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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 51 | Line 51
51   #include "integrators/DLM.hpp"
52   #include "utils/StringUtils.hpp"
53  
54 < namespace oopse {
55 < VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
54 > namespace OpenMD {
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() {
59 >  }
60 >  
61 >  VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62      delete rotAlgo;
63      delete rattle;
64 < }
65 <
66 < void VelocityVerletIntegrator::initialize(){
67 <
64 >  }
65 >  
66 >  void VelocityVerletIntegrator::initialize(){
67 >    
68      forceMan_->init();
69 <
70 <    // remove center of mass drift velocity (in case we passed in a configuration
71 <    // that was drifting
69 >    
70 >    // remove center of mass drift velocity (in case we passed in a
71 >    // configuration that was drifting)
72      velocitizer_->removeComDrift();
73 <
73 >    
74      // initialize the forces before the first step
75      calcForce(true, true);
76 <
77 <    //execute constraint algorithm to make sure at the very beginning the system is constrained  
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 <        info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
80 >      rattle->constraintA();
81 >      calcForce(true, true);
82 >      rattle->constraintB();      
83 >      //copy the current snapshot to previous snapshot
84 >      info_->getSnapshotManager()->advance();
85      }
86 <
86 >    
87      if (needVelocityScaling) {
88 <        velocitizer_->velocitize(targetScalingTemp);
88 >      velocitizer_->velocitize(targetScalingTemp);
89      }
90      
91      dumpWriter = createDumpWriter();
92 <
92 >    
93      statWriter = createStatWriter();
94 <
94 >
95      dumpWriter->writeDumpAndEor();
96 <    
96 >
97      //save statistics, before writeStat,  we must save statistics
98      thermo.saveStat();
99      saveConservedQuantity();
100 <    statWriter->writeStat(currentSnapshot_->statData);
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();
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 < }
107 <        
108 < void VelocityVerletIntegrator::doIntegrate() {
116 >    
117 >  }
118  
119 <
119 >  void VelocityVerletIntegrator::doIntegrate() {
120 >  
121 >  
122      initialize();
123 <
123 >  
124      while (currentSnapshot_->getTime() < runTime) {
125 <        
126 <        preStep();
127 <
128 <        integrateStep();
129 <        
130 <        postStep();
131 <
125 >    
126 >      preStep();
127 >    
128 >      integrateStep();
129 >    
130 >      postStep();
131 >    
132      }
133 <
133 >  
134      finalize();
135 <    
136 < }
135 >  
136 >  }
137  
138  
139 < void VelocityVerletIntegrator::preStep() {
140 <        double difference = currentSnapshot_->getTime() + dt - currStatus;
139 >  void VelocityVerletIntegrator::preStep() {
140 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141 >  
142 >    if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
143 >      needPotential = true;
144 >      needStress = true;  
145 >    }
146 >  }
147  
148 <        if (difference > 0 || fabs(difference) < oopse::epsilon) {
132 <            needPotential = true;
133 <            needStress = true;  
134 <        }
148 >  void VelocityVerletIntegrator::postStep() {
149  
150 < }
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 < void VelocityVerletIntegrator::postStep() {
181 >      if (simParams->getUseRNEMD()) {
182 >        rnemd_->getStatus();
183 >      }
184  
185 <        //save snapshot
186 <        info_->getSnapshotManager()->advance();
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  
143 –        //increase time
144 –        currentSnapshot_->increaseTime(dt);        
145 –        
146 –        if (needVelocityScaling) {
147 –            if (currentSnapshot_->getTime() >= currThermal) {
148 –                velocitizer_->velocitize(targetScalingTemp);
149 –                currThermal += thermalTime;
150 –            }
151 –        }
198  
199 <        if (currentSnapshot_->getTime() >= currSample) {
200 <            dumpWriter->writeDumpAndEor();
201 <            currSample += sampleTime;
156 <        }
157 <
158 <        if (currentSnapshot_->getTime() >= currStatus) {
159 <            //save statistics, before writeStat,  we must save statistics
160 <            thermo.saveStat();
161 <            saveConservedQuantity();
162 <            statWriter->writeStat(currentSnapshot_->statData);
163 <
164 <            needPotential = false;
165 <            needStress = false;
166 <            currStatus += statusTime;
167 <        }
168 <
169 <        
170 < }
171 <
172 <
173 < void VelocityVerletIntegrator::finalize() {
174 <     dumpWriter->writeEor();
175 <
199 >  void VelocityVerletIntegrator::finalize() {
200 >    dumpWriter->writeEor();
201 >  
202      delete dumpWriter;
203      delete statWriter;
204 <
204 >  
205      dumpWriter = NULL;
206      statWriter = NULL;
207 <    
208 < }
207 >  
208 >  }
209  
210 < void VelocityVerletIntegrator::integrateStep() {
211 <
210 >  void VelocityVerletIntegrator::integrateStep() {
211 >  
212      moveA();
213      calcForce(needPotential, needStress);
214      moveB();
215 < }
215 >  }
216  
217  
218 < void VelocityVerletIntegrator::calcForce(bool needPotential,
219 <                                         bool needStress) {
218 >  void VelocityVerletIntegrator::calcForce(bool needPotential,
219 >                                           bool needStress) {
220      forceMan_->calcForces(needPotential, needStress);
221 < }
221 >  }
222  
223 < DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
223 >  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224      return new DumpWriter(info_);
225 < }
225 >  }
226  
227 < StatWriter* VelocityVerletIntegrator::createStatWriter() {
202 <    return new StatWriter(info_->getStatFileName());
203 < }
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 < } //end namespace oopse
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 OpenMD

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