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
    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();
    flucQ_->applyConstraints();
  }

  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->getPrintHeatFlux()) {
      mask.set(Stats::HEATFLUX_X);
      mask.set(Stats::HEATFLUX_Y);
      mask.set(Stats::HEATFLUX_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:	1723
Committed:	Thu May 24 20:59:54 2012 UTC (12 years, 11 months ago) by gezelter
File size:	8407 byte(s)
Log Message:	Bug fixes for heat flux import
#	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			thermo.saveStat();
102			saveConservedQuantity();
103	skuang	1341	if (simParams->getUseRNEMD())
104	skuang	1368	rnemd_->getStarted();
105	skuang	1341
106	gezelter	246	statWriter->writeStat(currentSnapshot_->statData);
107	chrisfen	417
108	gezelter	246	currSample = sampleTime + currentSnapshot_->getTime();
109	gezelter	1329	currStatus = statusTime + currentSnapshot_->getTime();
110	tim	546	currThermal = thermalTime + currentSnapshot_->getTime();
111			if (needReset) {
112			currReset = resetTime + currentSnapshot_->getTime();
113			}
114	gezelter	1329	if (simParams->getUseRNEMD()){
115	skuang	1368	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->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	1715	while (currentSnapshot_->getTime() < runTime) {
127			preStep();
128			integrateStep();
129			postStep();
130			}
131	gezelter	507	finalize();
132			}
133	gezelter	246
134
135	gezelter	507	void VelocityVerletIntegrator::preStep() {
136	tim	963	RealType difference = currentSnapshot_->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	gezelter	507	//save snapshot
147			info_->getSnapshotManager()->advance();
148	chrisfen	417
149	gezelter	507	//increase time
150			currentSnapshot_->increaseTime(dt);
151	chrisfen	993
152	gezelter	507	if (needVelocityScaling) {
153			if (currentSnapshot_->getTime() >= currThermal) {
154			velocitizer_->velocitize(targetScalingTemp);
155			currThermal += thermalTime;
156			}
157	chrisfen	417	}
158	gezelter	1329	if (useRNEMD) {
159			if (currentSnapshot_->getTime() >= currRNEMD) {
160	skuang	1368	rnemd_->doRNEMD();
161			currRNEMD += RNEMD_exchangeTime;
162	gezelter	1329	}
163	gezelter	1396	rnemd_->collectData();
164	gezelter	1329	}
165
166	gezelter	507	if (currentSnapshot_->getTime() >= currSample) {
167			dumpWriter->writeDumpAndEor();
168	gezelter	1329
169	gezelter	507	currSample += sampleTime;
170			}
171	gezelter	1329
172	gezelter	507	if (currentSnapshot_->getTime() >= currStatus) {
173			//save statistics, before writeStat, we must save statistics
174			thermo.saveStat();
175			saveConservedQuantity();
176	skuang	1341
177	skuang	1368	if (simParams->getUseRNEMD()) {
178	skuang	1338	rnemd_->getStatus();
179	skuang	1368	}
180	skuang	1341
181			statWriter->writeStat(currentSnapshot_->statData);
182	gezelter	1413
183			progressBar->setStatus(currentSnapshot_->getTime(), runTime);
184			progressBar->update();
185
186	gezelter	507	needPotential = false;
187			needStress = false;
188			currStatus += statusTime;
189			}
190	gezelter	1329
191			if (needReset && currentSnapshot_->getTime() >= currReset) {
192			resetIntegrator();
193			currReset += resetTime;
194			}
195	gezelter	507	}
196	gezelter	246
197
198	gezelter	507	void VelocityVerletIntegrator::finalize() {
199			dumpWriter->writeEor();
200	chrisfen	417
201	gezelter	507	delete dumpWriter;
202			delete statWriter;
203	chrisfen	417
204	gezelter	507	dumpWriter = NULL;
205			statWriter = NULL;
206			}
207	gezelter	246
208	gezelter	507	void VelocityVerletIntegrator::integrateStep() {
209	chrisfen	417
210	gezelter	507	moveA();
211	gezelter	1464	calcForce();
212	gezelter	507	moveB();
213			}
214	gezelter	246
215
216	gezelter	1464	void VelocityVerletIntegrator::calcForce() {
217			forceMan_->calcForces();
218	gezelter	1718	flucQ_->applyConstraints();
219	gezelter	507	}
220	gezelter	246
221	gezelter	507	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
222			return new DumpWriter(info_);
223			}
224	gezelter	246
225	gezelter	507	StatWriter* VelocityVerletIntegrator::createStatWriter() {
226	tim	681
227			std::string statFileFormatString = simParams->getStatFileFormat();
228			StatsBitSet mask = parseStatFileFormat(statFileFormatString);
229	cli2	1360
230			// if we're doing a thermodynamic integration, we'll want the raw
231			// potential as well as the full potential:
232
233
234			if (simParams->getUseThermodynamicIntegration())
235	gezelter	507	mask.set(Stats::VRAW);
236	cli2	1360
237			// if we've got restraints turned on, we'll also want a report of the
238			// total harmonic restraints
239			if (simParams->getUseRestraints()){
240	gezelter	507	mask.set(Stats::VHARM);
241			}
242	tim	541
243	chrisfen	993	if (simParams->havePrintPressureTensor() &&
244			simParams->getPrintPressureTensor()){
245	gezelter	1291	mask.set(Stats::PRESSURE_TENSOR_XX);
246			mask.set(Stats::PRESSURE_TENSOR_XY);
247			mask.set(Stats::PRESSURE_TENSOR_XZ);
248			mask.set(Stats::PRESSURE_TENSOR_YX);
249			mask.set(Stats::PRESSURE_TENSOR_YY);
250			mask.set(Stats::PRESSURE_TENSOR_YZ);
251			mask.set(Stats::PRESSURE_TENSOR_ZX);
252			mask.set(Stats::PRESSURE_TENSOR_ZY);
253			mask.set(Stats::PRESSURE_TENSOR_ZZ);
254	tim	541	}
255
256	chrisfen	998	if (simParams->getAccumulateBoxDipole()) {
257			mask.set(Stats::BOX_DIPOLE_X);
258			mask.set(Stats::BOX_DIPOLE_Y);
259			mask.set(Stats::BOX_DIPOLE_Z);
260			}
261	gezelter	1723
262			if (simParams->getPrintHeatFlux()) {
263			mask.set(Stats::HEATFLUX_X);
264			mask.set(Stats::HEATFLUX_Y);
265			mask.set(Stats::HEATFLUX_Z);
266			}
267	gezelter	1329
268	gezelter	1291	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
269			if (simParams->getPrintTaggedPairDistance()) {
270			mask.set(Stats::TAGGED_PAIR_DISTANCE);
271			}
272			}
273	gezelter	1329
274			if (simParams->getUseRNEMD()) {
275	skuang	1368	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
276	gezelter	1329	}
277	skuang	1368
278	chrisfen	998
279	skuang	1368	return new StatWriter(info_->getStatFileName(), mask);
280	chrisfen	417	}
281	gezelter	246
282
283	gezelter	1390	} //end namespace OpenMD