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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @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"

namespace oopse {
  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_->init();
    
    // 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(true, true);
    
    // execute the constraint algorithm to make sure that the system is
    // constrained at the very beginning  
    if (info_->getNGlobalConstraints() > 0) {
      rattle->constraintA();
      calcForce(true, true);
      rattle->constraintB();      
      //copy the current snapshot to previous snapshot
      info_->getSnapshotManager()->advance();
    }
    
    if (needVelocityScaling) {
      velocitizer_->velocitize(targetScalingTemp);
    }
    
    dumpWriter = createDumpWriter();
    
    statWriter = createStatWriter();
 
    dumpWriter->writeDumpAndEor();

    //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) < oopse::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) {
      rnemd_->collectData();
      if (currentSnapshot_->getTime() >= currRNEMD) {
        rnemd_->doRNEMD();
        currRNEMD += RNEMD_exchangeTime;
      }
    }
    
    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);
      
      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(needPotential, needStress);
    moveB();
  }


  void VelocityVerletIntegrator::calcForce(bool needPotential,
                                           bool needStress) { 
    forceMan_->calcForces(needPotential, needStress);
  }

  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 oopse
Revision:	3541
Committed:	Mon Oct 19 13:39:04 2009 UTC (15 years, 6 months ago) by skuang
File size:	8103 byte(s)
Log Message:	added RNEMD scaling
#	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. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file VelocityVerletIntegrator.cpp
44	* @author tlin
45	* @date 11/09/2004
46	* @time 16:16am
47	* @version 1.0
48	*/
49
50	#include "integrators/VelocityVerletIntegrator.hpp"
51	#include "integrators/DLM.hpp"
52	#include "utils/StringUtils.hpp"
53
54	namespace oopse {
55	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56	dt2 = 0.5 * dt;
57	rotAlgo = new DLM();
58	rattle = new Rattle(info);
59	}
60
61	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	delete rotAlgo;
63	delete rattle;
64	}
65
66	void VelocityVerletIntegrator::initialize(){
67
68	forceMan_->init();
69
70	// remove center of mass drift velocity (in case we passed in a
71	// configuration that was drifting)
72	velocitizer_->removeComDrift();
73
74	// initialize the forces before the first step
75	calcForce(true, true);
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(true, true);
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	//save statistics, before writeStat, we must save statistics
98	thermo.saveStat();
99	saveConservedQuantity();
100	if (simParams->getUseRNEMD())
101	rnemd_->getStarted();
102
103	statWriter->writeStat(currentSnapshot_->statData);
104
105	currSample = sampleTime + currentSnapshot_->getTime();
106	currStatus = statusTime + currentSnapshot_->getTime();
107	currThermal = thermalTime + currentSnapshot_->getTime();
108	if (needReset) {
109	currReset = resetTime + currentSnapshot_->getTime();
110	}
111	if (simParams->getUseRNEMD()){
112	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
113	}
114	needPotential = false;
115	needStress = false;
116
117	}
118
119	void VelocityVerletIntegrator::doIntegrate() {
120
121
122	initialize();
123
124	while (currentSnapshot_->getTime() < runTime) {
125
126	preStep();
127
128	integrateStep();
129
130	postStep();
131
132	}
133
134	finalize();
135
136	}
137
138
139	void VelocityVerletIntegrator::preStep() {
140	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141
142	if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
143	needPotential = true;
144	needStress = true;
145	}
146	}
147
148	void VelocityVerletIntegrator::postStep() {
149
150	//save snapshot
151	info_->getSnapshotManager()->advance();
152
153	//increase time
154	currentSnapshot_->increaseTime(dt);
155
156	if (needVelocityScaling) {
157	if (currentSnapshot_->getTime() >= currThermal) {
158	velocitizer_->velocitize(targetScalingTemp);
159	currThermal += thermalTime;
160	}
161	}
162	if (useRNEMD) {
163	rnemd_->collectData();
164	if (currentSnapshot_->getTime() >= currRNEMD) {
165	rnemd_->doRNEMD();
166	currRNEMD += RNEMD_exchangeTime;
167	}
168	}
169
170	if (currentSnapshot_->getTime() >= currSample) {
171	dumpWriter->writeDumpAndEor();
172
173	currSample += sampleTime;
174	}
175
176	if (currentSnapshot_->getTime() >= currStatus) {
177	//save statistics, before writeStat, we must save statistics
178	thermo.saveStat();
179	saveConservedQuantity();
180
181	if (simParams->getUseRNEMD()) {
182	rnemd_->getStatus();
183	}
184
185	statWriter->writeStat(currentSnapshot_->statData);
186
187	needPotential = false;
188	needStress = false;
189	currStatus += statusTime;
190	}
191
192	if (needReset && currentSnapshot_->getTime() >= currReset) {
193	resetIntegrator();
194	currReset += resetTime;
195	}
196	}
197
198
199	void VelocityVerletIntegrator::finalize() {
200	dumpWriter->writeEor();
201
202	delete dumpWriter;
203	delete statWriter;
204
205	dumpWriter = NULL;
206	statWriter = NULL;
207
208	}
209
210	void VelocityVerletIntegrator::integrateStep() {
211
212	moveA();
213	calcForce(needPotential, needStress);
214	moveB();
215	}
216
217
218	void VelocityVerletIntegrator::calcForce(bool needPotential,
219	bool needStress) {
220	forceMan_->calcForces(needPotential, needStress);
221	}
222
223	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224	return new DumpWriter(info_);
225	}
226
227	StatWriter* VelocityVerletIntegrator::createStatWriter() {
228
229	std::string statFileFormatString = simParams->getStatFileFormat();
230	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
231
232	// if we're doing a thermodynamic integration, we'll want the raw
233	// potential as well as the full potential:
234
235
236	if (simParams->getUseThermodynamicIntegration())
237	mask.set(Stats::VRAW);
238
239	// if we've got restraints turned on, we'll also want a report of the
240	// total harmonic restraints
241	if (simParams->getUseRestraints()){
242	mask.set(Stats::VHARM);
243	}
244
245	if (simParams->havePrintPressureTensor() &&
246	simParams->getPrintPressureTensor()){
247	mask.set(Stats::PRESSURE_TENSOR_XX);
248	mask.set(Stats::PRESSURE_TENSOR_XY);
249	mask.set(Stats::PRESSURE_TENSOR_XZ);
250	mask.set(Stats::PRESSURE_TENSOR_YX);
251	mask.set(Stats::PRESSURE_TENSOR_YY);
252	mask.set(Stats::PRESSURE_TENSOR_YZ);
253	mask.set(Stats::PRESSURE_TENSOR_ZX);
254	mask.set(Stats::PRESSURE_TENSOR_ZY);
255	mask.set(Stats::PRESSURE_TENSOR_ZZ);
256	}
257
258	if (simParams->getAccumulateBoxDipole()) {
259	mask.set(Stats::BOX_DIPOLE_X);
260	mask.set(Stats::BOX_DIPOLE_Y);
261	mask.set(Stats::BOX_DIPOLE_Z);
262	}
263
264	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
265	if (simParams->getPrintTaggedPairDistance()) {
266	mask.set(Stats::TAGGED_PAIR_DISTANCE);
267	}
268	}
269
270	if (simParams->getUseRNEMD()) {
271	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272	}
273
274
275	return new StatWriter(info_->getStatFileName(), mask);
276	}
277
278
279	} //end namespace oopse