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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
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|
* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
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< |
* 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 |
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< |
* 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 |
|
* |
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< |
* 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 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
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|
* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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#include "integrators/VelocityVerletIntegrator.hpp" |
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#include "integrators/DLM.hpp" |
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#include "utils/StringUtils.hpp" |
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+ |
#include "utils/ProgressBar.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
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dt2 = 0.5 * dt; |
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rotAlgo = new DLM(); |
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|
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void VelocityVerletIntegrator::initialize(){ |
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|
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< |
forceMan_->init(); |
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> |
forceMan_->initialize(); |
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|
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// remove center of mass drift velocity (in case we passed in a |
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// configuration that was drifting) |
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velocitizer_->removeComDrift(); |
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|
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// initialize the forces before the first step |
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calcForce(true, true); |
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> |
calcForce(); |
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|
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// execute the constraint algorithm to make sure that the system is |
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// constrained at the very beginning |
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if (info_->getNGlobalConstraints() > 0) { |
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rattle->constraintA(); |
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calcForce(true, true); |
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> |
calcForce(); |
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rattle->constraintB(); |
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//copy the current snapshot to previous snapshot |
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info_->getSnapshotManager()->advance(); |
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|
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dumpWriter->writeDumpAndEor(); |
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|
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< |
if (simParams->getUseSolidThermInt()) { |
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< |
restWriter = createRestWriter(); |
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< |
restWriter->writeZAngFile(); |
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< |
} |
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< |
|
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> |
progressBar = new ProgressBar(); |
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> |
|
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|
//save statistics, before writeStat, we must save statistics |
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thermo.saveStat(); |
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saveConservedQuantity(); |
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if (simParams->getUseRNEMD()) |
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< |
rnemd_->getStatus(); |
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> |
rnemd_->getStarted(); |
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|
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statWriter->writeStat(currentSnapshot_->statData); |
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|
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currReset = resetTime + currentSnapshot_->getTime(); |
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} |
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if (simParams->getUseRNEMD()){ |
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< |
currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime(); |
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> |
currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime(); |
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} |
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needPotential = false; |
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needStress = false; |
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|
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} |
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< |
|
| 122 |
> |
|
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void VelocityVerletIntegrator::doIntegrate() { |
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|
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|
|
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integrateStep(); |
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|
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postStep(); |
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< |
|
| 135 |
> |
|
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|
} |
| 137 |
|
|
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|
finalize(); |
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|
void VelocityVerletIntegrator::preStep() { |
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RealType difference = currentSnapshot_->getTime() + dt - currStatus; |
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|
| 146 |
< |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
| 146 |
> |
if (difference > 0 || fabs(difference) < OpenMD::epsilon) { |
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|
needPotential = true; |
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|
needStress = true; |
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|
} |
| 165 |
|
} |
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if (useRNEMD) { |
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|
if (currentSnapshot_->getTime() >= currRNEMD) { |
| 168 |
< |
rnemd_->doSwap(); |
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< |
currRNEMD += RNEMD_swapTime; |
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> |
rnemd_->doRNEMD(); |
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> |
currRNEMD += RNEMD_exchangeTime; |
| 170 |
|
} |
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+ |
rnemd_->collectData(); |
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|
} |
| 173 |
|
|
| 174 |
|
if (currentSnapshot_->getTime() >= currSample) { |
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|
dumpWriter->writeDumpAndEor(); |
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|
|
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– |
if (simParams->getUseSolidThermInt()) |
| 178 |
– |
restWriter->writeZAngFile(); |
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– |
|
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|
currSample += sampleTime; |
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|
} |
| 179 |
|
|
| 182 |
|
thermo.saveStat(); |
| 183 |
|
saveConservedQuantity(); |
| 184 |
|
|
| 185 |
< |
if (simParams->getUseRNEMD()) |
| 185 |
> |
if (simParams->getUseRNEMD()) { |
| 186 |
|
rnemd_->getStatus(); |
| 187 |
+ |
} |
| 188 |
|
|
| 189 |
|
statWriter->writeStat(currentSnapshot_->statData); |
| 190 |
< |
|
| 190 |
> |
|
| 191 |
> |
progressBar->setStatus(currentSnapshot_->getTime(), runTime); |
| 192 |
> |
progressBar->update(); |
| 193 |
> |
|
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|
needPotential = false; |
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|
needStress = false; |
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|
currStatus += statusTime; |
| 206 |
|
void VelocityVerletIntegrator::finalize() { |
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|
dumpWriter->writeEor(); |
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|
|
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– |
if (simParams->getUseSolidThermInt()) { |
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– |
restWriter->writeZAngFile(); |
| 210 |
– |
delete restWriter; |
| 211 |
– |
restWriter = NULL; |
| 212 |
– |
} |
| 213 |
– |
|
| 209 |
|
delete dumpWriter; |
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|
delete statWriter; |
| 211 |
|
|
| 217 |
|
void VelocityVerletIntegrator::integrateStep() { |
| 218 |
|
|
| 219 |
|
moveA(); |
| 220 |
< |
calcForce(needPotential, needStress); |
| 220 |
> |
calcForce(); |
| 221 |
|
moveB(); |
| 222 |
|
} |
| 223 |
|
|
| 224 |
|
|
| 225 |
< |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
| 226 |
< |
bool needStress) { |
| 232 |
< |
forceMan_->calcForces(needPotential, needStress); |
| 225 |
> |
void VelocityVerletIntegrator::calcForce() { |
| 226 |
> |
forceMan_->calcForces(); |
| 227 |
|
} |
| 228 |
|
|
| 229 |
|
DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
| 234 |
|
|
| 235 |
|
std::string statFileFormatString = simParams->getStatFileFormat(); |
| 236 |
|
StatsBitSet mask = parseStatFileFormat(statFileFormatString); |
| 237 |
< |
|
| 238 |
< |
// if solidThermInt is true, add extra information to the statfile |
| 239 |
< |
if (simParams->getUseSolidThermInt()){ |
| 237 |
> |
|
| 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 |
|
mask.set(Stats::VRAW); |
| 244 |
+ |
|
| 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 |
|
mask.set(Stats::VHARM); |
| 249 |
|
} |
| 250 |
|
|
| 274 |
|
} |
| 275 |
|
|
| 276 |
|
if (simParams->getUseRNEMD()) { |
| 277 |
< |
mask.set(Stats::RNEMD_SWAP_TOTAL); |
| 277 |
> |
mask.set(Stats::RNEMD_EXCHANGE_TOTAL); |
| 278 |
|
} |
| 279 |
< |
|
| 279 |
> |
|
| 280 |
|
|
| 281 |
< |
return new StatWriter(info_->getStatFileName(), mask); |
| 281 |
> |
return new StatWriter(info_->getStatFileName(), mask); |
| 282 |
|
} |
| 283 |
|
|
| 283 |
– |
RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
| 284 |
– |
return new RestWriter(info_); |
| 285 |
– |
} |
| 284 |
|
|
| 285 |
< |
|
| 288 |
< |
} //end namespace oopse |
| 285 |
> |
} //end namespace OpenMD |
