			// find the initial fluctuating charges.
72			flucQ_->initialize();
73	chrisfen	417
74	gezelter	246	// initialize the forces before the first step
75	gezelter	1464	calcForce();
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	gezelter	1715	rattle_->constraintA();
81	gezelter	1464	calcForce();
82	gezelter	1715	rattle_->constraintB();
83	chrisfen	993	//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	gezelter	1413	progressBar = new ProgressBar();
98
99	gezelter	246	//save statistics, before writeStat, we must save statistics
100			saveConservedQuantity();
101	gezelter	1764	stats->collectStats();
102
103	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD())
104	skuang	1368	rnemd_->getStarted();
105	skuang	1341
106	gezelter	1764	statWriter->writeStat();
107	chrisfen	417
108	gezelter	1764	currSample = sampleTime + snap->getTime();
109			currStatus = statusTime + snap->getTime();
110			currThermal = thermalTime + snap->getTime();
111	tim	546	if (needReset) {
112	gezelter	1764	currReset = resetTime + snap->getTime();
113	tim	546	}
114	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD()){
115	gezelter	1764	currRNEMD = RNEMD_exchangeTime + snap->getTime();
116	gezelter	1329	}
117	gezelter	246	needPotential = false;
118			needStress = false;
119	chrisfen	417
120	gezelter	507	}
121	gezelter	1413
122	gezelter	507	void VelocityVerletIntegrator::doIntegrate() {
123	chrisfen	417
124	gezelter	507	initialize();
125	chrisfen	417
126	gezelter	1764	while (snap->getTime() < runTime) {
127	gezelter	1715	preStep();
128			integrateStep();
129			postStep();
130			}
131	gezelter	507	finalize();
132			}
133	gezelter	246
134
135	gezelter	507	void VelocityVerletIntegrator::preStep() {
136	gezelter	1764	RealType difference = snap->getTime() + dt - currStatus;
137	chrisfen	417
138	gezelter	1390	if (difference > 0 \|\| fabs(difference) < OpenMD::epsilon) {
139	gezelter	507	needPotential = true;
140			needStress = true;
141			}
142	chrisfen	417	}
143	gezelter	246
144	gezelter	507	void VelocityVerletIntegrator::postStep() {
145	tim	749
146	chrisfen	993
147	gezelter	507	if (needVelocityScaling) {
148	gezelter	1764	if (snap->getTime() >= currThermal) {
149	gezelter	507	velocitizer_->velocitize(targetScalingTemp);
150			currThermal += thermalTime;
151			}
152	chrisfen	417	}
153	gezelter	1329	if (useRNEMD) {
154	gezelter	1764	if (snap->getTime() >= currRNEMD) {
155	skuang	1368	rnemd_->doRNEMD();
156			currRNEMD += RNEMD_exchangeTime;
157	gezelter	1329	}
158	gezelter	1396	rnemd_->collectData();
159	gezelter	1329	}
160
161	gezelter	1764	if (snap->getTime() >= currSample) {
162	gezelter	507	dumpWriter->writeDumpAndEor();
163	gezelter	1329
164	gezelter	507	currSample += sampleTime;
165			}
166	gezelter	1329
167	gezelter	1764	if (snap->getTime() >= currStatus) {
168	gezelter	507	//save statistics, before writeStat, we must save statistics
169	gezelter	1852	saveConservedQuantity();
170	gezelter	1764	stats->collectStats();
171	skuang	1341
172	gezelter	1731	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173	gezelter	1773	rnemd_->writeOutputFile();
174	skuang	1368	}
175	skuang	1341
176	gezelter	1764	statWriter->writeStat();
177	gezelter	1413
178	gezelter	1764	progressBar->setStatus(snap->getTime(), runTime);
179	gezelter	1413	progressBar->update();
180
181	gezelter	507	needPotential = false;
182			needStress = false;
183			currStatus += statusTime;
184			}
185	gezelter	1329
186	gezelter	1764	if (needReset && snap->getTime() >= currReset) {
187	gezelter	1329	resetIntegrator();
188			currReset += resetTime;
189			}
190	gezelter	1856	//save snapshot
191			info_->getSnapshotManager()->advance();
192
193			//increase time
194			snap->increaseTime(dt);
195
196	gezelter	507	}
197	gezelter	246
198
199	gezelter	507	void VelocityVerletIntegrator::finalize() {
200			dumpWriter->writeEor();
201	gezelter	1776	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202			rnemd_->writeOutputFile();
203			}
204
205	gezelter	507	delete dumpWriter;
206			delete statWriter;
207	chrisfen	417
208	gezelter	507	dumpWriter = NULL;
209			statWriter = NULL;
210			}
211	gezelter	246
212	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
213	chrisfen	417
214	gezelter	507	moveA();
215	gezelter	1464	calcForce();
216	gezelter	507	moveB();
217			}
218	gezelter	246
219
220	gezelter	1464	void VelocityVerletIntegrator::calcForce() {
221			forceMan_->calcForces();
222	gezelter	1718	flucQ_->applyConstraints();
223	gezelter	507	}
224	gezelter	246
225	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
226			return new DumpWriter(info_);
227			}
228	gezelter	246
229	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
230	tim	541
231	gezelter	1764	stats = new Stats(info_);
232			statWriter = new StatWriter(info_->getStatFileName(), stats);
233	skuang	1368
234	gezelter	1764	return statWriter;
235	chrisfen	417	}
236	gezelter	246
237	gezelter	1390	} //end namespace OpenMD