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:	1878
Committed:	Thu Jun 13 14:26:09 2013 UTC (11 years, 10 months ago) by gezelter
File size:	6782 byte(s)
Log Message:	Fixed a DumpWriter parallel bug.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	#include "utils/StringUtils.hpp"
53	#include "utils/ProgressBar.hpp"
54
55	namespace OpenMD {
56	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
57	dt2 = 0.5 * dt;
58	}
59
60	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61	}
62
63	void VelocityVerletIntegrator::initialize(){
64
65	forceMan_->initialize();
66
67	// remove center of mass drift velocity (in case we passed in a
68	// configuration that was drifting)
69	velocitizer_->removeComDrift();
70
71	// find the initial fluctuating charges.
72	flucQ_->initialize();
73
74	// initialize the forces before the first step
75	calcForce();
76
77	// execute the constraint algorithm to make sure that the system is
78	// constrained at the very beginning
79	if (info_->getNGlobalConstraints() > 0) {
80	rattle_->constraintA();
81	calcForce();
82	rattle_->constraintB();
83	//copy the current snapshot to previous snapshot
84	info_->getSnapshotManager()->advance();
85	}
86
87	if (needVelocityScaling) {
88	velocitizer_->velocitize(targetScalingTemp);
89	}
90
91	dumpWriter = createDumpWriter();
92
93	statWriter = createStatWriter();
94
95	dumpWriter->writeDumpAndEor();
96
97	progressBar = new ProgressBar();
98
99	//save statistics, before writeStat, we must save statistics
100	saveConservedQuantity();
101	stats->collectStats();
102
103	if (simParams->getRNEMDParameters()->getUseRNEMD())
104	rnemd_->getStarted();
105
106	statWriter->writeStat();
107
108	currSample = sampleTime + snap->getTime();
109	currStatus = statusTime + snap->getTime();
110	currThermal = thermalTime + snap->getTime();
111	if (needReset) {
112	currReset = resetTime + snap->getTime();
113	}
114	if (simParams->getRNEMDParameters()->getUseRNEMD()){
115	currRNEMD = RNEMD_exchangeTime + snap->getTime();
116	}
117	needPotential = false;
118	needStress = false;
119
120	}
121
122	void VelocityVerletIntegrator::doIntegrate() {
123
124	initialize();
125
126	while (snap->getTime() < runTime) {
127	preStep();
128	integrateStep();
129	postStep();
130	}
131	finalize();
132	}
133
134
135	void VelocityVerletIntegrator::preStep() {
136	RealType difference = snap->getTime() + dt - currStatus;
137
138	if (difference > 0 \|\| fabs(difference) < OpenMD::epsilon) {
139	needPotential = true;
140	needStress = true;
141	}
142	}
143
144	void VelocityVerletIntegrator::postStep() {
145
146
147	if (needVelocityScaling) {
148	if (snap->getTime() >= currThermal) {
149	velocitizer_->velocitize(targetScalingTemp);
150	currThermal += thermalTime;
151	}
152	}
153	if (useRNEMD) {
154	if (snap->getTime() >= currRNEMD) {
155	rnemd_->doRNEMD();
156	currRNEMD += RNEMD_exchangeTime;
157	}
158	rnemd_->collectData();
159	}
160
161	if (snap->getTime() >= currSample) {
162	dumpWriter->writeDumpAndEor();
163
164	currSample += sampleTime;
165	}
166
167	if (snap->getTime() >= currStatus) {
168	//save statistics, before writeStat, we must save statistics
169	saveConservedQuantity();
170	stats->collectStats();
171
172	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173	rnemd_->writeOutputFile();
174	}
175
176	statWriter->writeStat();
177
178	progressBar->setStatus(snap->getTime(), runTime);
179	progressBar->update();
180
181	needPotential = false;
182	needStress = false;
183	currStatus += statusTime;
184	}
185
186	if (needReset && snap->getTime() >= currReset) {
187	resetIntegrator();
188	currReset += resetTime;
189	}
190	//save snapshot
191	info_->getSnapshotManager()->advance();
192
193	//increase time
194	snap->increaseTime(dt);
195
196	}
197
198
199	void VelocityVerletIntegrator::finalize() {
200	dumpWriter->writeEor();
201	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202	rnemd_->writeOutputFile();
203	}
204
205	delete dumpWriter;
206	delete statWriter;
207
208	dumpWriter = NULL;
209	statWriter = NULL;
210	}
211
212	void VelocityVerletIntegrator::integrateStep() {
213
214	moveA();
215	calcForce();
216	moveB();
217	}
218
219
220	void VelocityVerletIntegrator::calcForce() {
221	forceMan_->calcForces();
222	flucQ_->applyConstraints();
223	}
224
225	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
226	return new DumpWriter(info_);
227	}
228
229	StatWriter* VelocityVerletIntegrator::createStatWriter() {
230
231	stats = new Stats(info_);
232	statWriter = new StatWriter(info_->getStatFileName(), stats);
233
234	return statWriter;
235	}
236
237	} //end namespace OpenMD