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), rotAlgo(NULL) { 
    dt2 = 0.5 * dt;
    rotAlgo = new DLM();
    rattle = new Rattle(info);
  }
  
  VelocityVerletIntegrator::~VelocityVerletIntegrator() { 
    delete rotAlgo;
    delete rattle;
  }
  
  void VelocityVerletIntegrator::initialize(){
    
    forceMan_->initialize();
    
    // 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();
    
    // 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
    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) < OpenMD::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_->doRNEMD();
        currRNEMD += RNEMD_exchangeTime;
      }
      rnemd_->collectData();
    }
    
    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);

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

      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();
    moveB();
  }


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

  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 OpenMD
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	8272 byte(s)
Log Message:	updated copyright notices
#	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	chrisfen	417	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
58	gezelter	246	dt2 = 0.5 * dt;
59			rotAlgo = new DLM();
60			rattle = new Rattle(info);
61	chrisfen	417	}
62
63			VelocityVerletIntegrator::~VelocityVerletIntegrator() {
64	gezelter	246	delete rotAlgo;
65			delete rattle;
66	chrisfen	417	}
67
68			void VelocityVerletIntegrator::initialize(){
69
70	gezelter	1576	forceMan_->initialize();
71	chrisfen	417
72	chrisfen	993	// remove center of mass drift velocity (in case we passed in a
73			// configuration that was drifting)
74	gezelter	246	velocitizer_->removeComDrift();
75	chrisfen	417
76	gezelter	246	// initialize the forces before the first step
77	gezelter	1464	calcForce();
78	chrisfen	417
79	chrisfen	993	// execute the constraint algorithm to make sure that the system is
80			// constrained at the very beginning
81	gezelter	246	if (info_->getNGlobalConstraints() > 0) {
82	chrisfen	417	rattle->constraintA();
83	gezelter	1464	calcForce();
84	chrisfen	993	rattle->constraintB();
85			//copy the current snapshot to previous snapshot
86			info_->getSnapshotManager()->advance();
87	gezelter	246	}
88	chrisfen	417
89	gezelter	246	if (needVelocityScaling) {
90	chrisfen	417	velocitizer_->velocitize(targetScalingTemp);
91	gezelter	246	}
92
93			dumpWriter = createDumpWriter();
94	chrisfen	417
95	gezelter	246	statWriter = createStatWriter();
96	chrisfen	993
97			dumpWriter->writeDumpAndEor();
98
99	gezelter	1413	progressBar = new ProgressBar();
100
101	gezelter	246	//save statistics, before writeStat, we must save statistics
102			thermo.saveStat();
103			saveConservedQuantity();
104	skuang	1341	if (simParams->getUseRNEMD())
105	skuang	1368	rnemd_->getStarted();
106	skuang	1341
107	gezelter	246	statWriter->writeStat(currentSnapshot_->statData);
108	chrisfen	417
109	gezelter	246	currSample = sampleTime + currentSnapshot_->getTime();
110	gezelter	1329	currStatus = statusTime + currentSnapshot_->getTime();
111	tim	546	currThermal = thermalTime + currentSnapshot_->getTime();
112			if (needReset) {
113			currReset = resetTime + currentSnapshot_->getTime();
114			}
115	gezelter	1329	if (simParams->getUseRNEMD()){
116	skuang	1368	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->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
126	gezelter	507	initialize();
127	chrisfen	417
128	gezelter	507	while (currentSnapshot_->getTime() < runTime) {
129	gezelter	246
130	gezelter	507	preStep();
131	chrisfen	417
132	gezelter	507	integrateStep();
133	chrisfen	417
134	gezelter	507	postStep();
135	gezelter	1413
136	gezelter	507	}
137	chrisfen	417
138	gezelter	507	finalize();
139	chrisfen	417
140	gezelter	507	}
141	gezelter	246
142
143	gezelter	507	void VelocityVerletIntegrator::preStep() {
144	tim	963	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
145	chrisfen	417
146	gezelter	1390	if (difference > 0 \|\| fabs(difference) < OpenMD::epsilon) {
147	gezelter	507	needPotential = true;
148			needStress = true;
149			}
150	chrisfen	417	}
151	gezelter	246
152	gezelter	507	void VelocityVerletIntegrator::postStep() {
153	tim	749
