| 6 |
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* 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. |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 51 |
|
#include "integrators/VelocityVerletIntegrator.hpp" |
| 52 |
|
#include "integrators/DLM.hpp" |
| 53 |
|
#include "utils/StringUtils.hpp" |
| 54 |
+ |
#include "utils/ProgressBar.hpp" |
| 55 |
|
|
| 56 |
< |
namespace oopse { |
| 56 |
> |
namespace OpenMD { |
| 57 |
|
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
| 58 |
|
dt2 = 0.5 * dt; |
| 59 |
|
rotAlgo = new DLM(); |
| 67 |
|
|
| 68 |
|
void VelocityVerletIntegrator::initialize(){ |
| 69 |
|
|
| 70 |
< |
forceMan_->init(); |
| 70 |
> |
forceMan_->initialize(); |
| 71 |
|
|
| 72 |
< |
// remove center of mass drift velocity (in case we passed in a configuration |
| 73 |
< |
// that was drifting |
| 72 |
> |
// remove center of mass drift velocity (in case we passed in a |
| 73 |
> |
// configuration that was drifting) |
| 74 |
|
velocitizer_->removeComDrift(); |
| 75 |
|
|
| 76 |
|
// initialize the forces before the first step |
| 77 |
< |
calcForce(true, true); |
| 77 |
> |
calcForce(); |
| 78 |
|
|
| 79 |
< |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
| 79 |
> |
// execute the constraint algorithm to make sure that the system is |
| 80 |
> |
// constrained at the very beginning |
| 81 |
|
if (info_->getNGlobalConstraints() > 0) { |
| 82 |
|
rattle->constraintA(); |
| 83 |
< |
calcForce(true, true); |
| 84 |
< |
rattle->constraintB(); |
| 85 |
< |
info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
| 83 |
> |
calcForce(); |
| 84 |
> |
rattle->constraintB(); |
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> |
//copy the current snapshot to previous snapshot |
| 86 |
> |
info_->getSnapshotManager()->advance(); |
| 87 |
|
} |
| 88 |
|
|
| 89 |
|
if (needVelocityScaling) { |
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|
dumpWriter = createDumpWriter(); |
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|
|
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|
statWriter = createStatWriter(); |
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< |
|
| 93 |
< |
if (simParams->getUseSolidThermInt()) { |
| 94 |
< |
restWriter = createRestWriter(); |
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< |
restWriter->writeZangle(); |
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< |
} |
| 97 |
< |
|
| 96 |
> |
|
| 97 |
|
dumpWriter->writeDumpAndEor(); |
| 98 |
< |
|
| 99 |
< |
|
| 98 |
> |
|
| 99 |
> |
progressBar = new ProgressBar(); |
| 100 |
> |
|
| 101 |
|
//save statistics, before writeStat, we must save statistics |
| 102 |
|
thermo.saveStat(); |
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|
saveConservedQuantity(); |
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+ |
if (simParams->getUseRNEMD()) |
| 105 |
+ |
rnemd_->getStarted(); |
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+ |
|
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|
statWriter->writeStat(currentSnapshot_->statData); |
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|
|
| 109 |
|
currSample = sampleTime + currentSnapshot_->getTime(); |
| 110 |
< |
currStatus = statusTime + currentSnapshot_->getTime();; |
| 110 |
> |
currStatus = statusTime + currentSnapshot_->getTime(); |
| 111 |
|
currThermal = thermalTime + currentSnapshot_->getTime(); |
| 112 |
|
if (needReset) { |
| 113 |
|
currReset = resetTime + currentSnapshot_->getTime(); |
| 114 |
|
} |
| 115 |
+ |
if (simParams->getUseRNEMD()){ |
| 116 |
+ |
currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime(); |
| 117 |
+ |
} |
| 118 |
|
needPotential = false; |
| 119 |
|
needStress = false; |
| 120 |
|
|
| 121 |
|
} |
| 122 |
< |
|
| 122 |
> |
|
| 123 |
|
void VelocityVerletIntegrator::doIntegrate() { |
| 124 |
|
|
| 125 |
|
|
| 132 |
|
integrateStep(); |
| 133 |
|
|
| 134 |
|
postStep(); |
| 135 |
< |
|
| 135 |
> |
|
| 136 |
|
} |
| 137 |
|
|
| 138 |
|
finalize(); |
| 141 |
|
|
| 142 |
|
|