154	gezelter	507	//save snapshot
155			info_->getSnapshotManager()->advance();
156	chrisfen	417
157	gezelter	507	//increase time
158			currentSnapshot_->increaseTime(dt);
159	chrisfen	993
160	gezelter	507	if (needVelocityScaling) {
161			if (currentSnapshot_->getTime() >= currThermal) {
162			velocitizer_->velocitize(targetScalingTemp);
163			currThermal += thermalTime;
164			}
165	chrisfen	417	}
166	gezelter	1329	if (useRNEMD) {
167			if (currentSnapshot_->getTime() >= currRNEMD) {
168	skuang	1368	rnemd_->doRNEMD();
169			currRNEMD += RNEMD_exchangeTime;
170	gezelter	1329	}
171	gezelter	1396	rnemd_->collectData();
172	gezelter	1329	}
173
174	gezelter	507	if (currentSnapshot_->getTime() >= currSample) {
175			dumpWriter->writeDumpAndEor();
176	gezelter	1329
177	gezelter	507	currSample += sampleTime;
178			}
179	gezelter	1329
180	gezelter	507	if (currentSnapshot_->getTime() >= currStatus) {
181			//save statistics, before writeStat, we must save statistics
182			thermo.saveStat();
183			saveConservedQuantity();
184	skuang	1341
185	skuang	1368	if (simParams->getUseRNEMD()) {
186	skuang	1338	rnemd_->getStatus();
187	skuang	1368	}
188	skuang	1341
189			statWriter->writeStat(currentSnapshot_->statData);
190	gezelter	1413
191			progressBar->setStatus(currentSnapshot_->getTime(), runTime);
192			progressBar->update();
193
194	gezelter	507	needPotential = false;
195			needStress = false;
196			currStatus += statusTime;
197			}
198	gezelter	1329
199			if (needReset && currentSnapshot_->getTime() >= currReset) {
200			resetIntegrator();
201			currReset += resetTime;
202			}
203	gezelter	507	}
204	gezelter	246
205
206	gezelter	507	void VelocityVerletIntegrator::finalize() {
207			dumpWriter->writeEor();
208	chrisfen	417
209	gezelter	507	delete dumpWriter;
210			delete statWriter;
211	chrisfen	417
212	gezelter	507	dumpWriter = NULL;
213			statWriter = NULL;
214	chrisfen	417
215	gezelter	507	}
216	gezelter	246
217	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
218	chrisfen	417
219	gezelter	507	moveA();
220	gezelter	1464	calcForce();
221	gezelter	507	moveB();
222			}
223	gezelter	246
224
225	gezelter	1464	void VelocityVerletIntegrator::calcForce() {
226			forceMan_->calcForces();
227	gezelter	507	}
228	gezelter	246
229	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
230			return new DumpWriter(info_);
231			}
232	gezelter	246
233	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
234	tim	681
235			std::string statFileFormatString = simParams->getStatFileFormat();
236			StatsBitSet mask = parseStatFileFormat(statFileFormatString);
237	cli2	1360
238			// if we're doing a thermodynamic integration, we'll want the raw
239			// potential as well as the full potential:
240
241
242			if (simParams->getUseThermodynamicIntegration())
243	gezelter	507	mask.set(Stats::VRAW);
244	cli2	1360
245			// if we've got restraints turned on, we'll also want a report of the
246			// total harmonic restraints
247			if (simParams->getUseRestraints()){
248	gezelter	507	mask.set(Stats::VHARM);
249			}
250	tim	541
251	chrisfen	993	if (simParams->havePrintPressureTensor() &&
252			simParams->getPrintPressureTensor()){
253	gezelter	1291	mask.set(Stats::PRESSURE_TENSOR_XX);
254			mask.set(Stats::PRESSURE_TENSOR_XY);
255			mask.set(Stats::PRESSURE_TENSOR_XZ);
256			mask.set(Stats::PRESSURE_TENSOR_YX);
257			mask.set(Stats::PRESSURE_TENSOR_YY);
258			mask.set(Stats::PRESSURE_TENSOR_YZ);
259			mask.set(Stats::PRESSURE_TENSOR_ZX);
260			mask.set(Stats::PRESSURE_TENSOR_ZY);
261			mask.set(Stats::PRESSURE_TENSOR_ZZ);
262	tim	541	}
263
264	chrisfen	998	if (simParams->getAccumulateBoxDipole()) {
265			mask.set(Stats::BOX_DIPOLE_X);
266			mask.set(Stats::BOX_DIPOLE_Y);
267			mask.set(Stats::BOX_DIPOLE_Z);
268			}
269	gezelter	1329
270	gezelter	1291	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
271			if (simParams->getPrintTaggedPairDistance()) {
272			mask.set(Stats::TAGGED_PAIR_DISTANCE);
273			}
274			}
275	gezelter	1329
276			if (simParams->getUseRNEMD()) {
277	skuang	1368	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
278	gezelter	1329	}
279	skuang	1368
280	chrisfen	998
281	skuang	1368	return new StatWriter(info_->getStatFileName(), mask);
282	chrisfen	417	}
283	gezelter	246
284
285	gezelter	1390	} //end namespace OpenMD