| 143 |
|
void VelocityVerletIntegrator::preStep() { |
| 144 |
< |
double difference = currentSnapshot_->getTime() + dt - currStatus; |
| 144 |
> |
RealType difference = currentSnapshot_->getTime() + dt - currStatus; |
| 145 |
|
|
| 146 |
< |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
| 146 |
> |
if (difference > 0 || fabs(difference) < OpenMD::epsilon) { |
| 147 |
|
needPotential = true; |
| 148 |
|
needStress = true; |
| 149 |
|
} |
| 144 |
– |
|
| 150 |
|
} |
| 151 |
|
|
| 152 |
|
void VelocityVerletIntegrator::postStep() { |
| 156 |
|
|
| 157 |
|
//increase time |
| 158 |
|
currentSnapshot_->increaseTime(dt); |
| 159 |
< |
|
| 159 |
> |
|
| 160 |
|
if (needVelocityScaling) { |
| 161 |
|
if (currentSnapshot_->getTime() >= currThermal) { |
| 162 |
|
velocitizer_->velocitize(targetScalingTemp); |
| 163 |
|
currThermal += thermalTime; |
| 164 |
|
} |
| 165 |
|
} |
| 166 |
< |
|
| 166 |
> |
if (useRNEMD) { |
| 167 |
> |
if (currentSnapshot_->getTime() >= currRNEMD) { |
| 168 |
> |
rnemd_->doRNEMD(); |
| 169 |
> |
currRNEMD += RNEMD_exchangeTime; |
| 170 |
> |
} |
| 171 |
> |
rnemd_->collectData(); |
| 172 |
> |
} |
| 173 |
> |
|
| 174 |
|
if (currentSnapshot_->getTime() >= currSample) { |
| 175 |
|
dumpWriter->writeDumpAndEor(); |
| 176 |
< |
|
| 165 |
< |
if (simParams->getUseSolidThermInt()) |
| 166 |
< |
restWriter->writeZangle(); |
| 167 |
< |
|
| 176 |
> |
|
| 177 |
|
currSample += sampleTime; |
| 178 |
|
} |
| 179 |
< |
|
| 179 |
> |
|
| 180 |
|
if (currentSnapshot_->getTime() >= currStatus) { |
| 181 |
|
//save statistics, before writeStat, we must save statistics |
| 182 |
|
thermo.saveStat(); |
| 183 |
|
saveConservedQuantity(); |
| 184 |
+ |
|
| 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 |
> |
|
| 194 |
|
needPotential = false; |
| 195 |
|
needStress = false; |
| 196 |
|
currStatus += statusTime; |
| 197 |
|
} |
| 198 |
< |
|
| 199 |
< |
if (needReset && currentSnapshot_->getTime() >= currReset) { |
| 200 |
< |
resetIntegrator(); |
| 201 |
< |
currReset += resetTime; |
| 202 |
< |
} |
| 186 |
< |
|
| 198 |
> |
|
| 199 |
> |
if (needReset && currentSnapshot_->getTime() >= currReset) { |
| 200 |
> |
resetIntegrator(); |
| 201 |
> |
currReset += resetTime; |
| 202 |
> |
} |
| 203 |
|
} |
| 204 |
|
|
| 205 |
|
|
| 206 |
|
void VelocityVerletIntegrator::finalize() { |
| 207 |
|
dumpWriter->writeEor(); |
| 208 |
|
|
| 193 |
– |
if (simParams->getUseSolidThermInt()) { |
| 194 |
– |
restWriter->writeZangle(); |
| 195 |
– |
delete restWriter; |
| 196 |
– |
restWriter = NULL; |
| 197 |
– |
} |
| 198 |
– |
|
| 209 |
|
delete dumpWriter; |
| 210 |
|
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) { |
| 217 |
< |
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 |
|
|
| 251 |
< |
if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){ |
| 252 |
< |
mask.set(Stats::PRESSURE_TENSOR_X); |
| 253 |
< |
mask.set(Stats::PRESSURE_TENSOR_Y); |
| 254 |
< |
mask.set(Stats::PRESSURE_TENSOR_Z); |
| 251 |
> |
if (simParams->havePrintPressureTensor() && |
| 252 |
> |
simParams->getPrintPressureTensor()){ |
| 253 |
> |
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 |
|
} |
| 263 |
|
|
| 264 |
< |
return new StatWriter(info_->getStatFileName(), mask); |
| 265 |
< |
} |
| 264 |
> |
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 |
> |
|
| 270 |
> |
if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) { |
| 271 |
> |
if (simParams->getPrintTaggedPairDistance()) { |
| 272 |
> |
mask.set(Stats::TAGGED_PAIR_DISTANCE); |
| 273 |
> |
} |
| 274 |
> |
} |
| 275 |
|
|
| 276 |
< |
RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
| 277 |
< |
return new RestWriter(info_); |
| 276 |
> |
if (simParams->getUseRNEMD()) { |
| 277 |
> |
mask.set(Stats::RNEMD_EXCHANGE_TOTAL); |
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
|
| 281 |
> |
return new StatWriter(info_->getStatFileName(), mask); |
| 282 |
|
} |
| 283 |
|
|
| 284 |
|
|
| 285 |
< |
} //end namespace oopse |
| 285 |
> |
} //end namespace OpenMD |
